From 977094ebeae3ac42b78fbbbf161b7495348bcd4d Mon Sep 17 00:00:00 2001 From: "Carter T. Butts" Date: Sat, 7 Dec 2024 00:28:03 -0800 Subject: [PATCH] Changes for the 1.19.0 submission. This should not only resolve the issues spotted by the CRAN checks, but also extra memory issues flagged by Ripley and Kalibera. Most of these are in the category of "things that should not go wrong if the package is used properly," but they have been tightened up nevertheless. --- ChangeLog | 8 + DESCRIPTION | 2 +- R/access.R | 8 +- R/as.edgelist.R | 2 +- R/coercion.R | 4 +- man/as.edgelist.Rd | 2 +- man/as.matrix.network.Rd | 4 +- revdep/.gitignore | 7 - revdep/README.md | 153 ---- revdep/cran.md | 18 - revdep/email.yml | 5 - revdep/failures.md | 26 - revdep/problems.md | 1719 -------------------------------------- src/access.c | 75 +- 14 files changed, 76 insertions(+), 1957 deletions(-) delete mode 100644 revdep/.gitignore delete mode 100644 revdep/README.md delete mode 100644 revdep/cran.md delete mode 100644 revdep/email.yml delete mode 100644 revdep/failures.md delete mode 100644 revdep/problems.md diff --git a/ChangeLog b/ChangeLog index 1669b9d..265adb6 100644 --- a/ChangeLog +++ b/ChangeLog @@ -3,6 +3,14 @@ v1.19.0 - Non-visible and documentation changes for CRAN compliance. - Internal argument handling changes; should generally be invisible, but may in some complex cases avoid problems when calling network(). + - Added more internal checks to edge allocation and handling. These should + not be visible for normal use, but should catch/avoid errors due to + improper use (e.g., trying to make/use network objects with malformed + edges). This is not expected to break any working code, but if you + have been doing things you shouldn't have been doing (e.g., edges + without both inl and outl elements), then you might find that you need + to fix things. (This usually takes effort, so you are not likely to + have done it by accident.) - Bolstered add.edge and add.edges against improper edge.check arguments. - Made get.inducedSubgraph() and permute.vertexIDs() generic. - Replaced now non-functional Pajek URLs with Internet Archive versions. diff --git a/DESCRIPTION b/DESCRIPTION index 200b8fe..6815361 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: network Version: 1.19.0 -Date: 2024-12-04 +Date: 2024-12-06 Title: Classes for Relational Data Authors@R: c( person("Carter T.", "Butts", role=c("aut","cre"), email="buttsc@uci.edu"), diff --git a/R/access.R b/R/access.R index 943ffdf..af49afe 100644 --- a/R/access.R +++ b/R/access.R @@ -656,11 +656,11 @@ get.edge.attribute.network <- function(x, attrname, unlist=TRUE, na.omit=FALSE, if (!is.list(x)) stop("x must be a network object or a list.") - if (!is.character(attrname)) + if (!is.character(attrname) || (length(attrname)==0)) stop("attrname must be a character vector.") if (!is.logical(unlist) || !is.logical(na.omit) || !is.logical(null.na) || - !is.logical(deleted.edges.omit)) + !is.logical(deleted.edges.omit) || (length(unlist)*length(na.omit)*length(null.na)*length(deleted.edges.omit)==0)) stop("na.omit, null.na, deleted.edges.omit must be a logical vector.") edges <- .Call(getEdgeAttribute_R,x,attrname,na.omit,null.na,deleted.edges.omit) @@ -1965,6 +1965,10 @@ set.edge.value.network <- function(x, attrname, value, e = seq_along(x$mel), ... } else if (min(dim(value)) < n) { stop("set.edge.value requires a matrix whose dimension is equal to or larger than the network size") } + #Ensure that the attribute name is legit + attrname<-as.character(attrname) + if(length(attrname)==0) + stop("Attribute name required in set.edge.value.network.") #Do the deed xn<-substitute(x) x<-.Call(setEdgeValue_R,x,attrname,value,e) diff --git a/R/as.edgelist.R b/R/as.edgelist.R index 3670b19..823a3d3 100644 --- a/R/as.edgelist.R +++ b/R/as.edgelist.R @@ -39,7 +39,7 @@ as.edgelist <- function(x, ...){ #' @aliases edgelist #' @param x a \code{network} object with additional class added indicating how #' it should be dispatched. -#' @param output return type: a \code{\link{matrix}} or a \code{\link{tibble}}; +#' @param output return type: a \code{\link{matrix}} or a \code{\link[tibble]{tibble}}; #' see \code{\link{as.matrix.network}} for the difference. #' @param attrname optionally, the name of an edge attribute to use for edge #' values; may be a vector of names if \code{output="tibble"} diff --git a/R/coercion.R b/R/coercion.R index 3066434..562c277 100644 --- a/R/coercion.R +++ b/R/coercion.R @@ -43,7 +43,7 @@ #' The \code{as.matrix} methods attempt to coerce their input to a matrix in #' adjacency, incidence, or edgelist form. Edge values (from a stored #' attribute) may be used if present. \code{\link[tibble:as_tibble]{as_tibble}} -#' coerces into an edgelist in \code{\link{tibble}} (a type of +#' coerces into an edgelist in \code{\link[tibble]{tibble}} (a type of #' \code{\link{data.frame}}) form; this can be especially useful if extrecting #' a character-type edge attribute. #' @@ -86,7 +86,7 @@ #' edglist form? #' @param na.rm logical; should missing edges/vertices be included in the #' edgelist formats? Ignored if \code{as.sna.edgelist=TRUE}. -#' @param unit whether a \code{\link{tibble}} of edge or vertex attributes +#' @param unit whether a \code{\link[tibble]{tibble}} of edge or vertex attributes #' should be returned. #' @param ... additional arguments. #' @return For \code{as.matrix} methods, an adjacency, incidence, or edgelist diff --git a/man/as.edgelist.Rd b/man/as.edgelist.Rd index 04afd8e..0a2b7c9 100644 --- a/man/as.edgelist.Rd +++ b/man/as.edgelist.Rd @@ -49,7 +49,7 @@ values; may be a vector of names if \code{output="tibble"}} \item{as.sna.edgelist}{logical; should the edgelist be returned in edgelist form expected by the sna package? Ignored if \code{output="tibble"}} -\item{output}{return type: a \code{\link{matrix}} or a \code{\link{tibble}}; +\item{output}{return type: a \code{\link{matrix}} or a \code{\link[tibble]{tibble}}; see \code{\link{as.matrix.network}} for the difference.} \item{\dots}{additional arguments to other methods} diff --git a/man/as.matrix.network.Rd b/man/as.matrix.network.Rd index 9c24b54..c695a65 100644 --- a/man/as.matrix.network.Rd +++ b/man/as.matrix.network.Rd @@ -63,7 +63,7 @@ as indices for selecting them from \code{\link{list.edge.attributes}(x)} or \code{\link{list.vertex.attributes}(x)} (depending on \code{unit}); passing \code{TRUE} therefore returns all edge attributes as columns} -\item{unit}{whether a \code{\link{tibble}} of edge or vertex attributes +\item{unit}{whether a \code{\link[tibble]{tibble}} of edge or vertex attributes should be returned.} \item{store.eid}{whether the edge ID should be stored in the third column (\code{.eid}).