diff --git a/DESCRIPTION b/DESCRIPTION index e5df44a..c985d1f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -30,7 +30,6 @@ Imports: rlang, scales License: GPL-2 -LazyData: true Suggests: Cairo, covr, @@ -72,6 +71,6 @@ Collate: 'stamp.R' 'themes.R' 'utils_ggplot2.R' -RoxygenNote: 7.1.1 +RoxygenNote: 7.2.3 Roxygen: list(markdown = TRUE) Encoding: UTF-8 diff --git a/R/cowplot.R b/R/cowplot.R index bf9dee8..08c3c6d 100644 --- a/R/cowplot.R +++ b/R/cowplot.R @@ -8,10 +8,9 @@ #' hence the name (Claus O. Wilke's plot package). It has also been used #' extensively in the book Fundamentals of Data Visualization. #' -#' @name cowplot -#' @docType package #' @import ggplot2 #' @import grid #' @import rlang -NULL +#' @keywords internal +"_PACKAGE" diff --git a/README.md b/README.md index 6673404..4b5dfaa 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ [![R build status](https://github.com/wilkelab/cowplot/workflows/R-CMD-check/badge.svg)](https://github.com/wilkelab/cowplot/actions) -[![Coverage Status](https://img.shields.io/codecov/c/github/wilkelab/cowplot/master.svg)](https://codecov.io/github/wilkelab/cowplot?branch=master) +[![Coverage Status](https://img.shields.io/codecov/c/github/wilkelab/cowplot/master.svg)](https://app.codecov.io/github/wilkelab/cowplot?branch=master) [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/cowplot)](https://CRAN.R-project.org/package=cowplot) [![CRAN\_Downloads\_Badge](https://cranlogs.r-pkg.org/badges/cowplot)](https://cranlogs.r-pkg.org/downloads/total/last-month/cowplot) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2533860.svg)](https://doi.org/10.5281/zenodo.2533860) diff --git a/cran-comments.md b/cran-comments.md index 47e2be1..9e9ab93 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,9 +1,9 @@ -Make sure tests don't fail just because vdiffr couldn't be installed, per request by Brian Ripley. +Minor bug fixes ## Test environments * ubuntu 20.04, devel and release -* windows, release +* windows, devel and release * macOS, release ## R CMD check results diff --git a/man/cowplot.Rd b/man/cowplot-package.Rd similarity index 65% rename from man/cowplot.Rd rename to man/cowplot-package.Rd index 97baacf..62eca6e 100644 --- a/man/cowplot.Rd +++ b/man/cowplot-package.Rd @@ -1,8 +1,9 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/cowplot.R \docType{package} -\name{cowplot} +\name{cowplot-package} \alias{cowplot} +\alias{cowplot-package} \title{Streamlined Plot Theme and Plot Annotations for 'ggplot2'} \description{ Provides various features that help with creating publication-quality @@ -13,3 +14,16 @@ package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization. } +\seealso{ +Useful links: +\itemize{ + \item \url{https://wilkelab.org/cowplot/} + \item Report bugs at \url{https://github.com/wilkelab/cowplot/issues} +} + +} +\author{ +\strong{Maintainer}: Claus O. Wilke \email{wilke@austin.utexas.edu} (\href{https://orcid.org/0000-0002-7470-9261}{ORCID}) + +} +\keyword{internal} diff --git a/revdep/README.md b/revdep/README.md index 15110fb..f482f1a 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -2,42 +2,55 @@ |field |value | |:--------|:----------------------------| -|version |R version 3.6.0 (2019-04-26) | -|os |macOS Mojave 10.14.5 | -|system |x86_64, darwin15.6.0 | +|version |R version 4.3.1 (2023-06-16) | +|os |macOS Ventura 13.6 | +|system |aarch64, darwin20 | |ui |X11 | |language |(EN) | |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | |tz |America/Chicago | -|date |2019-07-08 | +|date |2023-12-14 | +|pandoc |NA | # Dependencies -|package |old |new |Δ | -|:-------|:-----|:------|:--| -|cowplot |0.9.4 |0.9.99 |* | +|package |old |new |Δ | +|:-------|:-----|:-----|:--| +|cowplot |1.1.1 |1.1.2 |* | +|ggplot2 |NA |3.4.4 |* | +|scales |NA |1.3.0 |* | # Revdeps -## Failed to check (10) - -|package |version |error |warning |note | -|:----------------------------------|:-------|:------|:-------|:----| -|BASiCS |1.6.0 |1 | | | -|bigstatsr |0.9.1 |1 | | | -|BPRMeth |1.10.0 |1 | | | -|CaseBasedReasoning |0.1 |1 | | | -|cytometree |1.3.0 |1 | | | -|[foreSIGHT](failures.md#foresight) |0.9.6 |__+1__ | | | -|graper |1.0.0 |1 | | | -|MutationalPatterns |1.10.0 |1 | | | -|poppr |2.8.3 |1 | | | -|telefit |1.0.1 |1 | | | - -## New problems (1) - -|package |version |error |warning |note | -|:------------------------------------|:-------|:------|:-------|:----| -|[AneuFinder](problems.md#aneufinder) |1.12.0 |__+1__ | |1 | +## Failed to check (18) + +|package |version |error |warning |note | +|:-------------------|:-------|:-----|:-------|:----| +|ClassifyR |3.6.2 |1 |1 |3 | +|cola |? | | | | +|CoSMoS |2.1.0 |1 | | | +|fgsea |? | | | | +|GenomicPlot |1.0.0 |1 | | | +|HiLDA |1.16.0 |1 | | | +|mcmcabn |0.6 |1 | | | +|orthos |1.0.1 |2 |1 | | +|pareg |1.6.0 |1 | |2 | +|phemd |1.18.0 |1 | | | +|rliger |? | | | | +|scGPS |? | | | | +|seqArchRplus |1.2.0 |1 | | | +|simplifyEnrichment |? | | | | +|SpatialOmicsOverlay |1.2.1 |1 | | | +|stppSim |1.3.2 |1 | | | +|TOmicsVis |2.0.0 |1 | | | +|valse |0.1-0 |1 | | | + +## New problems (3) + +|package |version |error |warning |note | +|:----------|:-------|:------|:-------|:----| +|[dce](problems.md#dce)|1.10.0 |__+1__ | |3 | +|[multiWGCNA](problems.md#multiwgcna)|1.0.0 |__+1__ | |1 | +|[ORFik](problems.md#orfik)|1.22.1 |__+1__ |1 |4 | diff --git a/revdep/cran.md b/revdep/cran.md new file mode 100644 index 0000000..f4a83e1 --- /dev/null +++ b/revdep/cran.md @@ -0,0 +1,16 @@ +## revdepcheck results + +We checked 363 reverse dependencies (250 from CRAN + 113 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. + + * We saw 0 new problems + * We failed to check 5 packages + +Issues with CRAN packages are summarised below. + +### Failed to check + +* CoSMoS (NA) +* mcmcabn (NA) +* stppSim (NA) +* TOmicsVis (NA) +* valse (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 83c2641..3cc87ee 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1,24 +1,128 @@ -# BASiCS +# ClassifyR
-* Version: 1.6.0 -* Source code: https://github.com/cran/BASiCS -* URL: https://github.com/catavallejos/BASiCS -* BugReports: https://github.com/catavallejos/BASiCS/issues -* Date/Publication: 2019-05-02 -* Number of recursive dependencies: 122 +* Version: 3.6.2 +* GitHub: NA +* Source code: https://github.com/cran/ClassifyR +* Date/Publication: 2023-11-10 +* Number of recursive dependencies: 189 -Run `revdep_details(,"BASiCS")` for more info +Run `revdepcheck::revdep_details(, "ClassifyR")` for more info
## In both -* checking whether package ‘BASiCS’ can be installed ... ERROR +* R CMD check timed out + + +* checking whether package ‘ClassifyR’ can be installed ... WARNING + ``` + Found the following significant warnings: + coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] + coxformatrices.cpp:529:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] + coxformatrices.cpp:569:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] + coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] + coxformatrices.cpp:656:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] + coxformatrices.cpp:657:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] + Warning: package ‘S4Vectors’ was built under R version 4.3.2 + Warning: package ‘MultiAssayExperiment’ was built under R version 4.3.2 + Warning: package ‘SummarizedExperiment’ was built under R version 4.3.2 + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/ClassifyR/new/ClassifyR.Rcheck/00install.out’ for details. + ``` + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘ggupset’ + All declared Imports should be used. + ``` + +* checking R code for possible problems ... NOTE + ``` + .addUserLevels: no visible binding for global variable ‘median’ + .dmvnorm_diag: no visible global function definition for ‘dnorm’ + .doSelection : : : no visible global function + definition for ‘setNames’ + .doSelection : : : no visible global function + definition for ‘na.omit’ + .doSelection : : : no visible global function + definition for ‘median’ + .doSelection : : no visible binding for global variable + ‘trainParams’ + ... + real samplesTiers sd second setNames size splinefun test + testingMatrix top trainParams trainingMatrix trueClass type unqiue + upper useFeatures value var + Consider adding + importFrom("base", "grouping") + importFrom("stats", "aggregate", "chisq.test", "density", "dist", + "dnorm", "glm", "mad", "median", "model.matrix", "na.omit", + "pnorm", "prcomp", "predict", "quantile", "quasibinomial", + "sd", "setNames", "splinefun", "var") + to your NAMESPACE file. + ``` + +# cola + +
+ +* Version: +* GitHub: https://github.com/wilkelab/cowplot +* Source code: NA +* Number of recursive dependencies: 0 + +
+ +## Error before installation + +### Devel + +``` + + + +installing the source packages ‘hu6800.db’, ‘reactome.db’ + + + +``` +### CRAN + +``` + + + +installing the source packages ‘hu6800.db’, ‘reactome.db’ + + + +``` +# CoSMoS + +
+ +* Version: 2.1.0 +* GitHub: https://github.com/TycheLab/CoSMoS +* Source code: https://github.com/cran/CoSMoS +* Date/Publication: 2021-05-29 23:20:08 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::revdep_details(, "CoSMoS")` for more info + +
