diff --git a/cran-comments.md b/cran-comments.md index 3859d6e..bf89008 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,25 +1,12 @@ -The package version I submitted yesterday did not build successfully when the magick package wasn't installed: https://cran.r-project.org/web/checks/check_results_cowplot.html This submission fixes that issue. - -I have also fixed the problem (noted yesterday) of examples that take longer than 10s to run. No other changes were made. +This is a minor bugfix release that closes bugs related to plots showing up in the wrong places +in shiny apps and extra blank plots popping up in knitted documents. ## Test environments * R devel on win-builder [ via devtools::build_win() ] * local OS X install x86_64-apple-darwin15.6.0 (64-bit), R 3.4.2 ## R CMD check results -There were no ERRORs or WARNINGs. - -There was one NOTE: -Days since last update: 0 - -I'm resubmitting so quickly because I received a request to do so by Brian Ripley: - -"You have added Suggests: magick but not used it conditionally as required in §1.1.3.1 of the manual. - -ImageMagick is a large install; moreover the C++ interface which 'magick' unnecessarily requires is not normally installed. - -Please correct ASAP once all the results are in." - +There were no ERRORs, WARNINGs, or NOTEs. ## Downstream dependencies Seem fine, according to devtools::revdep_check(). @@ -28,28 +15,28 @@ not because of cowplot. Full results available at https://github.com/wilkelab/cowplot/blob/master/revdep/README.md -21 packages - |package |version | errors| warnings| notes| |:------------|:-------|------:|--------:|-----:| -|bigstatsr |0.2.2 | 1| 0| 0| +|bigstatsr |0.2.3 | 1| 0| 0| |deconvolveR |1.0-3 | 0| 0| 0| |DGCA |1.0.1 | 1| 0| 0| +|ESTER |0.2.0 | 0| 0| 0| |ggpubr |0.1.6 | 0| 0| 1| |IncucyteDRC |0.5.4 | 0| 0| 0| |jtools |0.9.0 | 0| 0| 1| -|JWileymisc |0.2.1 | 0| 0| 0| -|meme |0.0.7 | 0| 0| 0| +|JWileymisc |0.2.1 | 0| 1| 0| +|meme |0.1.1 | 0| 1| 1| |memery |0.3.1 | 0| 0| 0| |modcmfitr |0.1.0 | 0| 0| 0| -|oddsratio |1.0.0 | 0| 0| 0| -|pcr |1.0.1 | 0| 0| 0| +|oddsratio |1.0.2 | 0| 0| 0| +|pcr |1.1.0 | 0| 1| 0| |poppr |2.5.0 | 1| 0| 0| |preText |0.6.1 | 0| 0| 0| -|RNOmni |0.1.3 | 0| 0| 0| +|RNOmni |0.1.4 | 0| 0| 0| +|scatr |1.0.1 | 0| 0| 0| |Seurat |2.1.0 | 1| 0| 1| |sicegar |0.2.2 | 0| 0| 0| |survivALL |0.9.1 | 1| 0| 0| -|tadaatoolbox |0.14.0 | 0| 0| 1| +|tadaatoolbox |0.15.0 | 0| 0| 0| |valr |0.3.1 | 0| 0| 1| |vanddraabe |1.0.0 | 0| 0| 0| diff --git a/revdep/README.md b/revdep/README.md index 884180c..c9b3d7d 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -10,48 +10,58 @@ |language |(EN) | |collate |en_US.UTF-8 | |tz |America/Chicago | -|date |2017-11-15 | +|date |2017-12-16 | ## Packages -|package |* |version |date |source | -|:-------|:--|:-------|:----------|:---------------------------| -|covr | |3.0.1 |2017-11-07 |cran (@3.0.1) | -|cowplot | |0.9.0 |2017-11-15 |local (wilkelab/cowplot@NA) | -|dplyr |* |0.7.4 |2017-09-28 |cran (@0.7.4) | -|magick | |1.5 |2017-11-03 |cran (@1.5) | -|tidyr |* |0.7.2 |2017-10-16 |cran (@0.7.2) | -|vdiffr | |0.2.1 |2017-10-09 |cran (@0.2.1) | +|package |* |version |date |source | +|:--------|:--|:-------|:----------|:---------------------------| +|covr | |3.0.1 |2017-11-07 |cran (@3.0.1) | +|cowplot | |0.9.2 |2017-12-16 |local (wilkelab/cowplot@NA) | +|dplyr | |0.7.4 |2017-09-28 |cran (@0.7.4) | +|ggplot2 | |2.2.1 |2016-12-30 |cran (@2.2.1) | +|gtable | |0.2.0 |2016-02-26 |cran (@0.2.0) | +|knitr | |1.17 |2017-08-10 |cran (@1.17) | +|magick | |1.6 |2017-12-01 |cran (@1.6) | +|maps | |3.2.0 |2017-06-08 |cran (@3.2.0) | +|plyr | |1.8.4 |2016-06-08 |cran (@1.8.4) | +|scales | |0.5.0 |2017-08-24 |cran (@0.5.0) | +|testthat | |2.0.0 |2017-12-13 |cran (@2.0.0) | +|tidyr | |0.7.2 |2017-10-16 |cran (@0.7.2) | +|vdiffr | |0.2.1 |2017-10-09 |cran (@0.2.1) | +|viridis | |0.4.0 |2017-03-27 |cran (@0.4.0) | # Check results -21 packages +23 packages |package |version | errors| warnings| notes| |:------------|:-------|------:|--------:|-----:| -|bigstatsr |0.2.2 | 1| 0| 0| +|bigstatsr |0.2.3 | 1| 0| 0| |deconvolveR |1.0-3 | 0| 0| 0| |DGCA |1.0.1 | 1| 0| 0| +|ESTER |0.2.0 | 0| 0| 0| |ggpubr |0.1.6 | 0| 0| 1| |IncucyteDRC |0.5.4 | 0| 0| 0| |jtools |0.9.0 | 0| 0| 1| -|JWileymisc |0.2.1 | 0| 0| 0| -|meme |0.0.7 | 0| 0| 0| +|JWileymisc |0.2.1 | 0| 1| 0| +|meme |0.1.1 | 0| 1| 1| |memery |0.3.1 | 0| 0| 0| |modcmfitr |0.1.0 | 0| 0| 0| -|oddsratio |1.0.0 | 0| 0| 0| -|pcr |1.0.1 | 0| 0| 0| +|oddsratio |1.0.2 | 0| 0| 0| +|pcr |1.1.0 | 0| 1| 0| |poppr |2.5.0 | 1| 0| 0| |preText |0.6.1 | 0| 0| 0| -|RNOmni |0.1.3 | 0| 0| 0| +|RNOmni |0.1.4 | 0| 0| 0| +|scatr |1.0.1 | 0| 0| 0| |Seurat |2.1.0 | 1| 0| 1| |sicegar |0.2.2 | 0| 0| 0| |survivALL |0.9.1 | 1| 0| 0| -|tadaatoolbox |0.14.0 | 0| 0| 1| +|tadaatoolbox |0.15.0 | 0| 0| 0| |valr |0.3.1 | 0| 0| 1| |vanddraabe |1.0.0 | 0| 0| 0| -## bigstatsr (0.2.2) +## bigstatsr (0.2.3) Maintainer: Florian Privé Bug reports: https://github.com/privefl/bigstatsr/issues @@ -76,7 +86,7 @@ Maintainer: Andrew McKenzie ``` checking package dependencies ... ERROR -Packages required but not available: ‘WGCNA’ ‘matrixStats’ +Package required but not available: ‘WGCNA’ Packages suggested but not available for checking: ‘impute’ ‘fdrtool’ ‘GOstats’ ‘HGNChelper’ ‘org.Hs.eg.db’ @@ -86,6 +96,12 @@ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ``` +## ESTER (0.2.0) +Maintainer: Ladislas Nalborczyk +Bug reports: https://github.com/lnalborczyk/ESTER/issues + +0 errors | 0 warnings | 0 notes + ## ggpubr (0.1.6) Maintainer: Alboukadel Kassambara Bug reports: https://github.com/kassambara/ggpubr/issues @@ -118,13 +134,36 @@ Packages unavailable to check Rd xrefs: ‘effects’, ‘ReporteRs’, ‘arm Maintainer: Joshua F. Wiley Bug reports: https://github.com/JWiley/JWileymisc/issues -0 errors | 0 warnings | 0 notes +0 errors | 1 warning | 0 notes + +``` +checking whether package ‘JWileymisc’ can be installed ... WARNING +Found the following significant warnings: + Warning: package ‘foreach’ was built under R version 3.4.3 +See ‘/Users/wilke/github/cowplot/revdep/checks/JWileymisc.Rcheck/00install.out’ for details. +``` -## meme (0.0.7) +## meme (0.1.1) Maintainer: Guangchuang Yu Bug reports: https://github.com/GuangchuangYu/meme/issues -0 errors | 0 warnings | 0 notes +0 errors | 1 warning | 1 note + +``` +checking re-building of vignette outputs ... WARNING +Error in re-building vignettes: + ... +Quitting from lines 167-177 (meme.Rmd) +Error: processing vignette 'meme.Rmd' failed with diagnostics: +unused argument (data = d) +Execution halted + + +checking installed package size ... NOTE + installed size is 5.4Mb + sub-directories of 1Mb or more: + doc 4.9Mb +``` ## memery (0.3.1) Maintainer: Matthew Leonawicz @@ -137,17 +176,42 @@ Maintainer: Ed Wilson 0 errors | 0 warnings | 0 notes -## oddsratio (1.0.0) +## oddsratio (1.0.2) Maintainer: Patrick Schratz Bug reports: https://github.com/pat-s/oddsratio/issues 0 errors | 0 warnings | 0 notes -## pcr (1.0.1) +## pcr (1.1.0) Maintainer: Mahmoud Ahmed Bug reports: https://github.com/MahShaaban/pcr/issues -0 errors | 0 warnings | 0 notes +0 errors | 1 warning | 0 notes + +``` +checking re-building of vignette outputs ... WARNING +Error in re-building vignettes: + ... +Joining, by = c("group", "gene") +Joining, by = c("group", "gene") +Joining, by = "gene" +Joining, by = c("group", "gene") +Joining, by = c("group", "gene") +Parsed with column specification: +cols( +... 8 lines ... +! LaTeX Error: \caption outside float. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.528 \caption + +Error: processing vignette 'qpcr_analysis.Rmd' failed with diagnostics: +pandoc document conversion failed with error 43 +Execution halted +``` ## poppr (2.5.0) Maintainer: Zhian N. Kamvar @@ -166,11 +230,17 @@ Maintainer: Matthew J. Denny 0 errors | 0 warnings | 0 notes -## RNOmni (0.1.3) +## RNOmni (0.1.4) Maintainer: Zachary McCaw 0 errors | 0 warnings | 0 notes +## scatr (1.0.1) +Maintainer: Ravi Selker +Bug reports: https://github.com/raviselker/scatr/issues + +0 errors | 0 warnings | 0 notes + ## Seurat (2.1.0) Maintainer: Paul Hoffman Bug reports: https://github.com/satijalab/seurat/issues @@ -201,7 +271,7 @@ Maintainer: Dominic Pearce ``` checking package dependencies ... ERROR Packages required but not available: - ‘survcomp’ ‘survsim’ ‘Biobase’ ‘desiR’ ‘ggthemes’ ‘pander’ + ‘survcomp’ ‘survsim’ ‘Biobase’ ‘desiR’ ‘pander’ Package suggested but not available for checking: ‘GGally’ @@ -209,16 +279,11 @@ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ``` -## tadaatoolbox (0.14.0) +## tadaatoolbox (0.15.0) Maintainer: Lukas Burk Bug reports: https://github.com/tadaadata/tadaatoolbox/issues -0 errors | 0 warnings | 1 note - -``` -checking Rd cross-references ... NOTE -Package unavailable to check Rd xrefs: ‘rmdformats’ -``` +0 errors | 0 warnings | 0 notes ## valr (0.3.1) Maintainer: Jay Hesselberth diff --git a/revdep/checks.rds b/revdep/checks.rds index b65f787..bd51c99 100644 Binary files a/revdep/checks.rds and b/revdep/checks.rds differ diff --git a/revdep/problems.md