} @@ -78,7 +78,7 @@ the edge ID, and whose subsequent columns are the requested edge attributes. The \code{as.matrix} methods attempt to coerce their input to a matrix in adjacency, incidence, or edgelist form. Edge values (from a stored attribute) may be used if present. \code{\link[tibble:as_tibble]{as_tibble}} -coerces into an edgelist in \code{\link{tibble}} (a type of +coerces into an edgelist in \code{\link[tibble]{tibble}} (a type of \code{\link{data.frame}}) form; this can be especially useful if extrecting a character-type edge attribute. } diff --git a/revdep/.gitignore b/revdep/.gitignore deleted file mode 100644 index bc768ae..0000000 --- a/revdep/.gitignore +++ /dev/null @@ -1,7 +0,0 @@ -checks -library -checks.noindex -library.noindex -data.sqlite -*.html -cloud.noindex diff --git a/revdep/README.md b/revdep/README.md deleted file mode 100644 index 9fd9629..0000000 --- a/revdep/README.md +++ /dev/null @@ -1,153 +0,0 @@ -# Platform - -|field |value | -|:--------|:----------------------------| -|version |R version 4.2.0 (2022-04-22) | -|os |CentOS Linux 7 (Core) | -|system |x86_64, linux-gnu | -|ui |X11 | -|language |(EN) | -|collate |en_US.UTF-8 | -|ctype |en_US.UTF-8 | -|tz |Australia/Sydney | -|date |2022-10-01 | -|pandoc |1.12.3.1 @ /bin/pandoc | - -# Dependencies - -|package |old |new |Δ | -|:-------|:------|:----------|:--| -|network |1.17.2 |1.17.2-748 |* | - -# Revdeps - -## Failed to check (1) - -|package |version |error |warning |note | -|:-------|:-------|:-----|:-------|:----| -|[lolog](failures.md#lolog)|1.3 |1 | |1 | - -## New problems (1) - -|package |version |error |warning |note | -|:-------|:-------|:---------|:-------|:----| -|[leiden](problems.md#leiden)|0.4.3 |-1 __+1__ | |1 | - -## All (113) - -|package |version |error |warning |note | -|:------------------|:--------|:---------|:-------|:----| -|amen |1.4.4 | | | | -|[BasketballAnalyzeR](problems.md#basketballanalyzer)|0.5.0 | | |1 | -|Bergm |5.0.5 | | | | -|[BGGM](problems.md#bggm)|2.0.4 | | |1 | -|[bingat](problems.md#bingat)|1.3 | | |1 | -|[Blaunet](problems.md#blaunet)|2.2.1 |1 | | | -|[bootcluster](problems.md#bootcluster)|0.3.2 | | |1 | -|[broom](problems.md#broom)|1.0.1 | | |2 | -|btergm |1.10.6 | | | | -|[CEMiTool](problems.md#cemitool)|1.20.0 | | |2 | -|[CeTF](problems.md#cetf)|1.8.0 |-1 | |1 | -|[chorrrds](problems.md#chorrrds)|0.1.9.5 | | |2 | -|[CINNA](problems.md#cinna)|1.2.0 | | |1 | -|[CluMSID](problems.md#clumsid)|1.12.0 |1 | | | -|collpcm |1.2 | | | | -|[conserveR](problems.md#conserver)|1.0.4 | | |2 | -|degreenet |1.3-3 | | | | -|discourseGT |1.1.7 | | | | -|dnr |0.3.5 | | | | -|[edgebundle](problems.md#edgebundle)|0.4.0 | | |1 | -|EGAnet |1.2.3 | | | | -|egor |1.22.5 | | | | -|EloRating |0.46.11 | | | | -|EpiModel |2.3.0 | | | | -|epinet |2.1.8 | | | | -|[ergm](problems.md#ergm)|4.2.2 | | |1 | -|ergm.count |4.1.1 | | | | -|ergm.ego |1.0.1 | | | | -|ergm.rank |4.1.0 | | | | -|ergm.userterms |3.10.0 | | | | -|[ergMargins](problems.md#ergmargins)|0.1.3 | | |2 | -|[ergmito](problems.md#ergmito)|0.3-0 | | |1 | -|[fcoex](problems.md#fcoex)|1.10.0 |2 |2 |1 | -|fergm |1.1.4 | | | | -|fglsnet |1.0 | | | | -|[fssemR](problems.md#fssemr)|0.1.8 | | |2 | -|genBaRcode |1.2.5 | | | | -|[geomnet](problems.md#geomnet)|0.3.1 |2 | | | -|[GGally](problems.md#ggally)|2.1.2 | | |1 | -|[GGMncv](problems.md#ggmncv)|2.1.1 | | |1 | -|[GGMnonreg](problems.md#ggmnonreg)|1.0.0 | | |1 | -|GGMselect |0.1-12.5 | | | | -|[ggnetwork](problems.md#ggnetwork)|0.5.10 | | |1 | -|[GGPA](problems.md#ggpa)|1.8.0 | | |3 | -|[ggraph](problems.md#ggraph)|2.0.6 | | |1 | -|[GOxploreR](problems.md#goxplorer)|1.2.6 | | |1 | -|[GRENITS](problems.md#grenits)|1.48.0 | | |3 | -|[gwdegree](problems.md#gwdegree)|0.1.1 | | |2 | -|haplotypes |1.1.2 | | | | -|hergm |4.1-9 | | | | -|[ICON](problems.md#icon)|0.4.0 |1 | | | -|[InflectSSP](problems.md#inflectssp)|1.4.4 |1 | | | -|intergraph |2.0-2 | | | | -|interplex |0.1.0 | | | | -|ITNr |0.6.0 | | | | -|jlsm |0.1.0 | | | | -|[latentnet](problems.md#latentnet)|2.10.6 | | |1 | -|[leiden](problems.md#leiden)|0.4.3 |-1 __+1__ | |1 | -|Linkage |0.9 | | | | -|[lolog](failures.md#lolog)|1.3 |1 | |1 | -|lvm4net |0.3 | | | | -|[MBCbook](problems.md#mbcbook)|0.1.1 | | |1 | -|[migraph](problems.md#migraph)|0.12.0 |1 | |2 | -|mlergm |0.8 | | | | -|motifr |1.0.0 | | | | -|[mpa](problems.md#mpa)|0.7.3 | | |3 | -|MRPC |3.1.0 | | | | -|ndtv |0.13.2 | | | | -|[netdiffuseR](problems.md#netdiffuser)|1.22.4 | | |1 | -|[nethet](problems.md#nethet)|1.28.0 | |1 |1 | -|[netmap](problems.md#netmap)|0.1.1 |1 | | | -|[netmediate](problems.md#netmediate)|0.1.0 | | |1 | -|NetMix |0.2.0 | | | | -|netplot |0.1-1 | | | | -|networkABC |0.8-0 | | | | -|NetworkChange |0.8 | | | | -|NetworkDistance |0.3.4 | | | | -|networkDynamic |0.11.2 | | | | -|networkDynamicData |0.2.1 | | | | -|NetworkExtinction |0.1.1 | | | | -|[networksis](problems.md#networksis)|2.1-3 | | |1 | -|PAFit |1.2.5 | | | | -|[PDN](problems.md#pdn)|0.1.0 | | |1 | -|[PhosR](problems.md#phosr)|1.6.0 | | |3 | -|pkggraph |0.2.3 | | | | -|[predictionet](problems.md#predictionet)|1.40.0 | |1 |4 | -|[PubScore](problems.md#pubscore)|1.8.0 |-1 |1 |2 | -|pulsar |0.3.8 | | | | -|quanteda.textplots |0.94.2 | | | | -|QuantNorm |1.0.5 | | | | -|RDS |0.9-3 | | | | -|rgraph6 |2.0-2 | | | | -|RHMS |1.7 | | | | -|[RSiena](problems.md#rsiena)|1.3.0.1 | | |1 | -|[sand](problems.md#sand)|2.0.0 | | |1 | -|[SBICgraph](problems.md#sbicgraph)|1.0.0 | | |2 | -|sidier |4.1.0 | | | | -|sna |2.7 | | | | -|[sparsebnUtils](problems.md#sparsebnutils)|0.0.8 | | |1 | -|SparseTSCGM |4.0 | | | | -|statnet |2019.6 | | | | -|[statnetWeb](problems.md#statnetweb)|0.5.6 | | |1 | -|tergm |4.1.0 | | | | -|tergmLite |2.6.1 | | | | -|tidygraph |1.2.2 | | | | -|tsna |0.3.5 | | | | -|VBLPCM |2.4.8 | | | | -|VineCopula |2.4.4 | | | | -|[vivid](problems.md#vivid)|0.2.3 | | |2 | -|[wildlifeDI](problems.md#wildlifedi)|0.4.1 |1 | | | -|[WOTPLY](problems.md#wotply)|0.1.0 | | |1 | -|WRSS |3.1 | | | | -|[xergm.common](problems.md#xergmcommon)|1.7.8 | | |1 | - diff --git a/revdep/cran.md b/revdep/cran.md deleted file mode 100644 index 23fd474..0000000 --- a/revdep/cran.md +++ /dev/null @@ -1,18 +0,0 @@ -## revdepcheck results - -We checked 113 reverse dependencies (103 from CRAN + 10 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - - * We saw 1 new problems - * We failed to check 1 packages - -Issues with CRAN packages are summarised below. - -### New problems -(This reports the first line of each new failure) - -* leiden - checking tests ... - -### Failed to check - -* lolog (NA) diff --git a/revdep/email.yml b/revdep/email.yml deleted file mode 100644 index 0c5cef8..0000000 --- a/revdep/email.yml +++ /dev/null @@ -1,5 +0,0 @@ -release_date: ??? -rel_release_date: ??? -my_news_url: ??? -release_version: ??? -release_details: ??? diff --git a/revdep/failures.md b/revdep/failures.md deleted file mode 100644 index 2d93710..0000000 --- a/revdep/failures.md +++ /dev/null @@ -1,26 +0,0 @@ -# lolog - -
- -* Version: 1.3 -* GitHub: https://github.com/statnet/lolog -* Source code: https://github.com/cran/lolog -* Date/Publication: 2021-07-01 07:50:06 UTC -* Number of recursive dependencies: 80 - -Run `revdep_details(, "lolog")` for more info - -