+ +## In both + +* checking whether package ‘CoSMoS’ can be installed ... ERROR ``` Installation failed. - See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/BASiCS/new/BASiCS.Rcheck/00install.out’ for details. + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/CoSMoS/new/CoSMoS.Rcheck/00install.out’ for details. ``` ## Installation @@ -26,278 +130,100 @@ Run `revdep_details(,"BASiCS")` for more info ### Devel ``` -* installing *source* package ‘BASiCS’ ... +* installing *source* package ‘CoSMoS’ ... +** package ‘CoSMoS’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_DenoisedRates.cpp -o BASiCS_DenoisedRates.o -In file included from BASiCS_DenoisedRates.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_MCMCcpp.cpp -o BASiCS_MCMCcpp.o -In file included from BASiCS_MCMCcpp.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_MCMCcppNoSpikes.cpp -o BASiCS_MCMCcppNoSpikes.o -In file included from BASiCS_MCMCcppNoSpikes.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_MCMCcppReg.cpp -o BASiCS_MCMCcppReg.o -In file included from BASiCS_MCMCcppReg.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_MCMCcppRegNoSpikes.cpp -o BASiCS_MCMCcppRegNoSpikes.o -In file included from BASiCS_MCMCcppRegNoSpikes.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c general_utils.cpp -o general_utils.o -In file included from general_utils.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils_MCMCcpp.cpp -o utils_MCMCcpp.o -In file included from utils_MCMCcpp.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils_MCMCcppNoSpikes.cpp -o utils_MCMCcppNoSpikes.o -In file included from utils_MCMCcppNoSpikes.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils_MCMCcppReg.cpp -o utils_MCMCcppReg.o -In file included from utils_MCMCcppReg.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils_MCMCcppRegNoSpikes.cpp -o utils_MCMCcppRegNoSpikes.o -In file included from utils_MCMCcppRegNoSpikes.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BASiCS.so BASiCS_DenoisedRates.o BASiCS_MCMCcpp.o BASiCS_MCMCcppNoSpikes.o BASiCS_MCMCcppReg.o BASiCS_MCMCcppRegNoSpikes.o RcppExports.o general_utils.o utils_MCMCcpp.o utils_MCMCcppNoSpikes.o utils_MCMCcppReg.o utils_MCMCcppRegNoSpikes.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [BASiCS.so] Error 1 -ERROR: compilation failed for package ‘BASiCS’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/BASiCS/new/BASiCS.Rcheck/BASiCS’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +tcltk DLL is linked to '/opt/X11/lib/libX11.6.dylib' +Error: .onLoad failed in loadNamespace() for 'tcltk', details: + call: fun(libname, pkgname) + error: X11 library is missing: install XQuartz from www.xquartz.org +Execution halted +ERROR: lazy loading failed for package ‘CoSMoS’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/CoSMoS/new/CoSMoS.Rcheck/CoSMoS’ + ``` ### CRAN ``` -* installing *source* package ‘BASiCS’ ... +* installing *source* package ‘CoSMoS’ ... +** package ‘CoSMoS’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_DenoisedRates.cpp -o BASiCS_DenoisedRates.o -In file included from BASiCS_DenoisedRates.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_MCMCcpp.cpp -o BASiCS_MCMCcpp.o -In file included from BASiCS_MCMCcpp.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_MCMCcppNoSpikes.cpp -o BASiCS_MCMCcppNoSpikes.o -In file included from BASiCS_MCMCcppNoSpikes.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_MCMCcppReg.cpp -o BASiCS_MCMCcppReg.o -In file included from BASiCS_MCMCcppReg.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BASiCS_MCMCcppRegNoSpikes.cpp -o BASiCS_MCMCcppRegNoSpikes.o -In file included from BASiCS_MCMCcppRegNoSpikes.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c general_utils.cpp -o general_utils.o -In file included from general_utils.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils_MCMCcpp.cpp -o utils_MCMCcpp.o -In file included from utils_MCMCcpp.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils_MCMCcppNoSpikes.cpp -o utils_MCMCcppNoSpikes.o -In file included from utils_MCMCcppNoSpikes.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils_MCMCcppReg.cpp -o utils_MCMCcppReg.o -In file included from utils_MCMCcppReg.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils_MCMCcppRegNoSpikes.cpp -o utils_MCMCcppRegNoSpikes.o -In file included from utils_MCMCcppRegNoSpikes.cpp:1: -In file included from ./utils.h:1: -In file included from ./MCMCcpp.h:15: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/RcppCommon.h:128: -/Users/clauswilke/github/cowplot/revdep/library.noindex/BASiCS/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion] - inline void warning(const std::string& message) { // #nocov start - ^ -1 warning generated. -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BASiCS.so BASiCS_DenoisedRates.o BASiCS_MCMCcpp.o BASiCS_MCMCcppNoSpikes.o BASiCS_MCMCcppReg.o BASiCS_MCMCcppRegNoSpikes.o RcppExports.o general_utils.o utils_MCMCcpp.o utils_MCMCcppNoSpikes.o utils_MCMCcppReg.o utils_MCMCcppRegNoSpikes.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [BASiCS.so] Error 1 -ERROR: compilation failed for package ‘BASiCS’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/BASiCS/old/BASiCS.Rcheck/BASiCS’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +tcltk DLL is linked to '/opt/X11/lib/libX11.6.dylib' +Error: .onLoad failed in loadNamespace() for 'tcltk', details: + call: fun(libname, pkgname) + error: X11 library is missing: install XQuartz from www.xquartz.org +Execution halted +ERROR: lazy loading failed for package ‘CoSMoS’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/CoSMoS/old/CoSMoS.Rcheck/CoSMoS’ + + +``` +# fgsea + +
+ +* Version: +* GitHub: https://github.com/wilkelab/cowplot +* Source code: NA +* Number of recursive dependencies: 0 + +
+ +## Error before installation + +### Devel + +``` + + + +installing the source package ‘reactome.db’ + + ``` -# bigstatsr +### CRAN + +``` + + + +installing the source package ‘reactome.db’ + + + +``` +# GenomicPlot
-* Version: 0.9.1 -* Source code: https://github.com/cran/bigstatsr -* URL: https://privefl.github.io/bigstatsr -* BugReports: https://github.com/privefl/bigstatsr/issues -* Date/Publication: 2019-03-03 17:30:13 UTC -* Number of recursive dependencies: 81 +* Version: 1.0.0 +* GitHub: https://github.com/shuye2009/GenomicPlot +* Source code: https://github.com/cran/GenomicPlot +* Date/Publication: 2023-10-30 +* Number of recursive dependencies: 220 -Run `revdep_details(,"bigstatsr")` for more info +Run `revdepcheck::revdep_details(, "GenomicPlot")` for more info
## In both -* checking whether package ‘bigstatsr’ can be installed ... ERROR +* checking whether package ‘GenomicPlot’ can be installed ... ERROR ``` Installation failed. - See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/bigstatsr/new/bigstatsr.Rcheck/00install.out’ for details. + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/GenomicPlot/new/GenomicPlot.Rcheck/00install.out’ for details. ``` ## Installation @@ -305,94 +231,65 @@ Run `revdep_details(,"bigstatsr")` for more info ### Devel ``` -* installing *source* package ‘bigstatsr’ ... -** package ‘bigstatsr’ successfully unpacked and MD5 sums checked +* installing *source* package ‘GenomicPlot’ ... ** using staged installation -** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c AUC.cpp -o AUC.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FBM-extract.cpp -o FBM-extract.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FBM-file.cpp -o FBM-file.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FBM-replace.cpp -o FBM-replace.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FBM-xptr.cpp -o FBM-xptr.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c arma-prod.cpp -o arma-prod.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c biglassoLin.cpp -o biglassoLin.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c biglassoLog.cpp -o biglassoLog.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c biglassoUtils.cpp -o biglassoUtils.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c colstats.cpp -o colstats.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c counts.cpp -o counts.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c decode.cpp -o decode.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c errorMsgs.cpp -o errorMsgs.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c prodMatVec.cpp -o prodMatVec.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c transpose.cpp -o transpose.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c univRegLin5.cpp -o univRegLin5.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c univRegLog.cpp -o univRegLog.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils-mat.cpp -o utils-mat.o -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o bigstatsr.so AUC.o FBM-extract.o FBM-file.o FBM-replace.o FBM-xptr.o RcppExports.o arma-prod.o biglassoLin.o biglassoLog.o biglassoUtils.o colstats.o counts.o decode.o errorMsgs.o prodMatVec.o transpose.o univRegLin5.o univRegLog.o utils-mat.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [bigstatsr.so] Error 1 -ERROR: compilation failed for package ‘bigstatsr’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/bigstatsr/new/bigstatsr.Rcheck/bigstatsr’ +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Warning message: +package ‘S4Vectors’ was built under R version 4.3.2 +Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘ggseqlogo’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘GenomicPlot’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/GenomicPlot/new/GenomicPlot.Rcheck/GenomicPlot’ + ``` ### CRAN ``` -* installing *source* package ‘bigstatsr’ ... -** package ‘bigstatsr’ successfully unpacked and MD5 sums checked +* installing *source* package ‘GenomicPlot’ ... ** using staged installation -** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c AUC.cpp -o AUC.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FBM-extract.cpp -o FBM-extract.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FBM-file.cpp -o FBM-file.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FBM-replace.cpp -o FBM-replace.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FBM-xptr.cpp -o FBM-xptr.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c arma-prod.cpp -o arma-prod.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c biglassoLin.cpp -o biglassoLin.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c biglassoLog.cpp -o biglassoLog.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c biglassoUtils.cpp -o biglassoUtils.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c colstats.cpp -o colstats.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c counts.cpp -o counts.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c decode.cpp -o decode.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c errorMsgs.cpp -o errorMsgs.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c prodMatVec.cpp -o prodMatVec.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c transpose.cpp -o transpose.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c univRegLin5.cpp -o univRegLin5.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c univRegLog.cpp -o univRegLog.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DARMA_DONT_PRINT_CXX11_WARNING -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/bigstatsr/rmio/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils-mat.cpp -o utils-mat.o -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o bigstatsr.so AUC.o FBM-extract.o FBM-file.o FBM-replace.o FBM-xptr.o RcppExports.o arma-prod.o biglassoLin.o biglassoLog.o biglassoUtils.o colstats.o counts.o decode.o errorMsgs.o prodMatVec.o transpose.o univRegLin5.o univRegLog.o utils-mat.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [bigstatsr.so] Error 1 -ERROR: compilation failed for package ‘bigstatsr’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/bigstatsr/old/bigstatsr.Rcheck/bigstatsr’ +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Warning message: +package ‘S4Vectors’ was built under R version 4.3.2 +Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘ggseqlogo’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘GenomicPlot’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/GenomicPlot/old/GenomicPlot.Rcheck/GenomicPlot’ + ``` -# BPRMeth +# HiLDA
-* Version: 1.10.0 -* Source code: https://github.com/cran/BPRMeth -* Date/Publication: 2019-05-02 -* Number of recursive dependencies: 83 +* Version: 1.16.0 +* GitHub: https://github.com/USCbiostats/HiLDA +* Source code: https://github.com/cran/HiLDA +* Date/Publication: 2023-10-24 +* Number of recursive dependencies: 144 -Run `revdep_details(,"BPRMeth")` for more info +Run `revdepcheck::revdep_details(, "HiLDA")` for more info