b/revdep/problems.md index bcc387a..619e4e1 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -10,32 +10,43 @@ |language |(EN) | |collate |en_US.UTF-8 | |tz |America/Chicago | -|date |2017-11-15 | +|date |2017-12-16 | ## Packages -|package |* |version |date |source | -|:-------|:--|:-------|:----------|:---------------------------| -|covr | |3.0.1 |2017-11-07 |cran (@3.0.1) | -|cowplot | |0.9.0 |2017-11-15 |local (wilkelab/cowplot@NA) | -|dplyr |* |0.7.4 |2017-09-28 |cran (@0.7.4) | -|magick | |1.5 |2017-11-03 |cran (@1.5) | -|tidyr |* |0.7.2 |2017-10-16 |cran (@0.7.2) | -|vdiffr | |0.2.1 |2017-10-09 |cran (@0.2.1) | +|package |* |version |date |source | +|:--------|:--|:-------|:----------|:---------------------------| +|covr | |3.0.1 |2017-11-07 |cran (@3.0.1) | +|cowplot | |0.9.2 |2017-12-16 |local (wilkelab/cowplot@NA) | +|dplyr | |0.7.4 |2017-09-28 |cran (@0.7.4) | +|ggplot2 | |2.2.1 |2016-12-30 |cran (@2.2.1) | +|gtable | |0.2.0 |2016-02-26 |cran (@0.2.0) | +|knitr | |1.17 |2017-08-10 |cran (@1.17) | +|magick | |1.6 |2017-12-01 |cran (@1.6) | +|maps | |3.2.0 |2017-06-08 |cran (@3.2.0) | +|plyr | |1.8.4 |2016-06-08 |cran (@1.8.4) | +|scales | |0.5.0 |2017-08-24 |cran (@0.5.0) | +|testthat | |2.0.0 |2017-12-13 |cran (@2.0.0) | +|tidyr | |0.7.2 |2017-10-16 |cran (@0.7.2) | +|vdiffr | |0.2.1 |2017-10-09 |cran (@0.2.1) | +|viridis | |0.4.0 |2017-03-27 |cran (@0.4.0) | # Check results -5 packages with problems +8 packages with problems -|package |version | errors| warnings| notes| -|:---------|:-------|------:|--------:|-----:| -|bigstatsr |0.2.2 | 1| 0| 0| -|DGCA |1.0.1 | 1| 0| 0| -|poppr |2.5.0 | 1| 0| 0| -|Seurat |2.1.0 | 1| 0| 1| -|survivALL |0.9.1 | 1| 0| 0| +|package |version | errors| warnings| notes| +|:----------|:-------|------:|--------:|-----:| +|bigstatsr |0.2.3 | 1| 0| 0| +|DGCA |1.0.1 | 1| 0| 0| +|JWileymisc |0.2.1 | 0| 1| 0| +|meme |0.1.1 | 0| 1| 1| +|pcr |1.1.0 | 0| 1| 0| +|poppr |2.5.0 | 1| 0| 0| +|Seurat |2.1.0 | 1| 0| 1| +|survivALL |0.9.1 | 1| 0| 0| -## bigstatsr (0.2.2) +## bigstatsr (0.2.3) Maintainer: Florian Privé Bug reports: https://github.com/privefl/bigstatsr/issues @@ -54,7 +65,7 @@ Maintainer: Andrew McKenzie ``` checking package dependencies ... ERROR -Packages required but not available: ‘WGCNA’ ‘matrixStats’ +Package required but not available: ‘WGCNA’ Packages suggested but not available for checking: ‘impute’ ‘fdrtool’ ‘GOstats’ ‘HGNChelper’ ‘org.Hs.eg.db’ @@ -64,6 +75,72 @@ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ``` +## JWileymisc (0.2.1) +Maintainer: Joshua F. Wiley +Bug reports: https://github.com/JWiley/JWileymisc/issues + +0 errors | 1 warning | 0 notes + +``` +checking whether package ‘JWileymisc’ can be installed ... WARNING +Found the following significant warnings: + Warning: package ‘foreach’ was built under R version 3.4.3 +See ‘/Users/wilke/github/cowplot/revdep/checks/JWileymisc.Rcheck/00install.out’ for details. +``` + +## meme (0.1.1) +Maintainer: Guangchuang Yu +Bug reports: https://github.com/GuangchuangYu/meme/issues + +0 errors | 1 warning | 1 note + +``` +checking re-building of vignette outputs ... WARNING +Error in re-building vignettes: + ... +Quitting from lines 167-177 (meme.Rmd) +Error: processing vignette 'meme.Rmd' failed with diagnostics: +unused argument (data = d) +Execution halted + + +checking installed package size ... NOTE + installed size is 5.4Mb + sub-directories of 1Mb or more: + doc 4.9Mb +``` + +## pcr (1.1.0) +Maintainer: Mahmoud Ahmed +Bug reports: https://github.com/MahShaaban/pcr/issues + +0 errors | 1 warning | 0 notes + +``` +checking re-building of vignette outputs ... WARNING +Error in re-building vignettes: + ... +Joining, by = c("group", "gene") +Joining, by = c("group", "gene") +Joining, by = "gene" +Joining, by = c("group", "gene") +Joining, by = c("group", "gene") +Parsed with column specification: +cols( +... 8 lines ... +! LaTeX Error: \caption outside float. + +See the LaTeX manual or LaTeX Companion for explanation. +Type H for immediate help. + ... + +l.528 \caption + +Error: processing vignette 'qpcr_analysis.Rmd' failed with diagnostics: +pandoc document conversion failed with error 43 +Execution halted +``` + ## poppr (2.5.0) Maintainer: Zhian N. Kamvar Bug reports: https://github.com/grunwaldlab/poppr/issues @@ -100,7 +177,7 @@ Maintainer: Dominic Pearce ``` checking package dependencies ... ERROR Packages required but not available: - ‘survcomp’ ‘survsim’ ‘Biobase’ ‘desiR’ ‘ggthemes’ ‘pander’ + ‘survcomp’ ‘survsim’ ‘Biobase’ ‘desiR’ ‘pander’ Package suggested but not available for checking: ‘GGally’ diff --git a/revdep/timing.md b/revdep/timing.md index 5d80cd7..edaf650 100644 --- a/revdep/timing.md +++ b/revdep/timing.md @@ -2,26 +2,28 @@ | |package |version | check_time| |:--|:------------|:-------|----------:| -|15 |RNOmni |0.1.3 | 213.4| -|20 |valr |0.3.1 | 137.1| -|2 |deconvolveR |1.0-3 | 127.1| -|6 |jtools |0.9.0 | 99.2| -|19 |tadaatoolbox |0.14.0 | 86| -|4 |ggpubr |0.1.6 | 82.8| -|7 |JWileymisc |0.2.1 | 73.7| -|14 |preText |0.6.1 | 70| -|1 |bigstatsr |0.2.2 | 68.7| -|11 |oddsratio |1.0.0 | 51.9| -|17 |sicegar |0.2.2 | 51.4| -|5 |IncucyteDRC |0.5.4 | 48.1| -|10 |modcmfitr |0.1.0 | 47.7| -|12 |pcr |1.0.1 | 43| -|9 |memery |0.3.1 | 41.1| -|8 |meme |0.0.7 | 39.2| -|21 |vanddraabe |1.0.0 | 33.7| -|16 |Seurat |2.1.0 | 17.7| -|13 |poppr |2.5.0 | 6.3| -|18 |survivALL |0.9.1 | 2.9| -|3 |DGCA |1.0.1 | 2| +|2 |deconvolveR |1.0-3 | 120.1| +|22 |valr |0.3.1 | 115| +|7 |jtools |0.9.0 | 87.5| +|5 |ggpubr |0.1.6 | 79.1| +|21 |tadaatoolbox |0.15.0 | 73.3| +|8 |JWileymisc |0.2.1 | 64.2| +|1 |bigstatsr |0.2.3 | 60.9| +|15 |preText |0.6.1 | 59.3| +|4 |ESTER |0.2.0 | 58.1| +|6 |IncucyteDRC |0.5.4 | 48.7| +|12 |oddsratio |1.0.2 | 44.4| +|19 |sicegar |0.2.2 | 44.1| +|13 |pcr |1.1.0 | 41.8| +|11 |modcmfitr |0.1.0 | 39.4| +|10 |memery |0.3.1 | 37.3| +|16 |RNOmni |0.1.4 | 31| +|9 |meme |0.1.1 | 29.4| +|23 |vanddraabe |1.0.0 | 28.6| +|18 |Seurat |2.1.0 | 14.7| +|17 |scatr |1.0.1 | 9.9| +|14 |poppr |2.5.0 | 4.8| +|20 |survivALL |0.9.1 | 2.5| +|3 |DGCA |1.0.1 | 2.1|