- -## In both - -* R CMD check timed out - - -* checking installed package size ... NOTE - ``` - installed size is 24.8Mb - sub-directories of 1Mb or more: - libs 23.1Mb - ``` - diff --git a/revdep/problems.md b/revdep/problems.md deleted file mode 100644 index de4b408..0000000 --- a/revdep/problems.md +++ /dev/null @@ -1,1719 +0,0 @@ -# BasketballAnalyzeR - -
- -* Version: 0.5.0 -* GitHub: https://github.com/sndmrc/BasketballAnalyzeR -* Source code: https://github.com/cran/BasketballAnalyzeR -* Date/Publication: 2020-06-26 09:00:11 UTC -* Number of recursive dependencies: 76 - -Run `revdep_details(, "BasketballAnalyzeR")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’ - All declared Imports should be used. - ``` - -# BGGM - -
- -* Version: 2.0.4 -* GitHub: https://github.com/donaldRwilliams/BGGM -* Source code: https://github.com/cran/BGGM -* Date/Publication: 2021-08-20 15:50:06 UTC -* Number of recursive dependencies: 167 - -Run `revdep_details(, "BGGM")` for more info - -
- -## In both - -* checking installed package size ... NOTE - ``` - installed size is 12.8Mb - sub-directories of 1Mb or more: - doc 3.8Mb - help 1.1Mb - libs 7.2Mb - ``` - -# bingat - -
- -* Version: 1.3 -* GitHub: NA -* Source code: https://github.com/cran/bingat -* Date/Publication: 2017-07-05 18:30:37 UTC -* Number of recursive dependencies: 32 - -Run `revdep_details(, "bingat")` for more info - -
- -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘genalg’ - ``` - -# Blaunet - -
- -* Version: 2.2.1 -* GitHub: NA -* Source code: https://github.com/cran/Blaunet -* Date/Publication: 2022-09-27 08:10:08 UTC -* Number of recursive dependencies: 65 - -Run `revdep_details(, "Blaunet")` for more info - -
- -## In both - -* checking package dependencies ... ERROR - ``` - Package required but not available: ‘gWidgets2tcltk’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# bootcluster - -
- -* Version: 0.3.2 -* GitHub: NA -* Source code: https://github.com/cran/bootcluster -* Date/Publication: 2022-01-29 22:50:03 UTC -* Number of recursive dependencies: 69 - -Run `revdep_details(, "bootcluster")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘sna’ - All declared Imports should be used. - ``` - -# broom - -
- -* Version: 1.0.1 -* GitHub: https://github.com/tidymodels/broom -* Source code: https://github.com/cran/broom -* Date/Publication: 2022-08-29 21:00:08 UTC -* Number of recursive dependencies: 292 - -Run `revdep_details(, "broom")` for more info - -
- -## In both - -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: - 'epiR', 'spdep', 'spatialreg' - ``` - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘spatialreg’, ‘epiR’ - ``` - -# CEMiTool - -
- -* Version: 1.20.0 -* GitHub: NA -* Source code: https://github.com/cran/CEMiTool -* Date/Publication: 2022-04-26 -* Number of recursive dependencies: 194 - -Run `revdep_details(, "CEMiTool")` for more info - -
- -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.9Mb - sub-directories of 1Mb or more: - data 3.1Mb - doc 2.3Mb - extdata 2.8Mb - ``` - -* checking R code for possible problems ... NOTE - ``` - flip_vector: no visible global function definition for ‘setNames’ - select_genes: no visible global function definition for ‘var’ - get_hubs,CEMiTool : : no visible global function definition - for ‘head’ - get_merged_mods,CEMiTool: no visible global function definition for - ‘as.dist’ - get_mods,CEMiTool: no visible global function definition for ‘as.dist’ - get_phi,CEMiTool: no visible global function definition for ‘tail’ - get_phi,CEMiTool: no visible global function definition for ‘head’ - mod_gene_num,CEMiTool: no visible binding for global variable ‘modules’ - ... - save_plots,CEMiTool: no visible global function definition for - ‘dev.off’ - Undefined global functions or variables: - ..eq.label.. ..rr.label.. := Mean Variance as.dist data dev.off dist - head modules num_genes setNames tail var - Consider adding - importFrom("grDevices", "dev.off") - importFrom("stats", "as.dist", "dist", "setNames", "var") - importFrom("utils", "data", "head", "tail") - to your NAMESPACE file. - ``` - -# CeTF - -
- -* Version: 1.8.0 -* GitHub: NA -* Source code: https://github.com/cran/CeTF -* Date/Publication: 2022-04-26 -* Number of recursive dependencies: 228 - -Run `revdep_details(, "CeTF")` for more info - -
- -## Newly fixed - -* checking re-building of vignette outputs ...sh: line 1: 247279 Killed '/srv/scratch/z3528859/R-4.2.0/bin/R' --vanilla --no-echo > '/srv/scratch/z3528859/github/statnet/network/revdep/checks/CeTF/old/CeTF.Rcheck/build_vignettes.log' 2>&1 < '/scratch/pbs.3584821.kman.restech.unsw.edu.au/Rtmp5JkIUj/file375426c1496a9' - ``` - ERROR - Error(s) in re-building vignettes: - --- re-building ‘CeTF.Rmd’ using rmarkdown - - ======================================== - CeTF version 1.8.0 - Bioconductor page: http://bioconductor.org/packages/CeTF/ - Github page: https://github.com/cbiagii/CeTF or https://cbiagii.github.io/CeTF/ - Documentation: http://bioconductor.org/packages/CeTF/ - If you use it in published research, please cite: - ... - count - - The following objects are masked from 'package:stats': - - filter, lag - - The following objects are masked from 'package:base': - - intersect, setdiff, setequal, union - - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.6Mb - sub-directories of 1Mb or more: - data 1.5Mb - doc 3.0Mb - libs 2.5Mb - ``` - -# chorrrds - -
- -* Version: 0.1.9.5 -* GitHub: https://github.com/r-music/chorrrds -* Source code: https://github.com/cran/chorrrds -* Date/Publication: 2020-06-30 17:30:02 UTC -* Number of recursive dependencies: 72 - -Run `revdep_details(, "chorrrds")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘forcats’ - All declared Imports should be used. - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 4004 marked UTF-8 strings - ``` - -# CINNA - -
- -* Version: 1.2.0 -* GitHub: NA -* Source code: https://github.com/cran/CINNA -* Date/Publication: 2022-04-07 15:12:31 UTC -* Number of recursive dependencies: 145 - -Run `revdep_details(, "CINNA")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘circlize’ - All declared Imports should be used. - ``` - -# CluMSID - -
- -* Version: 1.12.0 -* GitHub: https://github.com/tdepke/CluMSID -* Source code: https://github.com/cran/CluMSID -* Date/Publication: 2022-04-26 -* Number of recursive dependencies: 182 - -Run `revdep_details(, "CluMSID")` for more info - -
- -## In both - -* checking package dependencies ... ERROR - ``` - Package required but not available: ‘MSnbase’ - - Packages suggested but not available for checking: 'metaMS', 'xcms' - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# conserveR - -