## In both -* checking whether package ‘BPRMeth’ can be installed ... ERROR +* checking whether package ‘HiLDA’ can be installed ... ERROR ``` Installation failed. - See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/BPRMeth/new/BPRMeth.Rcheck/00install.out’ for details. + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/HiLDA/new/HiLDA.Rcheck/00install.out’ for details. ``` ## Installation @@ -400,49 +297,77 @@ Run `revdep_details(,"BPRMeth")` for more info ### Devel ``` -* installing *source* package ‘BPRMeth’ ... +* installing *source* package ‘HiLDA’ ... ** using staged installation ** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BPRMeth/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BPRMeth/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang: error: unsupported option '-fopenmp' -make: *** [RcppExports.o] Error 1 -ERROR: compilation failed for package ‘BPRMeth’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/BPRMeth/new/BPRMeth.Rcheck/BPRMeth’ +using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ +using SDK: ‘’ +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c EMalgorithm.cpp -o EMalgorithm.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c checkBoundary.cpp -o checkBoundary.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convertFromToVector.cpp -o convertFromToVector.o +clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o HiLDA.so EMalgorithm.o RcppExports.o checkBoundary.o convertFromToVector.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation +... +** byte-compile and prepare package for lazy loading +Error: .onLoad failed in loadNamespace() for 'rjags', details: + call: dyn.load(file, DLLpath = DLLpath, ...) + error: unable to load shared object '/Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/rjags/libs/rjags.so': + dlopen(/Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/rjags/libs/rjags.so, 0x000A): Library not loaded: /usr/local/lib/libjags.4.dylib + Referenced from: <621A7307-C96A-3A25-BE2B-B9C2339518AE> /Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/rjags/libs/rjags.so + Reason: tried: '/usr/local/lib/libjags.4.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libjags.4.dylib' (no such file), '/usr/local/lib/libjags.4.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libjags.4.dylib' (no such file), '/Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home/lib/server/libjags.4.dylib' (no such file) +Execution halted +ERROR: lazy loading failed for package ‘HiLDA’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/HiLDA/new/HiLDA.Rcheck/HiLDA’ + ``` ### CRAN ``` -* installing *source* package ‘BPRMeth’ ... +* installing *source* package ‘HiLDA’ ... ** using staged installation ** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BPRMeth/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/BPRMeth/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang: error: unsupported option '-fopenmp' -make: *** [RcppExports.o] Error 1 -ERROR: compilation failed for package ‘BPRMeth’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/BPRMeth/old/BPRMeth.Rcheck/BPRMeth’ +using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ +using SDK: ‘’ +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c EMalgorithm.cpp -o EMalgorithm.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c checkBoundary.cpp -o checkBoundary.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convertFromToVector.cpp -o convertFromToVector.o +clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o HiLDA.so EMalgorithm.o RcppExports.o checkBoundary.o convertFromToVector.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation +... +** byte-compile and prepare package for lazy loading +Error: .onLoad failed in loadNamespace() for 'rjags', details: + call: dyn.load(file, DLLpath = DLLpath, ...) + error: unable to load shared object '/Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/rjags/libs/rjags.so': + dlopen(/Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/rjags/libs/rjags.so, 0x000A): Library not loaded: /usr/local/lib/libjags.4.dylib + Referenced from: <621A7307-C96A-3A25-BE2B-B9C2339518AE> /Users/clauswilke/github/cowplot/revdep/library.noindex/HiLDA/rjags/libs/rjags.so + Reason: tried: '/usr/local/lib/libjags.4.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libjags.4.dylib' (no such file), '/usr/local/lib/libjags.4.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libjags.4.dylib' (no such file), '/Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home/lib/server/libjags.4.dylib' (no such file) +Execution halted +ERROR: lazy loading failed for package ‘HiLDA’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/HiLDA/old/HiLDA.Rcheck/HiLDA’ + ``` -# CaseBasedReasoning +# mcmcabn
-* Version: 0.1 -* Source code: https://github.com/cran/CaseBasedReasoning -* BugReports: https://github.com/sipemu/case-based-reasoning/issues -* Date/Publication: 2018-06-12 10:34:11 UTC -* Number of recursive dependencies: 120 +* Version: 0.6 +* GitHub: NA +* Source code: https://github.com/cran/mcmcabn +* Date/Publication: 2023-09-28 12:20:02 UTC +* Number of recursive dependencies: 129 -Run `revdep_details(,"CaseBasedReasoning")` for more info +Run `revdepcheck::revdep_details(, "mcmcabn")` for more info
## In both -* checking whether package ‘CaseBasedReasoning’ can be installed ... ERROR +* checking whether package ‘mcmcabn’ can be installed ... ERROR ``` Installation failed. - See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/CaseBasedReasoning/new/CaseBasedReasoning.Rcheck/00install.out’ for details. + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/mcmcabn/new/mcmcabn.Rcheck/00install.out’ for details. ``` ## Installation @@ -450,285 +375,174 @@ Run `revdep_details(,"CaseBasedReasoning")` for more info ### Devel ``` -* installing *source* package ‘CaseBasedReasoning’ ... -** package ‘CaseBasedReasoning’ successfully unpacked and MD5 sums checked +* installing *source* package ‘mcmcabn’ ... +** package ‘mcmcabn’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c distanceAPI.cpp -o distanceAPI.o -In file included from distanceAPI.cpp:1: -./distanceAPI.h:134:16: warning: 'rfDepthXYDistanceAPI::calc' hides overloaded virtual function [-Woverloaded-virtual] - virtual void calc(arma::mat& xNodeIDs, arma::mat& yNodeIDs); - ^ -./distanceAPI.h:121:16: note: hidden overloaded virtual function 'rfDepthDistanceAPI::calc' declared here: different number of parameters (1 vs 2) - virtual void calc(arma::mat& xNodeIDs); - ^ -In file included from distanceAPI.cpp:1: -In file included from ./distanceAPI.h:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include/RcppCommon.h:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include/Rcpp/r/headers.h:59: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include/Rcpp/platform/compiler.h:153: -In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/unordered_map:384: -In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/__hash_table:16: -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3706:5: warning: destructor called on non-final 'weightedDistance' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] - __data_.second().~_Tp(); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3667:9: note: in instantiation of member function 'std::__1::__shared_ptr_emplace >::__on_zero_shared' requested here - __shared_ptr_emplace(_Alloc __a, _Args&& ...__args) - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:4327:26: note: in instantiation of function template specialization 'std::__1::__shared_ptr_emplace >::__shared_ptr_emplace' requested here - ::new(__hold2.get()) _CntrlBlk(__a2, _VSTD::forward<_Args>(__args)...); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:4706:29: note: in instantiation of function template specialization 'std::__1::shared_ptr::make_shared' requested here - return shared_ptr<_Tp>::make_shared(_VSTD::forward<_Args>(__args)...); - ^ -distanceAPI.cpp:27:16: note: in instantiation of function template specialization 'std::__1::make_shared' requested here - dist_ = std::make_shared(dist); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3706:23: note: qualify call to silence this warning - __data_.second().~_Tp(); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3706:5: warning: destructor called on non-final 'rangerProximity' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] - __data_.second().~_Tp(); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3667:9: note: in instantiation of member function 'std::__1::__shared_ptr_emplace >::__on_zero_shared' requested here - __shared_ptr_emplace(_Alloc __a, _Args&& ...__args) - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:4327:26: note: in instantiation of function template specialization 'std::__1::__shared_ptr_emplace >::__shared_ptr_emplace' requested here - ::new(__hold2.get()) _CntrlBlk(__a2, _VSTD::forward<_Args>(__args)...); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:4706:29: note: in instantiation of function template specialization 'std::__1::shared_ptr::make_shared' requested here - return shared_ptr<_Tp>::make_shared(_VSTD::forward<_Args>(__args)...); - ^ -distanceAPI.cpp:89:16: note: in instantiation of function template specialization 'std::__1::make_shared' requested here - dist_ = std::make_shared(dist); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3706:23: note: qualify call to silence this warning - __data_.second().~_Tp(); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3706:5: warning: destructor called on non-final 'rfDepthDistance' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] - __data_.second().