- -* Version: 1.0.4 -* GitHub: https://github.com/azizka/conserveR -* Source code: https://github.com/cran/conserveR -* Date/Publication: 2021-08-02 09:10:06 UTC -* Number of recursive dependencies: 51 - -Run `revdep_details(, "conserveR")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘scales’ ‘sna’ - All declared Imports should be used. - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 244 marked UTF-8 strings - ``` - -# edgebundle - -
- -* Version: 0.4.0 -* GitHub: https://github.com/schochastics/edgebundle -* Source code: https://github.com/cran/edgebundle -* Date/Publication: 2022-07-05 00:10:10 UTC -* Number of recursive dependencies: 53 - -Run `revdep_details(, "edgebundle")` for more info - -
- -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 22 marked UTF-8 strings - ``` - -# ergm - -
- -* Version: 4.2.2 -* GitHub: https://github.com/statnet/ergm -* Source code: https://github.com/cran/ergm -* Date/Publication: 2022-06-01 12:00:04 UTC -* Number of recursive dependencies: 89 - -Run `revdep_details(, "ergm")` for more info - -
- -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.3Mb - sub-directories of 1Mb or more: - R 1.1Mb - doc 1.7Mb - libs 3.8Mb - ``` - -# ergMargins - -
- -* Version: 0.1.3 -* GitHub: NA -* Source code: https://github.com/cran/ergMargins -* Date/Publication: 2021-06-30 07:40:02 UTC -* Number of recursive dependencies: 58 - -Run `revdep_details(, "ergMargins")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘methods’ ‘sna’ ‘statnet.common’ - All declared Imports should be used. - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘margins’ - ``` - -# ergmito - -
- -* Version: 0.3-0 -* GitHub: https://github.com/muriteams/ergmito -* Source code: https://github.com/cran/ergmito -* Date/Publication: 2020-08-10 21:40:02 UTC -* Number of recursive dependencies: 65 - -Run `revdep_details(, "ergmito")` for more info - -
- -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.1Mb - sub-directories of 1Mb or more: - libs 5.7Mb - ``` - -# fcoex - -
- -* Version: 1.10.0 -* GitHub: NA -* Source code: https://github.com/cran/fcoex -* Date/Publication: 2022-04-26 -* Number of recursive dependencies: 298 - -Run `revdep_details(, "fcoex")` for more info - -
- -## In both - -* checking examples ... ERROR - ``` - Running examples in ‘fcoex-Ex.R’ failed - The error most likely occurred in: - - > ### Name: mod_ora - > ### Title: Over Representation Analysis (ORA) - > ### Aliases: mod_ora mod_ora,fcoex-method - > - > ### ** Examples - > - > data("fc") - ... - > gmt_fname <- system.file("extdata", "pathways.gmt", package = "CEMiTool") - > gmt_in <- pathwayPCA::read_gmt(gmt_fname) - Warning in file(con, "rb") : - file("") only supports open = "w+" and open = "w+b": using the former - Warning in readChar(file, nchars = nChars, useBytes = TRUE) : - text connection used with readChar(), results may be incorrect - Error in readChar(file, nchars = nChars, useBytes = TRUE) : - invalid 'nchars' argument - Calls: -> readChar - Execution halted - ``` - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - --- re-building ‘fcoex.Rmd’ using rmarkdown - - - Attaching package: 'MatrixGenerics' - - The following objects are masked from 'package:matrixStats': - - colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, - colCounts, colCummaxs, colCummins, colCumprods, colCumsums, - ... - Quitting from lines 67-75 (fcoex_and_seurat.Rmd) - Error: processing vignette 'fcoex_and_seurat.Rmd' failed with diagnostics: - invalid 'nchars' argument - --- failed re-building ‘fcoex_and_seurat.Rmd’ - - SUMMARY: processing the following files failed: - ‘fcoex.Rmd’ ‘fcoex_and_seurat.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -* checking whether package ‘fcoex’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘fcoex’ - See ‘/srv/scratch/z3528859/github/statnet/network/revdep/checks/fcoex/new/fcoex.Rcheck/00install.out’ for details. - ``` - -* checking Rd \usage sections ... WARNING - ``` - Documented arguments not in \usage in documentation object '.plot_one_interaction': - ‘...’ - - Functions with \usage entries need to have the appropriate \alias - entries, and all their arguments documented. - The \usage entries must correspond to syntactically valid R code. - See chapter ‘Writing R documentation files’ in the ‘Writing R - Extensions’ manual. - ``` - -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: 'TENxPBMCData', 'schex' - ``` - -# fssemR - -
- -* Version: 0.1.8 -* GitHub: https://github.com/Ivis4ml/fssemR -* Source code: https://github.com/cran/fssemR -* Date/Publication: 2022-02-11 13:00:02 UTC -* Number of recursive dependencies: 87 - -Run `revdep_details(, "fssemR")` for more info - -
- -## In both - -* checking installed package size ... NOTE - ``` - installed size is 15.2Mb - sub-directories of 1Mb or more: - libs 14.5Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘qpdf’ - All declared Imports should be used. - ``` - -# geomnet - -
- -* Version: 0.3.1 -* GitHub: https://github.com/sctyner/geomnet -* Source code: https://github.com/cran/geomnet -* Date/Publication: 2020-11-26 11:00:06 UTC -* Number of recursive dependencies: 98 - -Run `revdep_details(, "geomnet")` for more info - -
- -## In both - -* checking examples ... ERROR - ``` - Running examples in ‘geomnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: football - > ### Title: College football games network (undirected) - > ### Aliases: football - > ### Keywords: datasets - > - > ### ** Examples - > - ... - + scale_colour_brewer("Conference", palette = "Paired") - Error: `loops` is `FALSE`, but `x` contains loops. - The following values are affected: - - `x[604, 1:2]` - - `x[605, 1:2]` - - `x[610, 1:2]` - - `x[615, 1:2]` - - `x[617, 1:2]` - - `x[618, 1:2]` - Execution halted - ``` - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘geomnet-vignette.Rmd’ using rmarkdown - Quitting from lines 15-112 (geomnet-vignette.Rmd) - Error: processing vignette 'geomnet-vignette.Rmd' failed with diagnostics: - The first two columns of `x` must be of the same type. - --- failed re-building ‘geomnet-vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘geomnet-vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# GGally - -
- -* Version: 2.1.2 -* GitHub: https://github.com/ggobi/ggally -* Source code: https://github.com/cran/GGally -* Date/Publication: 2021-06-21 04:40:10 UTC -* Number of recursive dependencies: 147 - -Run `revdep_details(, "GGally")` for more info - -
- -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘scagnostics’ - ``` - -# GGMncv - -
- -* Version: 2.1.1 -* GitHub: https://github.com/donaldRwilliams/GGMncv -* Source code: https://github.com/cran/GGMncv -* Date/Publication: 2021-12-15 07:40:28 UTC -* Number of recursive dependencies: 152 - -Run `revdep_details(, "GGMncv")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘Rdpack’ ‘mathjaxr’ - All declared Imports should be used. - ``` - -# GGMnonreg - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/GGMnonreg -* Date/Publication: 2021-04-08 11:30:06 UTC -* Number of recursive dependencies: 112 - -Run `revdep_details(, "GGMnonreg")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘Matrix’ ‘Rdpack’ - All declared Imports should be used. - ``` - -# ggnetwork - -
- -* Version: 0.5.10 -* GitHub: https://github.com/briatte/ggnetwork -* Source code: https://github.com/cran/ggnetwork -* Date/Publication: 2021-07-06 05:30:02 UTC -* Number of recursive dependencies: 70 - -Run `revdep_details(, "ggnetwork")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘sna’ ‘utils’ - All declared Imports should be used. - ``` - -# GGPA - -
- -* Version: 1.8.0 -* GitHub: https://github.com/dongjunchung/GGPA -* Source code: https://github.com/cran/GGPA -* Date/Publication: 2022-04-26 -* Number of recursive dependencies: 74 - -Run `revdep_details(, "GGPA")` for more info - -
- -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.8Mb - sub-directories of 1Mb or more: - doc 1.6Mb - libs 3.9Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Packages in Depends field not imported from: - ‘network’ ‘scales’ ‘sna’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - ``` - -* checking compiled code ... NOTE - ``` - File ‘GGPA/libs/GGPA.so’: - Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) - Object: ‘3_Param.o’ - - Compiled code should not call entry points which might terminate R nor - write to stdout/stderr instead of to the console, nor use Fortran I/O - nor system RNGs. - - See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. - ``` - -# ggraph - -
- -* Version: 2.0.6 -* GitHub: https://github.com/thomasp85/ggraph -* Source code: https://github.com/cran/ggraph -* Date/Publication: 2022-08-08 11:40:02 UTC -* Number of recursive dependencies: 96 - -Run `revdep_details(, "ggraph")` for more info - -
- -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.9Mb - sub-directories of 1Mb or more: - doc 3.6Mb - libs 4.0Mb - ``` - -# GOxploreR - -
- -* Version: 1.2.6 -* GitHub: NA -* Source code: https://github.com/cran/GOxploreR -* Date/Publication: 2022-04-19 14:02:33 UTC -* Number of recursive dependencies: 114 - -Run `revdep_details(, "GOxploreR")` for more info - -
- -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.7Mb - sub-directories of 1Mb or more: - R 6.1Mb - ``` - -# GRENITS - -
- -* Version: 1.48.0 -* GitHub: NA -* Source code: https://github.com/cran/GRENITS -* Date/Publication: 2022-04-26 -* Number of recursive dependencies: 38 - -Run `revdep_details(, "GRENITS")` for more info - -
- -## In both - -* checking installed package size ... NOTE - ``` - installed size is 10.9Mb - sub-directories of 1Mb or more: - libs 10.6Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Packages in Depends field not imported from: - ‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - ``` - -* checking R code for possible problems ... NOTE - ``` - .heatMap.ggplot: no visible global function definition for ‘ggplot’ - .heatMap.ggplot: no visible global function definition for ‘aes’ - .heatMap.ggplot: no visible binding for global variable ‘Var2’ - .heatMap.ggplot: no visible binding for global variable ‘Var1’ - .heatMap.ggplot: no visible global function definition for ‘geom_tile’ - .heatMap.ggplot: no visible binding for global variable ‘value’ - .heatMap.ggplot: no visible global function definition for - ‘scale_fill_gradient’ - .heatMap.ggplot: no visible global function definition for ‘theme’ - .heatMap.ggplot: no visible global function definition for - ... - .plotDistribParents.LargeMat: no visible global function definition for - ‘scale_x_discrete’ - .plotDistribParents.LargeMat: no visible global function definition for - ‘scale_y_discrete’ - .plotDistribParents.LargeMat: no visible global function definition for - ‘facet_wrap’ - Undefined global functions or variables: - GeneNames Var1 Var2 aes element_blank element_text facet_wrap - geom_tile ggplot ggtitle labs scale_fill_gradient scale_x_discrete - scale_y_discrete theme value variable - ``` - -# gwdegree - -
- -* Version: 0.1.1 -* GitHub: https://github.com/michaellevy/gwdegree -* Source code: https://github.com/cran/gwdegree -* Date/Publication: 2016-07-09 10:46:45 -* Number of recursive dependencies: 89 - -Run `revdep_details(, "gwdegree")` for more info - -
- -## In both - -* checking R code for possible problems ... NOTE - ``` - simCCCent : : no visible global function definition for - ‘simulate.formula’ - Undefined global functions or variables: - simulate.formula - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# ICON - -
- -* Version: 0.4.0 -* GitHub: https://github.com/rrrlw/ICON -* Source code: https://github.com/cran/ICON -* Date/Publication: 2020-10-23 23:00:02 UTC -* Number of recursive dependencies: 80 - -Run `revdep_details(, "ICON")` for more info - -
- -## In both - -* checking tests ... - ``` - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ══ Skipped tests ═══════════════════════════════════════════════════════════════ - • On CRAN (1) - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure (test-s3-network.R:21:3): as.network.ICON generic works ───────────── - network::get.edge.attribute(converted_network, "attrib") not equal to test_obj$attrib. - Lengths differ: 21 is not 25 - ── Failure (test-s3-network.R:24:3): as.network.ICON generic works ───────────── - network::network.edgecount(converted_network) not equal to `NROW`. - 1/1 mismatches - [1] 21 - 25 == -4 - - [ FAIL 2 | WARN 0 | SKIP 1 | PASS 11 ] - Error: Test failures - Execution halted - ``` - -# InflectSSP - -
- -* Version: 1.4.4 -* GitHub: NA -* Source code: https://github.com/cran/InflectSSP -* Date/Publication: 2022-03-18 14:40:02 UTC -* Number of recursive dependencies: 84 - -Run `revdep_details(, "InflectSSP")` for more info - -
- -## In both - -* checking package dependencies ... ERROR - ``` - Package required but not available: ‘xlsx’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# latentnet - -
- -* Version: 2.10.6 -* GitHub: https://github.com/statnet/latentnet -* Source code: https://github.com/cran/latentnet -* Date/Publication: 2022-05-11 12:30:05 UTC -* Number of recursive dependencies: 112 - -Run `revdep_details(, "latentnet")` for more info - -
- -## In both - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# leiden - -
- -* Version: 0.4.3 -* GitHub: https://github.com/TomKellyGenetics/leiden -* Source code: https://github.com/cran/leiden -* Date/Publication: 2022-09-10 17:22:53 UTC -* Number of recursive dependencies: 146 - -Run `revdep_details(, "leiden")` for more info - -
- -## Newly broken - -* checking tests ... - ``` - Running ‘spelling.R’ - Running ‘testthat.R’/srv/scratch/z3528859/R-4.2.0/bin/BATCH: line 60: 67256 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 - - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library("testthat") - > library("leiden") - Unable to set up conda environment r-reticulate - run in terminal: - conda init - conda create -n r-reticulate - conda environment r-reticulate installed - Unable to install python modules igraph and leidenalg - run in terminal: - conda install -n r-reticulate -c conda-forge vtraag python-igraph pandas umap learn - python modules igraph and leidenalg installed - > - > test_check("leiden") - ``` - -## Newly fixed - -* R CMD check timed out - - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.0Mb - sub-directories of 1Mb or more: - doc 5.9Mb - ``` - -# lolog - -