~_Tp(); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3667:9: note: in instantiation of member function 'std::__1::__shared_ptr_emplace >::__on_zero_shared' requested here - __shared_ptr_emplace(_Alloc __a, _Args&& ...__args) - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:4327:26: note: in instantiation of function template specialization 'std::__1::__shared_ptr_emplace >::__shared_ptr_emplace' requested here - ::new(__hold2.get()) _CntrlBlk(__a2, _VSTD::forward<_Args>(__args)...); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:4706:29: note: in instantiation of function template specialization 'std::__1::shared_ptr::make_shared' requested here - return shared_ptr<_Tp>::make_shared(_VSTD::forward<_Args>(__args)...); - ^ -distanceAPI.cpp:124:16: note: in instantiation of function template specialization 'std::__1::make_shared' requested here - dist_ = std::make_shared(dist); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3706:23: note: qualify call to silence this warning - __data_.second().~_Tp(); - ^ -4 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c distances.cpp -o distances.o -In file included from distances.cpp:4: -./distanceAPI.h:134:16: warning: 'rfDepthXYDistanceAPI::calc' hides overloaded virtual function [-Woverloaded-virtual] - virtual void calc(arma::mat& xNodeIDs, arma::mat& yNodeIDs); - ^ -./distanceAPI.h:121:16: note: hidden overloaded virtual function 'rfDepthDistanceAPI::calc' declared here: different number of parameters (1 vs 2) - virtual void calc(arma::mat& xNodeIDs); - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c kNN.cpp -o kNN.o -kNN.cpp:25:19: warning: 'sort_index >' is deprecated [-Wdeprecated-declarations] - order = arma::sort_index(tmpDist, sortDirection); - ^ -/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:40:1: note: 'sort_index >' has been explicitly marked deprecated here -arma_deprecated -^ -/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:303:44: note: expanded from macro 'arma_deprecated' - #define arma_deprecated __attribute__((__deprecated__)) - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c order.cpp -o order.o -order.cpp:26:21: warning: 'sort_index >' is deprecated [-Wdeprecated-declarations] - order = arma::sort_index(x_.col(i), sortDirection_); - ^ -/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:40:1: note: 'sort_index >' has been explicitly marked deprecated here -arma_deprecated -^ -/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:303:44: note: expanded from macro 'arma_deprecated' - #define arma_deprecated __attribute__((__deprecated__)) - ^ -order.cpp:75:28: warning: 'sort_index >' is deprecated [-Wdeprecated-declarations] - arma::uvec order = arma::sort_index(x, sortDirection) + 1; - ^ -/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:40:1: note: 'sort_index >' has been explicitly marked deprecated here -arma_deprecated -^ -/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:303:44: note: expanded from macro 'arma_deprecated' - #define arma_deprecated __attribute__((__deprecated__)) - ^ -2 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c parallelTerminalNodeID.cpp -o parallelTerminalNodeID.o -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CaseBasedReasoning.so RcppExports.o distanceAPI.o distances.o kNN.o order.o parallelTerminalNodeID.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [CaseBasedReasoning.so] Error 1 -ERROR: compilation failed for package ‘CaseBasedReasoning’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/CaseBasedReasoning/new/CaseBasedReasoning.Rcheck/CaseBasedReasoning’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: .onLoad failed in loadNamespace() for 'rjags', details: + call: dyn.load(file, DLLpath = DLLpath, ...) + error: unable to load shared object '/Users/clauswilke/github/cowplot/revdep/library.noindex/mcmcabn/rjags/libs/rjags.so': + dlopen(/Users/clauswilke/github/cowplot/revdep/library.noindex/mcmcabn/rjags/libs/rjags.so, 0x000A): Library not loaded: /usr/local/lib/libjags.4.dylib + Referenced from: <621A7307-C96A-3A25-BE2B-B9C2339518AE> /Users/clauswilke/github/cowplot/revdep/library.noindex/mcmcabn/rjags/libs/rjags.so + Reason: tried: '/usr/local/lib/libjags.4.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libjags.4.dylib' (no such file), '/usr/local/lib/libjags.4.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libjags.4.dylib' (no such file), '/Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home/lib/server/libjags.4.dylib' (no such file) +Execution halted +ERROR: lazy loading failed for package ‘mcmcabn’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/mcmcabn/new/mcmcabn.Rcheck/mcmcabn’ + ``` ### CRAN ``` -* installing *source* package ‘CaseBasedReasoning’ ... -** package ‘CaseBasedReasoning’ successfully unpacked and MD5 sums checked +* installing *source* package ‘mcmcabn’ ... +** package ‘mcmcabn’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c distanceAPI.cpp -o distanceAPI.o -In file included from distanceAPI.cpp:1: -./distanceAPI.h:134:16: warning: 'rfDepthXYDistanceAPI::calc' hides overloaded virtual function [-Woverloaded-virtual] - virtual void calc(arma::mat& xNodeIDs, arma::mat& yNodeIDs); - ^ -./distanceAPI.h:121:16: note: hidden overloaded virtual function 'rfDepthDistanceAPI::calc' declared here: different number of parameters (1 vs 2) - virtual void calc(arma::mat& xNodeIDs); - ^ -In file included from distanceAPI.cpp:1: -In file included from ./distanceAPI.h:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/RcppArmadillo.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/RcppArmadilloForward.h:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include/RcppCommon.h:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include/Rcpp/r/headers.h:59: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include/Rcpp/platform/compiler.h:153: -In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/unordered_map:384: -In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/__hash_table:16: -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3706:5: warning: destructor called on non-final 'weightedDistance' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] - __data_.second().~_Tp(); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3667:9: note: in instantiation of member function 'std::__1::__shared_ptr_emplace >::__on_zero_shared' requested here - __shared_ptr_emplace(_Alloc __a, _Args&& ...__args) - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:4327:26: note: in instantiation of function template specialization 'std::__1::__shared_ptr_emplace >::__shared_ptr_emplace' requested here - ::new(__hold2.get()) _CntrlBlk(__a2, _VSTD::forward<_Args>(__args)...); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:4706:29: note: in instantiation of function template specialization 'std::__1::shared_ptr::make_shared' requested here - return shared_ptr<_Tp>::make_shared(_VSTD::forward<_Args>(__args)...); - ^ -distanceAPI.cpp:27:16: note: in instantiation of function template specialization 'std::__1::make_shared' requested here - dist_ = std::make_shared(dist); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3706:23: note: qualify call to silence this warning - __data_.second().~_Tp(); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3706:5: warning: destructor called on non-final 'rangerProximity' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] - __data_.second().~_Tp(); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3667:9: note: in instantiation of member function 'std::__1::__shared_ptr_emplace >::__on_zero_shared' requested here - __shared_ptr_emplace(_Alloc __a, _Args&& ...__args) - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:4327:26: note: in instantiation of function template specialization 'std::__1::__shared_ptr_emplace >::__shared_ptr_emplace' requested here - ::new(__hold2.get()) _CntrlBlk(__a2, _VSTD::forward<_Args>(__args)...); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:4706:29: note: in instantiation of function template specialization 'std::__1::shared_ptr::make_shared' requested here - return shared_ptr<_Tp>::make_shared(_VSTD::forward<_Args>(__args)...); - ^ -distanceAPI.cpp:89:16: note: in instantiation of function template specialization 'std::__1::make_shared' requested here - dist_ = std::make_shared(dist); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3706:23: note: qualify call to silence this warning - __data_.second().~_Tp(); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3706:5: warning: destructor called on non-final 'rfDepthDistance' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor] - __data_.second().~_Tp(); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3667:9: note: in instantiation of member function 'std::__1::__shared_ptr_emplace >::__on_zero_shared' requested here - __shared_ptr_emplace(_Alloc __a, _Args&& ...__args) - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:4327:26: note: in instantiation of function template specialization 'std::__1::__shared_ptr_emplace >::__shared_ptr_emplace' requested here - ::new(__hold2.get()) _CntrlBlk(__a2, _VSTD::forward<_Args>(__args)...); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:4706:29: note: in instantiation of function template specialization 'std::__1::shared_ptr::make_shared' requested here - return shared_ptr<_Tp>::make_shared(_VSTD::forward<_Args>(__args)...); - ^ -distanceAPI.cpp:124:16: note: in instantiation of function template specialization 'std::__1::make_shared' requested here - dist_ = std::make_shared(dist); - ^ -/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:3706:23: note: qualify call to silence this warning - __data_.second().