- -* Version: 1.3 -* GitHub: https://github.com/statnet/lolog -* Source code: https://github.com/cran/lolog -* Date/Publication: 2021-07-01 07:50:06 UTC -* Number of recursive dependencies: 80 - -Run `revdep_details(, "lolog")` for more info - -
- -## In both - -* R CMD check timed out - - -* checking installed package size ... NOTE - ``` - installed size is 24.8Mb - sub-directories of 1Mb or more: - libs 23.1Mb - ``` - -# MBCbook - -
- -* Version: 0.1.1 -* GitHub: NA -* Source code: https://github.com/cran/MBCbook -* Date/Publication: 2019-07-02 07:00:03 UTC -* Number of recursive dependencies: 23 - -Run `revdep_details(, "MBCbook")` for more info - -
- -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 66 marked UTF-8 strings - ``` - -# migraph - -
- -* Version: 0.12.0 -* GitHub: https://github.com/snlab-ch/migraph -* Source code: https://github.com/cran/migraph -* Date/Publication: 2022-09-27 07:50:02 UTC -* Number of recursive dependencies: 131 - -Run `revdep_details(, "migraph")` for more info - -
- -## In both - -* checking tests ... - ``` - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure (test-viz_autographr.R:115:3): fancy node mods graph correctly ────── - class(testcolnodes) not equal to c("ggraph", "gg", "ggplot"). - Lengths differ: 1 is not 3 - ── Error (test-viz_autographr.R:116:3): fancy node mods graph correctly ──────── - Error in `round(testcolnodes$data$x[1])`: non-numeric argument to mathematical function - Backtrace: - ▆ - 1. └─testthat::expect_equal(round(testcolnodes$data$x[1]), 4) at test-viz_autographr.R:116:2 - 2. └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. └─rlang::eval_bare(expr, quo_get_env(quo)) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 526 ] - Error: Test failures - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘concaveman’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 5.1Mb - sub-directories of 1Mb or more: - doc 3.0Mb - ``` - -# mpa - -
- -* Version: 0.7.3 -* GitHub: NA -* Source code: https://github.com/cran/mpa -* Date/Publication: 2012-10-29 08:59:13 -* Number of recursive dependencies: 15 - -Run `revdep_details(, "mpa")` for more info - -
- -## In both - -* checking DESCRIPTION meta-information ... NOTE - ``` - Malformed Description field: should contain one or more complete sentences. - ``` - -* checking R code for possible problems ... NOTE - ``` - NB: .First.lib is obsolete and will not be used in R >= 3.0.0 - File ‘mpa/R/zzz.R’: - .First.lib calls: - cat("\n mpa: CoWords Method") - cat("\n ") - cat("\n Universidad Nacional de Colombia") - cat("\n ") - cat("\n Elaborado por: Daniel Rodriguez ") - cat("\n Campo Elias Pardo ") - cat("\n For help: ?mpa \n\n") - ... - generate messages. - See section ‘Good practice’ in '?.onAttach'. - - diagram.mpa: no visible global function definition for ‘abline’ - diagram.mpa: no visible global function definition for ‘text’ - Undefined global functions or variables: - abline text - Consider adding - importFrom("graphics", "abline", "text") - to your NAMESPACE file. - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 6 marked UTF-8 strings - ``` - -# netdiffuseR - -
- -* Version: 1.22.4 -* GitHub: https://github.com/USCCANA/netdiffuseR -* Source code: https://github.com/cran/netdiffuseR -* Date/Publication: 2022-09-20 07:46:13 UTC -* Number of recursive dependencies: 79 - -Run `revdep_details(, "netdiffuseR")` for more info - -
- -## In both - -* checking installed package size ... NOTE - ``` - installed size is 13.2Mb - sub-directories of 1Mb or more: - doc 2.5Mb - libs 8.8Mb - ``` - -# nethet - -
- -* Version: 1.28.0 -* GitHub: NA -* Source code: https://github.com/cran/nethet -* Date/Publication: 2022-04-26 -* Number of recursive dependencies: 102 - -Run `revdep_details(, "nethet")` for more info - -
- -## In both - -* checking whether package ‘nethet’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘mclust::dmvnorm’ by ‘mvtnorm::dmvnorm’ when loading ‘nethet’ - Warning: replacing previous import ‘multtest::update’ by ‘stats::update’ when loading ‘nethet’ - See ‘/srv/scratch/z3528859/github/statnet/network/revdep/checks/nethet/new/nethet.Rcheck/00install.out’ for details. - ``` - -* checking R code for possible problems ... NOTE - ``` - screen_shrink: no visible global function definition for - ‘performance.pcor’ - Undefined global functions or variables: - performance.pcor - ``` - -# netmap - -
- -* Version: 0.1.1 -* GitHub: https://github.com/artod83/netmap -* Source code: https://github.com/cran/netmap -* Date/Publication: 2022-03-18 16:00:02 UTC -* Number of recursive dependencies: 81 - -Run `revdep_details(, "netmap")` for more info - -
- -## In both - -* checking package dependencies ... ERROR - ``` - Package required but not available: ‘sf’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# netmediate - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/netmediate -* Date/Publication: 2022-08-31 07:50:02 UTC -* Number of recursive dependencies: 99 - -Run `revdep_details(, "netmediate")` for more info - -
- -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘mediation’ - ``` - -# networksis - -
- -* Version: 2.1-3 -* GitHub: NA -* Source code: https://github.com/cran/networksis -* Date/Publication: 2015-04-16 08:44:42 -* Number of recursive dependencies: 15 - -Run `revdep_details(, "networksis")` for more info - -
- -## In both - -* checking R code for possible problems ... NOTE - ``` - simulate.sisnetwork: no visible global function definition for ‘var’ - Undefined global functions or variables: - var - Consider adding - importFrom("stats", "var") - to your NAMESPACE file. - ``` - -# PDN - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/PDN -* Date/Publication: 2017-11-03 23:27:43 UTC -* Number of recursive dependencies: 60 - -Run `revdep_details(, "PDN")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘glmnet’ - All declared Imports should be used. - ``` - -# PhosR - -
- -* Version: 1.6.0 -* GitHub: NA -* Source code: https://github.com/cran/PhosR -* Date/Publication: 2022-04-26 -* Number of recursive dependencies: 182 - -Run `revdep_details(, "PhosR")` for more info - -
- -## In both - -* checking for hidden files and directories ... NOTE - ``` - Found the following hidden files and directories: - .travis.yml - These were most likely included in error. See section ‘Package - structure’ in the ‘Writing R Extensions’ manual. - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.4Mb - sub-directories of 1Mb or more: - data 3.3Mb - doc 2.2Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Unexported objects imported by ':::' calls: - ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::disableValidity’ - ‘SummarizedExperiment:::.SummarizedExperiment.charbound’ - See the note in ?`:::` about the use of this operator. - ``` - -# predictionet - -