~_Tp(); - ^ -4 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c distances.cpp -o distances.o -In file included from distances.cpp:4: -./distanceAPI.h:134:16: warning: 'rfDepthXYDistanceAPI::calc' hides overloaded virtual function [-Woverloaded-virtual] - virtual void calc(arma::mat& xNodeIDs, arma::mat& yNodeIDs); - ^ -./distanceAPI.h:121:16: note: hidden overloaded virtual function 'rfDepthDistanceAPI::calc' declared here: different number of parameters (1 vs 2) - virtual void calc(arma::mat& xNodeIDs); - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c kNN.cpp -o kNN.o -kNN.cpp:25:19: warning: 'sort_index >' is deprecated [-Wdeprecated-declarations] - order = arma::sort_index(tmpDist, sortDirection); - ^ -/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:40:1: note: 'sort_index >' has been explicitly marked deprecated here -arma_deprecated -^ -/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:303:44: note: expanded from macro 'arma_deprecated' - #define arma_deprecated __attribute__((__deprecated__)) - ^ -1 warning generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c order.cpp -o order.o -order.cpp:26:21: warning: 'sort_index >' is deprecated [-Wdeprecated-declarations] - order = arma::sort_index(x_.col(i), sortDirection_); - ^ -/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:40:1: note: 'sort_index >' has been explicitly marked deprecated here -arma_deprecated -^ -/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:303:44: note: expanded from macro 'arma_deprecated' - #define arma_deprecated __attribute__((__deprecated__)) - ^ -order.cpp:75:28: warning: 'sort_index >' is deprecated [-Wdeprecated-declarations] - arma::uvec order = arma::sort_index(x, sortDirection) + 1; - ^ -/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:40:1: note: 'sort_index >' has been explicitly marked deprecated here -arma_deprecated -^ -/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:303:44: note: expanded from macro 'arma_deprecated' - #define arma_deprecated __attribute__((__deprecated__)) - ^ -2 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/CaseBasedReasoning/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c parallelTerminalNodeID.cpp -o parallelTerminalNodeID.o -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CaseBasedReasoning.so RcppExports.o distanceAPI.o distances.o kNN.o order.o parallelTerminalNodeID.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [CaseBasedReasoning.so] Error 1 -ERROR: compilation failed for package ‘CaseBasedReasoning’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/CaseBasedReasoning/old/CaseBasedReasoning.Rcheck/CaseBasedReasoning’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: .onLoad failed in loadNamespace() for 'rjags', details: + call: dyn.load(file, DLLpath = DLLpath, ...) + error: unable to load shared object '/Users/clauswilke/github/cowplot/revdep/library.noindex/mcmcabn/rjags/libs/rjags.so': + dlopen(/Users/clauswilke/github/cowplot/revdep/library.noindex/mcmcabn/rjags/libs/rjags.so, 0x000A): Library not loaded: /usr/local/lib/libjags.4.dylib + Referenced from: <621A7307-C96A-3A25-BE2B-B9C2339518AE> /Users/clauswilke/github/cowplot/revdep/library.noindex/mcmcabn/rjags/libs/rjags.so + Reason: tried: '/usr/local/lib/libjags.4.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libjags.4.dylib' (no such file), '/usr/local/lib/libjags.4.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libjags.4.dylib' (no such file), '/Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home/lib/server/libjags.4.dylib' (no such file) +Execution halted +ERROR: lazy loading failed for package ‘mcmcabn’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/mcmcabn/old/mcmcabn.Rcheck/mcmcabn’ + ``` -# cytometree +# orthos + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/orthos +* Date/Publication: 2023-11-02 +* Number of recursive dependencies: 180 + +Run `revdepcheck::revdep_details(, "orthos")` for more info + +
+ +## In both + +* checking examples ... ERROR + ``` + Running examples in ‘orthos-Ex.R’ failed + The error most likely occurred in: + + > ### Name: loadContrastDatabase + > ### Title: Load contrast database + > ### Aliases: loadContrastDatabase + > + > ### ** Examples + > + > + ... + demo_decomposed_contrasts_mouse_hdf5 already present in cache at: /Users/clauswilke/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5 + updating resource /Users/clauswilke/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5 + Error in stop_if_bad_dir(dir, prefix) : Directory + "/Users/clauswilke/Library/Caches/org.R-project.R/R/ExperimentHub" does + not seem to contain an HDF5-based SummarizedExperiment object + previously saved with saveHDF5SummarizedExperiment(..., + prefix="mouse_v212_NDF_c100_DEMO"). Make sure you're using the same + 'prefix' that was used when the object was saved. + Calls: loadContrastDatabase -> -> stop_if_bad_dir + Execution halted + ``` + +* R CMD check timed out + + +* checking whether package ‘orthos’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘SummarizedExperiment’ was built under R version 4.3.2 + Warning: package ‘S4Vectors’ was built under R version 4.3.2 + Found the following additional notes/warnings: + Non-staged installation was used + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/orthos/new/orthos.Rcheck/00install.out’ for details. + ``` + +# pareg + +
+ +* Version: 1.6.0 +* GitHub: https://github.com/cbg-ethz/pareg +* Source code: https://github.com/cran/pareg +* Date/Publication: 2023-10-24 +* Number of recursive dependencies: 320 + +Run `revdepcheck::revdep_details(, "pareg")` for more info + +
+ +## In both + +* R CMD check timed out + + +* checking for portable file names ... NOTE + ``` + Found the following non-portable file paths: + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/config.yaml + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/params.csv + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/config.yaml + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/params.csv + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/config.yaml + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/params.csv + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/config.yaml + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/params.csv + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter/config.yaml + ... + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_response_distribution/params.csv + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/config.yaml + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/params.csv + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/workflow/scripts/compare_rocauc_vs_loss.R + pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter + + Tarballs are only required to store paths of up to 100 bytes and cannot + store those of more than 256 bytes, with restrictions including to 100 + bytes for the final component. + See section ‘Package structure’ in the ‘Writing R Extensions’ manual. + ``` + +* checking whether package ‘pareg’ can be installed ... NOTE + ``` + Found the following notes/warnings: + Non-staged installation was used + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/pareg/new/pareg.Rcheck/00install.out’ for details. + ``` + +# phemd
-* Version: 1.3.0 -* Source code: https://github.com/cran/cytometree -* BugReports: https://github.com/sistm/Cytometree/issues -* Date/Publication: 2019-01-12 13:10:03 UTC -* Number of recursive dependencies: 57 +* Version: 1.18.0 +* GitHub: NA +* Source code: https://github.com/cran/phemd +* Date/Publication: 2023-10-24 +* Number of recursive dependencies: 233 -Run `revdep_details(,"cytometree")` for more info +Run `revdepcheck::revdep_details(, "phemd")` for more info
## In both -* checking whether package ‘cytometree’ can be installed ... ERROR +* checking whether package ‘phemd’ can be installed ... ERROR ``` Installation failed. - See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/cytometree/new/cytometree.Rcheck/00install.out’ for details. + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/phemd/new/phemd.Rcheck/00install.out’ for details. ``` ## Installation @@ -736,60 +550,129 @@ Run `revdep_details(,"cytometree")` for more info ### Devel ``` -* installing *source* package ‘cytometree’ ... -** package ‘cytometree’ successfully unpacked and MD5 sums checked +* installing *source* package ‘phemd’ ... ** using staged installation -** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/cytometree/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/cytometree/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FmeasureC.cpp -o FmeasureC.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/cytometree/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/cytometree/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cytometree.so FmeasureC.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [cytometree.so] Error 1 -ERROR: compilation failed for package ‘cytometree’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/cytometree/new/cytometree.Rcheck/cytometree’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘monocle’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + there is no package called ‘qlcMatrix’ +Execution halted +ERROR: lazy loading failed for package ‘phemd’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/phemd/new/phemd.Rcheck/phemd’ + ``` ### CRAN ``` -* installing *source* package ‘cytometree’ ... -** package ‘cytometree’ successfully unpacked and MD5 sums checked +* installing *source* package ‘phemd’ ... ** using staged installation -** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/cytometree/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/cytometree/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FmeasureC.cpp -o FmeasureC.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/cytometree/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/cytometree/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cytometree.so FmeasureC.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [cytometree.so] Error 1 -ERROR: compilation failed for package ‘cytometree’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/cytometree/old/cytometree.Rcheck/cytometree’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘monocle’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + there is no package called ‘qlcMatrix’ +Execution halted +ERROR: lazy loading failed for package ‘phemd’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/phemd/old/phemd.Rcheck/phemd’ + ``` -# foreSIGHT +# rliger
-* Version: 0.9.6 -* Source code: https://github.com/cran/foreSIGHT -* Date/Publication: 2018-07-10 08:00:26 UTC -* Number of recursive dependencies: 55 +* Version: +* GitHub: https://github.com/wilkelab/cowplot +* Source code: NA +* Number of recursive dependencies: 0 + +
+ +## Error before installation + +### Devel + +``` + + + +installing the source package ‘reactome.db’ + + + +``` +### CRAN -Run `revdep_details(,"foreSIGHT")` for more info +``` + + + +installing the source package ‘reactome.db’ + + + +``` +# scGPS + +
+ +* Version: +* GitHub: https://github.com/wilkelab/cowplot +* Source code: NA +* Number of recursive dependencies: 0