- -* Version: 1.40.0 -* GitHub: NA -* Source code: https://github.com/cran/predictionet -* Date/Publication: 2021-10-26 -* Number of recursive dependencies: 36 - -Run `revdep_details(, "predictionet")` for more info - -
- -## In both - -* checking whether package ‘predictionet’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: Package 'predictionet' is deprecated and will be removed from - See ‘/srv/scratch/z3528859/github/statnet/network/revdep/checks/predictionet/new/predictionet.Rcheck/00install.out’ for details. - ``` - -* checking for hidden files and directories ... NOTE - ``` - Found the following hidden files and directories: - .BBSoptions - These were most likely included in error. See section ‘Package - structure’ in the ‘Writing R Extensions’ manual. - ``` - -* checking dependencies in R code ... NOTE - ``` - Packages in Depends field not imported from: - ‘catnet’ ‘igraph’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. - ``` - -* checking R code for possible problems ... NOTE - ``` - .build.regression.regrnet: no visible global function definition for - ‘formula’ - .build.regression.regrnet: no visible global function definition for - ‘lm’ - .build2.mim: no visible global function definition for ‘cor’ - .exportGML: no visible global function definition for ‘vcount’ - .exportGML: no visible global function definition for ‘ecount’ - .get.ii4triplets.gaussian: no visible global function definition for - ‘cor’ - .pred.onegene.bayesnet.fs : : no visible global function - ... - Undefined global functions or variables: - as cnMatParents coefficients complete.cases cor ecount formula lm - quantile sessionInfo vcount - Consider adding - importFrom("methods", "as") - importFrom("stats", "coefficients", "complete.cases", "cor", "formula", - "lm", "quantile") - importFrom("utils", "sessionInfo") - to your NAMESPACE file (and ensure that your DESCRIPTION Imports field - contains 'methods'). - ``` - -* checking compiled code ... NOTE - ``` - File ‘predictionet/libs/predictionet.so’: - Found ‘rand’, possibly from ‘rand’ (C) - Object: ‘mrnet_ensemble_standalone.o’ - Found ‘srand’, possibly from ‘srand’ (C) - Object: ‘mrnet_ensemble_standalone.o’ - - Compiled code should not call entry points which might terminate R nor - write to stdout/stderr instead of to the console, nor use Fortran I/O - nor system RNGs. - - See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. - ``` - -# PubScore - -
- -* Version: 1.8.0 -* GitHub: NA -* Source code: https://github.com/cran/PubScore -* Date/Publication: 2022-04-26 -* Number of recursive dependencies: 132 - -Run `revdep_details(, "PubScore")` for more info - -
- -## Newly fixed - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘PubScore_vignette.Rmd’ using rmarkdown - Quitting from lines 144-153 (PubScore_vignette.Rmd) - Error: processing vignette 'PubScore_vignette.Rmd' failed with diagnostics: - Gateway Timeout (HTTP 504). - --- failed re-building ‘PubScore_vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘PubScore_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking whether package ‘PubScore’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: Package 'PubScore' is deprecated and will be removed from Bioconductor - See ‘/srv/scratch/z3528859/github/statnet/network/revdep/checks/PubScore/new/PubScore.Rcheck/00install.out’ for details. - ``` - -* checking installed package size ... NOTE - ``` - installed size is 9.4Mb - sub-directories of 1Mb or more: - data 4.2Mb - doc 4.9Mb - ``` - -* checking R code for possible problems ... NOTE - ``` - get_literature_score: no visible binding for global variable - ‘gene2pubmed_db’ - get_literature_score: no visible binding for global variable - ‘hgcn_entrez_reference’ - get_sum_of_weights: no visible binding for global variable ‘Genes’ - get_sum_of_weights: no visible binding for global variable ‘Topic’ - plot_literature_score: no visible binding for global variable ‘Genes’ - plot_literature_score: no visible binding for global variable ‘Topic’ - plot_literature_score: no visible binding for global variable - ‘number_of_articles’ - show,PubScore: no visible binding for global variable ‘pub’ - Undefined global functions or variables: - Genes Topic gene2pubmed_db hgcn_entrez_reference number_of_articles - pub - ``` - -# RSiena - -
- -* Version: 1.3.0.1 -* GitHub: NA -* Source code: https://github.com/cran/RSiena -* Date/Publication: 2021-11-15 17:13:35 UTC -* Number of recursive dependencies: 19 - -Run `revdep_details(, "RSiena")` for more info - -
- -## In both - -* checking installed package size ... NOTE - ``` - installed size is 19.1Mb - sub-directories of 1Mb or more: - R 1.0Mb - libs 17.2Mb - ``` - -# sand - -
- -* Version: 2.0.0 -* GitHub: https://github.com/kolaczyk/sand -* Source code: https://github.com/cran/sand -* Date/Publication: 2020-07-02 07:20:06 UTC -* Number of recursive dependencies: 160 - -Run `revdep_details(, "sand")` for more info - -
- -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 6 marked UTF-8 strings - ``` - -# SBICgraph - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/SBICgraph -* Date/Publication: 2021-03-02 19:10:09 UTC -* Number of recursive dependencies: 47 - -Run `revdep_details(, "SBICgraph")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘network’ - All declared Imports should be used. - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# sparsebnUtils - -
- -* Version: 0.0.8 -* GitHub: https://github.com/itsrainingdata/sparsebnUtils -* Source code: https://github.com/cran/sparsebnUtils -* Date/Publication: 2021-01-27 06:30:02 UTC -* Number of recursive dependencies: 64 - -Run `revdep_details(, "sparsebnUtils")` for more info - -
- -## In both - -* checking Rd cross-references ... NOTE - ``` - Unknown package ‘sparsebn’ in Rd xrefs - ``` - -# statnetWeb - -
- -* Version: 0.5.6 -* GitHub: NA -* Source code: https://github.com/cran/statnetWeb -* Date/Publication: 2020-08-05 18:00:03 UTC -* Number of recursive dependencies: 65 - -Run `revdep_details(, "statnetWeb")` for more info - -
- -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# vivid - -
- -* Version: 0.2.3 -* GitHub: NA -* Source code: https://github.com/cran/vivid -* Date/Publication: 2021-11-20 01:30:02 UTC -* Number of recursive dependencies: 201 - -Run `revdep_details(, "vivid")` for more info - -
- -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘zenplots’ - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘RColorBrewer’ ‘colorspace’ ‘tidyr’ - All declared Imports should be used. - ``` - -# wildlifeDI - -