-## Newly broken +## Error before installation + +### Devel + +``` + -* checking whether package ‘foreSIGHT’ can be installed ... ERROR + +installing the source package ‘reactome.db’ + + + +``` +### CRAN + +``` + + + +installing the source package ‘reactome.db’ + + + +``` +# seqArchRplus + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/snikumbh/seqArchRplus +* Source code: https://github.com/cran/seqArchRplus +* Date/Publication: 2023-10-24 +* Number of recursive dependencies: 292 + +Run `revdepcheck::revdep_details(, "seqArchRplus")` for more info + +
+ +## In both + +* checking whether package ‘seqArchRplus’ can be installed ... ERROR ``` Installation failed. - See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/foreSIGHT/new/foreSIGHT.Rcheck/00install.out’ for details. + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/seqArchRplus/new/seqArchRplus.Rcheck/00install.out’ for details. ``` ## Installation @@ -797,58 +680,96 @@ Run `revdep_details(,"foreSIGHT")` for more info ### Devel ``` -* installing *source* package ‘foreSIGHT’ ... -** package ‘foreSIGHT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘seqArchRplus’ ... ** using staged installation ** R -** data ** inst ** byte-compile and prepare package for lazy loading -Error: object ‘ggsave’ is not exported by 'namespace:cowplot' +Warning message: +package ‘S4Vectors’ was built under R version 4.3.2 +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘ggseqlogo’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘foreSIGHT’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/foreSIGHT/new/foreSIGHT.Rcheck/foreSIGHT’ +ERROR: lazy loading failed for package ‘seqArchRplus’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/seqArchRplus/new/seqArchRplus.Rcheck/seqArchRplus’ + ``` ### CRAN ``` -* installing *source* package ‘foreSIGHT’ ... -** package ‘foreSIGHT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘seqArchRplus’ ... ** using staged installation ** R -** data ** inst ** byte-compile and prepare package for lazy loading -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (foreSIGHT) +Warning message: +package ‘S4Vectors’ was built under R version 4.3.2 +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘ggseqlogo’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘seqArchRplus’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/seqArchRplus/old/seqArchRplus.Rcheck/seqArchRplus’ + ``` -# graper +# simplifyEnrichment
-* Version: 1.0.0 -* Source code: https://github.com/cran/graper -* Date/Publication: 2019-05-02 -* Number of recursive dependencies: 58 +* Version: +* GitHub: https://github.com/wilkelab/cowplot +* Source code: NA +* Number of recursive dependencies: 0 + +
+ +## Error before installation + +### Devel -Run `revdep_details(,"graper")` for more info +``` + + + +installing the source packages ‘DO.db’, ‘hu6800.db’, ‘reactome.db’ + + + +``` +### CRAN + +``` + + + +installing the source packages ‘DO.db’, ‘hu6800.db’, ‘reactome.db’ + + + +``` +# SpatialOmicsOverlay + +
+ +* Version: 1.2.1 +* GitHub: NA +* Source code: https://github.com/cran/SpatialOmicsOverlay +* Date/Publication: 2023-10-26 +* Number of recursive dependencies: 185 + +Run `revdepcheck::revdep_details(, "SpatialOmicsOverlay")` for more info
## In both -* checking whether package ‘graper’ can be installed ... ERROR +* checking whether package ‘SpatialOmicsOverlay’ can be installed ... ERROR ``` Installation failed. - See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/graper/new/graper.Rcheck/00install.out’ for details. + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/SpatialOmicsOverlay/new/SpatialOmicsOverlay.Rcheck/00install.out’ for details. ``` ## Installation @@ -856,79 +777,139 @@ Run `revdep_details(,"graper")` for more info ### Devel ``` -* installing *source* package ‘graper’ ... +* installing *source* package ‘SpatialOmicsOverlay’ ... ** using staged installation -** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/graper/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/graper/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/graper/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/graper/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/graper/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/graper/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [graper.so] Error 1 -ERROR: compilation failed for package ‘graper’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/graper/new/graper.Rcheck/graper’ +** R +** inst +** byte-compile and prepare package for lazy loading +The operation couldn’t be completed. Unable to locate a Java Runtime. +Please visit http://www.java.com for information on installing Java. + +Warning in system("/usr/libexec/java_home", intern = TRUE) : + running command '/usr/libexec/java_home' had status 1 +Warning in fun(libname, pkgname) : + Cannot find JVM library 'NA/lib/server/libjvm.dylib' +Install Java and/or check JAVA_HOME (if in doubt, do NOT set it, it will be detected) +Error: .onLoad failed in loadNamespace() for 'rJava', details: + call: fun(libname, pkgname) + error: JVM could not be found +Execution halted +ERROR: lazy loading failed for package ‘SpatialOmicsOverlay’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/SpatialOmicsOverlay/new/SpatialOmicsOverlay.Rcheck/SpatialOmicsOverlay’ + ``` ### CRAN ``` -* installing *source* package ‘graper’ ... +* installing *source* package ‘SpatialOmicsOverlay’ ... ** using staged installation -** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/graper/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/graper/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/graper/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/graper/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/graper/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/graper/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c fit_graper.cpp -o fit_graper.o -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o graper.so RcppExports.o fit_graper.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [graper.so] Error 1 -ERROR: compilation failed for package ‘graper’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/graper/old/graper.Rcheck/graper’ +** R +** inst +** byte-compile and prepare package for lazy loading +The operation couldn’t be completed. Unable to locate a Java Runtime. +Please visit http://www.java.com for information on installing Java. + +Warning in system("/usr/libexec/java_home", intern = TRUE) : + running command '/usr/libexec/java_home' had status 1 +Warning in fun(libname, pkgname) : + Cannot find JVM library 'NA/lib/server/libjvm.dylib' +Install Java and/or check JAVA_HOME (if in doubt, do NOT set it, it will be detected) +Error: .onLoad failed in loadNamespace() for 'rJava', details: + call: fun(libname, pkgname) + error: JVM could not be found +Execution halted +ERROR: lazy loading failed for package ‘SpatialOmicsOverlay’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/SpatialOmicsOverlay/old/SpatialOmicsOverlay.Rcheck/SpatialOmicsOverlay’ + ``` -# MutationalPatterns +# stppSim
-* Version: 1.10.0 -* Source code: https://github.com/cran/MutationalPatterns -* URL: https://doi.org/10.1186/s13073-018-0539-0 -* Date/Publication: 2019-05-02 -* Number of recursive dependencies: 120 +* Version: 1.3.2 +* GitHub: https://github.com/Manalytics/stppSim +* Source code: https://github.com/cran/stppSim +* Date/Publication: 2023-10-29 21:20:02 UTC +* Number of recursive dependencies: 134 -Run `revdep_details(,"MutationalPatterns")` for more info +Run `revdepcheck::revdep_details(, "stppSim")` for more info
## In both -* R CMD check timed out - +* checking whether package ‘stppSim’ can be installed ... ERROR + ``` + Installation failed. + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/stppSim/new/stppSim.Rcheck/00install.out’ for details. + ``` -# poppr +## Installation + +### Devel + +``` +* installing *source* package ‘stppSim’ ... +** package ‘stppSim’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +tcltk DLL is linked to '/opt/X11/lib/libX11.6.dylib' +Error: .onLoad failed in loadNamespace() for 'tcltk', details: + call: fun(libname, pkgname) + error: X11 library is missing: install XQuartz from www.xquartz.org +Execution halted +ERROR: lazy loading failed for package ‘stppSim’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/stppSim/new/stppSim.Rcheck/stppSim’ + + +``` +### CRAN + +``` +* installing *source* package ‘stppSim’ ... +** package ‘stppSim’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +tcltk DLL is linked to '/opt/X11/lib/libX11.6.dylib' +Error: .onLoad failed in loadNamespace() for 'tcltk', details: + call: fun(libname, pkgname) + error: X11 library is missing: install XQuartz from www.xquartz.org +Execution halted +ERROR: lazy loading failed for package ‘stppSim’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/stppSim/old/stppSim.Rcheck/stppSim’ + + +``` +# TOmicsVis
-* Version: 2.8.3 -* Source code: https://github.com/cran/poppr -* URL: https://grunwaldlab.github.io/poppr, https://github.com/grunwaldlab/poppr, https://grunwaldlab.github.io/Population_Genetics_in_R/ -* BugReports: https://github.com/grunwaldlab/poppr/issues -* Date/Publication: 2019-06-18 16:21:21 UTC -* Number of recursive dependencies: 98 +* Version: 2.0.0 +* GitHub: https://github.com/benben-miao/TOmicsVis +* Source code: https://github.com/cran/TOmicsVis +* Date/Publication: 2023-08-28 18:30:02 UTC +* Number of recursive dependencies: 265 -Run `revdep_details(,"poppr")` for more info +Run `revdepcheck::revdep_details(, "TOmicsVis")` for more info