- -* Version: 0.4.1 -* GitHub: https://github.com/jedalong/wildlifeDI -* Source code: https://github.com/cran/wildlifeDI -* Date/Publication: 2021-06-16 15:20:02 UTC -* Number of recursive dependencies: 90 - -Run `revdep_details(, "wildlifeDI")` for more info - -
- -## In both - -* checking package dependencies ... ERROR - ``` - Package required but not available: ‘sf’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# WOTPLY - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/WOTPLY -* Date/Publication: 2022-09-12 07:43:01 UTC -* Number of recursive dependencies: 70 - -Run `revdep_details(, "WOTPLY")` for more info - -
- -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘sna’ - All declared Imports should be used. - ``` - -# xergm.common - -
- -* Version: 1.7.8 -* GitHub: https://github.com/leifeld/xergm.common -* Source code: https://github.com/cran/xergm.common -* Date/Publication: 2020-04-07 09:50:02 UTC -* Number of recursive dependencies: 35 - -Run `revdep_details(, "xergm.common")` for more info - -
- -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘RSiena’ - ``` - diff --git a/src/access.c b/src/access.c index c4a69b9..21d32d8 100644 --- a/src/access.c +++ b/src/access.c @@ -4,7 +4,7 @@ # access.c # # Written by Carter T. Butts -# Last Modified 01/24/23 +# Last Modified 12/06/24 # Licensed under the GNU General Public License version 2 (June, 1991) # or greater # @@ -550,7 +550,7 @@ SEXP setVertexAttribute(SEXP x, const char *attrname, SEXP value, int v) SEXP addEdges(SEXP x, SEXP tail, SEXP head, SEXP namesEval, SEXP valsEval, SEXP edgeCheck) /*Adds multiple edges to x. Note that we assume tail, head, et al. to be lists of identical length. By contrast, edgeCheck should be a single logical value.*/ { - int pc=0,opc,i,j,mnext,z; + int pc=0,opc,i,j,mnext,z,echeck; SEXP el,atl,atlnam,navec,inl,outl,elnam,mel,newmel,oel,iel,ptr,elem,mnptr,gal; char buf[64]; @@ -565,6 +565,10 @@ SEXP addEdges(SEXP x, SEXP tail, SEXP head, SEXP namesEval, SEXP valsEval, SEXP /*If necessary, verify that new edge satisfies existing graph requirements*/ PROTECT(edgeCheck = coerceVector(edgeCheck, LGLSXP)); pc++; + if(length(edgeCheck)<1) + echeck=0; + else + echeck=INTEGER(edgeCheck)[0]; /*Rprintf("addEdges: adding %d edges\n",length(tail));*/ for(z=0;z(double)networkSize(x)) ||(vecMax(outl)>(double)networkSize(x))) error("(edge check) Illegal vertex reference in addEdges_R. Exiting."); + if(length(inl)*length(outl)==0) + error("(edge check) Empty head/tail list in addEdges_R. Exiting."); - if(INTEGER(edgeCheck)[0]){ - if(length(inl)*length(outl)==0) - error("(edge check) Empty head/tail list in addEdges_R. Exiting."); + if(echeck){ if(!isHyper(x)) if(MAX(length(inl),length(outl))>1) error("(edge check) Attempted to add hyperedge where hyper==FALSE in addEdges_R. Exiting."); @@ -657,8 +661,13 @@ SEXP addEdges(SEXP x, SEXP tail, SEXP head, SEXP namesEval, SEXP valsEval, SEXP PROTECT(ptr=coerceVector(VECTOR_ELT(oel,INTEGER(outl)[i]-1),INTSXP)); pc++; if(length(ptr)>0){ PROTECT(elem = allocVector(INTSXP,length(ptr)+1)); pc++; - for(j=0;(j=INTEGER(outl)[0])) + break; INTEGER(elem)[j]=INTEGER(ptr)[j]; + } INTEGER(elem)[j++]=mnext; for(;(j-10){ PROTECT(elem = allocVector(INTSXP,length(ptr)+1)); pc++; - for(j=0;(j=INTEGER(inl)[0])) + break; INTEGER(elem)[j]=INTEGER(ptr)[j]; + } INTEGER(elem)[j++]=mnext; for(;(j-1(double)networkSize(x)) ||(vecMax(outl)>(double)networkSize(x))) error("(edge check) Illegal vertex reference in addEdge_R. Exiting."); + if(length(inl)*length(outl)==0) + error("(edge check) Empty head/tail list in addEdge_R. Exiting."); /*If necessary, verify that new edge satisfies existing graph requirements*/ PROTECT(edgeCheck = coerceVector(edgeCheck, LGLSXP)); pc++; - if(INTEGER(edgeCheck)[0]){ - if(length(inl)*length(outl)==0) - error("(edge check) Empty head/tail list in addEdge_R. Exiting."); + if(length(edgeCheck)==0) + echeck=0; + else + echeck=INTEGER(edgeCheck)[0]; + if(echeck){ if(!isHyper(x)) if(MAX(length(inl),length(outl))>1) error("(edge check) Attempted to add hyperedge where hyper==FALSE in addEdge_R. Exiting."); @@ -953,8 +971,13 @@ SEXP addEdge_R(SEXP x, SEXP tail, SEXP head, SEXP namesEval, SEXP valsEval, SEXP PROTECT(ptr=coerceVector(VECTOR_ELT(oel,INTEGER(outl)[i]-1),INTSXP)); pc++; if(length(ptr)>0){ PROTECT(elem = allocVector(INTSXP,length(ptr)+1)); pc++; - for(j=0;(j=INTEGER(outl)[0])) + break; INTEGER(elem)[j]=INTEGER(ptr)[j]; + } INTEGER(elem)[j++]=mnext; for(;(j-10){ PROTECT(elem = allocVector(INTSXP,length(ptr)+1)); pc++; - for(j=0;(j=INTEGER(inl)[0])) + break; INTEGER(elem)[j]=INTEGER(ptr)[j]; + } INTEGER(elem)[j++]=mnext; for(;(j-1n)|| (INTEGER(vj)[i]>n)) INTEGER(ans)[i]=NA_INTEGER; /*Return NA on a bad query*/ else - INTEGER(ans)[i]=isAdjacent(x,INTEGER(vi)[i],INTEGER(vj)[i], INTEGER(naOmit)[0]); + INTEGER(ans)[i]=isAdjacent(x,INTEGER(vi)[i],INTEGER(vj)[i], omitna); /*Return the result*/ UNPROTECT(pc); @@ -1466,14 +1498,17 @@ SEXP isNANetwork_R(SEXP x, SEXP y) SEXP networkEdgecount_R(SEXP x, SEXP naOmit) -/*Count the number of active edges in x. If naOmit==TRUE, then missing edges are not counted; otherwise, all edges are included.*/ +/*Count the number of active edges in x. If naOmit==TRUE (default), then missing edges are not counted; otherwise, all edges are included.*/ { int pc=0,naomit; SEXP ans; /*Take care of preliminaries*/ PROTECT(naOmit=coerceVector(naOmit,LGLSXP)); pc++; - naomit=INTEGER(naOmit)[0]; + if(length(naOmit)<1) + naomit=1; + else + naomit=INTEGER(naOmit)[0]; PROTECT(ans=allocVector(INTSXP,1)); pc++; /*Get the result*/ @@ -1540,7 +1575,7 @@ SEXP setEdgeAttribute_R(SEXP x, SEXP attrname, SEXP value, SEXP e) /* this version is essentially the same as above, but allows passing in lists of attrnames and lists of lists of values */ SEXP setEdgeAttributes_R(SEXP x, SEXP attrnames, SEXP values, SEXP e) -/*Sets the attribute in attrname to the values in (list) value, for each corresponding edge with respective ID in vector e. If an edge referred to in e does not actually exist (i.e., its entry in mel is NULL), then that edge (and the associated value) is silently skipped. Note that existing attribute entries are overwritten by this routine, where present...if the named attribute does not exist, a new entry is created for each edge in question.*/ +/*Sets the attribute in attrname to the values in (list) value, for each corresponding edgeb with respective ID in vector e. If an edge referred to in e does not actually exist (i.e., its entry in mel is NULL), then that edge (and the associated value) is silently skipped. Note that existing attribute entries are overwritten by this routine, where present...if the named attribute does not exist, a new entry is created for each edge in question.*/ { int i,j,pc=0; SEXP mel,el,atl, value; @@ -1737,7 +1772,7 @@ SEXP setVertexAttributes_R(SEXP x, SEXP attrnames, SEXP values, SEXP v) } SEXP nonEmptyEdges_R(SEXP el) -/* retrun all edges which are non NULL */ +/* return all edges which are non NULL */ { int i, elen, n=0; SEXP ans;