## In both -* checking whether package ‘poppr’ can be installed ... ERROR +* checking whether package ‘TOmicsVis’ can be installed ... ERROR ``` Installation failed. - See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/poppr/new/poppr.Rcheck/00install.out’ for details. + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/TOmicsVis/new/TOmicsVis.Rcheck/00install.out’ for details. ``` ## Installation @@ -936,50 +917,65 @@ Run `revdep_details(,"poppr")` for more info ### Devel ``` -* installing *source* package ‘poppr’ ... -** package ‘poppr’ successfully unpacked and MD5 sums checked +* installing *source* package ‘TOmicsVis’ ... +** package ‘TOmicsVis’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c adjust_missing.c -o adjust_missing.o -clang: error: unsupported option '-fopenmp' -make: *** [adjust_missing.o] Error 1 -ERROR: compilation failed for package ‘poppr’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/poppr/new/poppr.Rcheck/poppr’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +tcltk DLL is linked to '/opt/X11/lib/libX11.6.dylib' +Error: .onLoad failed in loadNamespace() for 'tcltk', details: + call: fun(libname, pkgname) + error: X11 library is missing: install XQuartz from www.xquartz.org +Execution halted +ERROR: lazy loading failed for package ‘TOmicsVis’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/TOmicsVis/new/TOmicsVis.Rcheck/TOmicsVis’ + ``` ### CRAN ``` -* installing *source* package ‘poppr’ ... -** package ‘poppr’ successfully unpacked and MD5 sums checked +* installing *source* package ‘TOmicsVis’ ... +** package ‘TOmicsVis’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c adjust_missing.c -o adjust_missing.o -clang: error: unsupported option '-fopenmp' -make: *** [adjust_missing.o] Error 1 -ERROR: compilation failed for package ‘poppr’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/poppr/old/poppr.Rcheck/poppr’ +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +tcltk DLL is linked to '/opt/X11/lib/libX11.6.dylib' +Error: .onLoad failed in loadNamespace() for 'tcltk', details: + call: fun(libname, pkgname) + error: X11 library is missing: install XQuartz from www.xquartz.org +Execution halted +ERROR: lazy loading failed for package ‘TOmicsVis’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/TOmicsVis/old/TOmicsVis.Rcheck/TOmicsVis’ + ``` -# telefit +# valse
-* Version: 1.0.1 -* Source code: https://github.com/cran/telefit -* Date/Publication: 2019-02-18 10:50:03 UTC -* Number of recursive dependencies: 78 +* Version: 0.1-0 +* GitHub: NA +* Source code: https://github.com/cran/valse +* Date/Publication: 2021-05-31 08:00:02 UTC +* Number of recursive dependencies: 55 -Run `revdep_details(,"telefit")` for more info +Run `revdepcheck::revdep_details(, "valse")` for more info
## In both -* checking whether package ‘telefit’ can be installed ... ERROR +* checking whether package ‘valse’ can be installed ... ERROR ``` Installation failed. - See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/telefit/new/telefit.Rcheck/00install.out’ for details. + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/valse/new/valse.Rcheck/00install.out’ for details. ``` ## Installation @@ -987,2100 +983,40 @@ Run `revdep_details(,"telefit")` for more info ### Devel ``` -* installing *source* package ‘telefit’ ... -** package ‘telefit’ successfully unpacked and MD5 sums checked +* installing *source* package ‘valse’ ... +** package ‘valse’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c GibbsSampler.cpp -o GibbsSampler.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RWSampler.cpp -o RWSampler.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -17 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c covs.cpp -o covs.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c distributions.cpp -o distributions.o -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -17 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c glm_gmrf.cpp -o glm_gmrf.o -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -17 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mcstat.cpp -o mcstat.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c numAlg.cpp -o numAlg.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c stpglmmod.cpp -o stpglmmod.o -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -17 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c stpmod.cpp -o stpmod.o -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -stpmod.cpp:967:8: warning: unused variable 'ncats' [-Wunused-variable] - int ncats = cat_breaks.n_elem + 1; - ^ -stpmod.cpp:470:32: warning: private field 'R' is not used [-Wunused-private-field] - double CProposed_logdet, one, R; - ^ -19 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c stpnotation.cpp -o stpnotation.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c svcMod.cpp -o svcMod.o -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -17 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c svcPredict.cpp -o svcPredict.o -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -17 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c transformations.cpp -o transformations.o -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o telefit.so GibbsSampler.o RWSampler.o RcppExports.o covs.o distributions.o glm_gmrf.o mcstat.o numAlg.o stpglmmod.o stpmod.o stpnotation.o svcMod.o svcPredict.o transformations.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [telefit.so] Error 1 -ERROR: compilation failed for package ‘telefit’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/telefit/new/telefit.Rcheck/telefit’ +using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ +using SDK: ‘’ +clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c EMGLLF.c -o EMGLLF.o +EMGLLF.c:4:10: fatal error: 'gsl/gsl_linalg.h' file not found +#include + ^~~~~~~~~~~~~~~~~~ +1 error generated. +make: *** [EMGLLF.o] Error 1 +ERROR: compilation failed for package ‘valse’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/valse/new/valse.Rcheck/valse’ + ``` ### CRAN ``` -* installing *source* package ‘telefit’ ... -** package ‘telefit’ successfully unpacked and MD5 sums checked +* installing *source* package ‘valse’ ... +** package ‘valse’ successfully unpacked and MD5 sums checked ** using staged installation ** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c GibbsSampler.cpp -o GibbsSampler.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RWSampler.cpp -o RWSampler.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from RcppExports.cpp:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -17 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c covs.cpp -o covs.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c distributions.cpp -o distributions.o -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from distributions.cpp:1: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -17 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c glm_gmrf.cpp -o glm_gmrf.o -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from glm_gmrf.cpp:1: -In file included from ./glm_gmrf.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -17 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mcstat.cpp -o mcstat.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c numAlg.cpp -o numAlg.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c stpglmmod.cpp -o stpglmmod.o -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpglmmod.cpp:9: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -17 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c stpmod.cpp -o stpmod.o -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from stpmod.cpp:4: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -stpmod.cpp:967:8: warning: unused variable 'ncats' [-Wunused-variable] - int ncats = cat_breaks.n_elem + 1; - ^ -stpmod.cpp:470:32: warning: private field 'R' is not used [-Wunused-private-field] - double CProposed_logdet, one, R; - ^ -19 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c stpnotation.cpp -o stpnotation.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c svcMod.cpp -o svcMod.o -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcMod.cpp:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -17 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c svcPredict.cpp -o svcPredict.o -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:1: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Core:535: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:2: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/LU:47: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:12: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Jacobi:29: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:3: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Cholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:4: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/QR:17: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Householder:27: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:5: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SVD:48: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:6: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Geometry:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:30: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Dense:7: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Eigenvalues:58: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:26: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCore:66: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:27: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/OrderingMethods:71: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:29: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseCholesky:43: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/SparseQR:35: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:31: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/Sparse:33: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/IterativeLinearSolvers:46: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:32: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/CholmodSupport:45: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:35: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:39: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/Polynomials:135: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -In file included from svcPredict.cpp:9: -In file included from ./distributions.h:8: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigen.h:25: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/RcppEigenForward.h:40: -In file included from /Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/SparseExtra:51: -/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] - #pragma clang diagnostic pop - ^ -17 warnings generated. -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/Rcpp/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppArmadillo/include" -I"/Users/clauswilke/github/cowplot/revdep/library.noindex/telefit/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c transformations.cpp -o transformations.o -clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o telefit.so GibbsSampler.o RWSampler.o RcppExports.o covs.o distributions.o glm_gmrf.o mcstat.o numAlg.o stpglmmod.o stpmod.o stpnotation.o svcMod.o svcPredict.o transformations.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -ld: library not found for -lgfortran -clang: error: linker command failed with exit code 1 (use -v to see invocation) -make: *** [telefit.so] Error 1 -ERROR: compilation failed for package ‘telefit’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/telefit/old/telefit.Rcheck/telefit’ +using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ +using SDK: ‘’ +clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c EMGLLF.c -o EMGLLF.o +EMGLLF.c:4:10: fatal error: 'gsl/gsl_linalg.h' file not found +#include + ^~~~~~~~~~~~~~~~~~ +1 error generated. +make: *** [EMGLLF.o] Error 1 +ERROR: compilation failed for package ‘valse’ +* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/valse/old/valse.Rcheck/valse’ + ``` diff --git a/revdep/problems.md b/revdep/problems.md index 9833b08..e2e182b 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,14 +1,14 @@ -# AneuFinder +# dce
-* Version: 1.12.0 -* Source code: https://github.com/cran/AneuFinder -* URL: https://github.com/ataudt/aneufinder.git -* Date/Publication: 2019-05-02 -* Number of recursive dependencies: 102 +* Version: 1.10.0 +* GitHub: https://github.com/cbg-ethz/dce +* Source code: https://github.com/cran/dce +* Date/Publication: 2023-10-24 +* Number of recursive dependencies: 324 -Run `revdep_details(,"AneuFinder")` for more info +Run `revdepcheck::revdep_details(, "dce")` for more info
@@ -16,27 +16,88 @@ Run `revdep_details(,"AneuFinder")` for more info * checking examples ... ERROR ``` + Running examples in ‘dce-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_pathway_info + > ### Title: Dataframe containing meta-information of pathways in database + > ### Aliases: get_pathway_info + > + > ### ** Examples + > + > head(get_pathway_info(database_list = c("kegg"))) ... - Subsetting specified chromosomes ... 0.01s - Calculating coverage ... 0.14s - Splitting into strands ... 0.03s - Counting overlaps for binsize_1e+06 ... 0.06s - Warning in bam2GRanges(file, bamindex, chromosomes = chromosomes, pairedEndReads = pairedEndReads, : - Not using chromosomes MMCHR1_RANDOM_CTG1, MMCHR1_RANDOM_CTG2, MMCHR1_RANDOM_CTG3, MMCHR1_RANDOM_CTG4, MMCHR1_RANDOM_CTG5, MMCHR4UN_CTG1, MMCHR4UN_CTG3, MMCHR4UN_CTG2, MMCHR4UN_CTG4, MMCHR4UN_CTG5, MMCHR4UN_CTG6, MMCHR5_RANDOM_CTG4, MMCHR5_RANDOM_CTG1, MMCHR5_RANDOM_CTG2, MMCHR5_RANDOM_CTG3, MMCHR5_RANDOM_CTG5, MMCHR7_RANDOM_CTG1, MMCHRX_RANDOM_CTG2, MMCHRY_CTGU1, MMCHRY_CTGU2, MMCHRY_CTGU3, MMCHRY_CTGU4, MSCHRUN_CTG1, MSCHRUN_CTG13, MSCHRUN_CTG14, MSCHRUN_CTG21, MSCHRUN_CTG2, MSCHRUN_CTG22, MSCHRUN_CTG19, MSCHRUN_CTG16, MSCHRUN_CTG3, MSCHRUN_CTG20, MSCHRUN_CTG4, MSCHRUN_CTG5, MSCHRUN_CTG6, MSCHRUN_CTG7, MSCHRUN_CTG17, MSCHRUN_CTG18, MSCHRUN_CTG9, MSCHRUN_CTG10, MSCHRUN_CTG11, MSCHRUN_CTG12, MSCHRUN_CTG15, MSCHRUN_CTG23 because they are not in the data. - Reading file BB150803_IV_074.bam ... 0.15s - Converting to GRanges ... 0.01s - Filtering reads ... 0.01s - Warning in binReads(file, assembly = assembly, min.mapq = min.mapq, pairedEndReads = pairedEndReads, : - Could not find chromosomes MMCHR1_RANDOM_CTG1, MMCHR1_RANDOM_CTG2, MMCHR1_RANDOM_CTG3, MMCHR1_RANDOM_CTG4, MMCHR1_RANDOM_CTG5, MMCHR4UN_CTG1, MMCHR4UN_CTG3, MMCHR4UN_CTG2, MMCHR4UN_CTG4, MMCHR4UN_CTG5, MMCHR4UN_CTG6, MMCHR5_RANDOM_CTG4, MMCHR5_RANDOM_CTG1, MMCHR5_RANDOM_CTG2, MMCHR5_RANDOM_CTG3, MMCHR5_RANDOM_CTG5, MMCHR7_RANDOM_CTG1, MMCHRX_RANDOM_CTG2, MMCHRY_CTGU1, MMCHRY_CTGU2, MMCHRY_CTGU3, MMCHRY_CTGU4, MSCHRUN_CTG1, MSCHRUN_CTG13, MSCHRUN_CTG14, MSCHRUN_CTG21, MSCHRUN_CTG2, MSCHRUN_CTG22, MSCHRUN_CTG19, MSCHRUN_CTG16, MSCHRUN_CTG3, MSCHRUN_CTG20, MSCHRUN_CTG4, MSCHRUN_CTG5, MSCHRUN_CTG6, MSCHRUN_CTG7, MSCHRUN_CTG17, MSCHRUN_CTG18, MSCHRUN_CTG9, MSCHRUN_CTG10, MSCHRUN_CTG11, MSCHRUN_CTG12, MSCHRUN_CTG15, MSCHRUN_CTG23. - Subsetting specified chromosomes ... 0.01s - Removing duplicate reads ... 0.05s - Calculating coverage ... 0.15s - Splitting into strands ... 0.01s - Counting overlaps for binsize_1e+06 ... 0.06s - > ## Plot a histogram to decide on a sensible cutoff - > qplot(pre.blacklist$ratio, binwidth=0.1) - Error in qplot(pre.blacklist$ratio, binwidth = 0.1) : - could not find function "qplot" + 11. │ └─graphite::pathways(query_species, database) + 12. │ └─graphite:::loadData(paste(species, database, sep = "-")) + 13. │ └─graphite:::archivePath(name) + 14. │ └─graphite:::archiveDir() + 15. │ └─base::stop("error creating directory: ", d) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.3Mb + sub-directories of 1Mb or more: + doc 3.5Mb + ``` + +* checking R code for possible problems ... NOTE + ``` + plot_network: no visible binding for global variable ‘.’ + Undefined global functions or variables: + . + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 3 marked UTF-8 strings + ``` + +# multiWGCNA + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/multiWGCNA +* Date/Publication: 2023-10-24 +* Number of recursive dependencies: 175 + +Run `revdepcheck::revdep_details(, "multiWGCNA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘multiWGCNA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cleanDatExpr + > ### Title: cleanDatExpr + > ### Aliases: cleanDatExpr + > + > ### ** Examples + > + > library(ExperimentHub) + ... + 'lattice', 'learnr', 'lpSolve', 'markdown', 'mgcv', 'nlme', 'plyr', 'ragg', + 'reticulate', 'rnaturalearth', 'rpart', 's2', 'sass', 'scales', 'shiny', + 'sp', 'spatial', 'stringi', 'stringr', 'survival', 'systemfonts', 'terra', + 'testthat', 'textshaping', 'tinytex', 'units', 'vroom', 'waldo', 'wk', 'xml2' + loading from cache + Error: failed to load resource + name: EH8223 + title: Astrocyte Ribotag SummarizedExperiment + reason: error in evaluating the argument 'x' in selecting a method for function 'get': error reading from connection Execution halted ``` @@ -44,66 +105,119 @@ Run `revdep_details(,"AneuFinder")` for more info * checking R code for possible problems ... NOTE ``` - Aneufinder: multiple local function definitions for ‘parallel.helper’ - with different formal arguments + bidirectionalBestMatches: no visible binding for global variable ‘mod1’ + bidirectionalBestMatches: no visible binding for global variable ‘mod2’ + bidirectionalBestMatches: no visible binding for global variable + ‘overlap’ + coexpressionLineGraph: no visible binding for global variable ‘Var1’ + coexpressionLineGraph: no visible binding for global variable ‘value’ + coexpressionLineGraph: no visible binding for global variable ‘Var2’ + computeOverlapsFromWGCNA: no visible binding for global variable ‘mod1’ + computeOverlapsFromWGCNA: no visible binding for global variable ‘mod2’ + continuousFlowPlot: no visible global function definition for ‘ulist’ + ... + ‘Zsum’ + preservationComparisonPlot: no visible binding for global variable + ‘trait’ + preservationComparisonPlot: no visible binding for global variable + ‘Module’ + topNGenes: no visible binding for global variable ‘kWithin’ + Undefined global functions or variables: + Correlation Expression Gene Module Sample Status Var1 Var2 Zscore + Zsum error kWithin layout_with_fr log10Pvalue mod1 mod2 overlap p.adj + stratum trait ulist uniqueSortedData value zScoreMatrix ``` -# foreSIGHT +# ORFik
-* Version: 0.9.6 -* Source code: https://github.com/cran/foreSIGHT -* Date/Publication: 2018-07-10 08:00:26 UTC -* Number of recursive dependencies: 55 +* Version: 1.22.1 +* GitHub: https://github.com/Roleren/ORFik +* Source code: https://github.com/cran/ORFik +* Date/Publication: 2023-12-08 +* Number of recursive dependencies: 156 -Run `revdep_details(,"foreSIGHT")` for more info +Run `revdepcheck::revdep_details(, "ORFik")` for more info
## Newly broken -* checking whether package ‘foreSIGHT’ can be installed ... ERROR - ``` - Installation failed. - See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/foreSIGHT/new/foreSIGHT.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘foreSIGHT’ ... -** package ‘foreSIGHT’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error: object ‘ggsave’ is not exported by 'namespace:cowplot' -Execution halted -ERROR: lazy loading failed for package ‘foreSIGHT’ -* removing ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/foreSIGHT/new/foreSIGHT.Rcheck/foreSIGHT’ - -``` -### CRAN - -``` -* installing *source* package ‘foreSIGHT’ ... -** package ‘foreSIGHT’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (foreSIGHT) - -``` +* checking examples ... ERROR + ``` + Running examples in ‘ORFik-Ex.R’ failed + The error most likely occurred in: + + > ### Name: download.SRA.metadata + > ### Title: Downloads metadata from SRA + > ### Aliases: download.SRA.metadata + > + > ### ** Examples + > + > ## Originally on SRA + > download.SRA.metadata("SRP226389") + Downloading metadata from: + https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&id=9232220,9232221,9232222,9232223,9232224,9232225&rettype=fasta&retmode=xml + Error in open.connection(x, "rb") : HTTP error 429. + Calls: download.SRA.metadata ... read_xml.character -> read_xml.connection -> open -> open.connection + Execution halted + ``` + +## In both + +* checking whether package ‘ORFik’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘S4Vectors’ was built under R version 4.3.2 + Warning: package ‘SummarizedExperiment’ was built under R version 4.3.2 + See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/ORFik/new/ORFik.Rcheck/00install.out’ for details. + ``` + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 9.3Mb + sub-directories of 1Mb or more: + R 1.0Mb + doc 5.6Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Unexported objects imported by ':::' calls: + ‘GenomicFeatures:::.merge_seqinfo_and_infer_missing_seqlengths’ + ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::normarg_mcols’ + ‘biomartr:::getENSEMBL.Seq’ ‘biomartr:::getENSEMBL.gtf’ + See the note in ?`:::` about the use of this operator. + ``` + +* checking R code for possible problems ... NOTE + ``` + DEG.plot.static: no visible binding for global variable ‘Regulation’ + DEG.plot.static: no visible binding for global variable ‘meanCounts’ + DEG.plot.static: no visible binding for global variable ‘LFC’ + DTEG.plot: no visible binding for global variable ‘Regulation’ + DTEG.plot: no visible binding for global variable ‘rna’ + DTEG.plot: no visible binding for global variable ‘rfp’ + QCplots: no visible binding for global variable ‘leaders’ + QCplots: no visible binding for global variable ‘trailers’ + QCstats.plot: no visible binding for global variable ‘variable’ + QCstats.plot: no visible binding for global variable ‘sample_total’ + ... + start2 startCodonCoverage startRegionRelative subtitle sum.count + sum_per_gene sum_txNorm te trailers uniprotswissprot + upstream_kozak_strength utr3_len utr5_len value var_txNorm variable + widths windowMean windowSD zscore + Consider adding + importFrom("base", "length") + importFrom("graphics", "frame") + importFrom("stats", "df") + importFrom("utils", "browseURL", "head") + to your NAMESPACE file. + ``` +