Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:26 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the tRanslatome package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tRanslatome.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1949/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tRanslatome 1.30.0 (landing page) Toma Tebaldi
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: tRanslatome |
Version: 1.30.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tRanslatome.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings tRanslatome_1.30.0.tar.gz |
StartedAt: 2021-10-15 06:51:45 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 06:58:58 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 433.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: tRanslatome.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tRanslatome.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings tRanslatome_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/tRanslatome.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'tRanslatome/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'tRanslatome' version '1.30.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'limma', 'sigPathway', 'anota', 'DESeq2', 'edgeR', 'RankProd', 'topGO', 'org.Hs.eg.db', 'GOSemSim', 'Heatplus', 'gplots', 'plotrix', 'Biobase' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'tRanslatome' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE computeGeneListEnrichment: no visible global function definition for 'data' computeGeneListEnrichment: no visible binding for global variable 'tRanslatomeSampleData' computeGeneListEnrichment: no visible global function definition for 'fisher.test' computeGeneListEnrichment: no visible global function definition for 'p.adjust' createspecifictable: no visible global function definition for 'str' createspecifictable: no visible global function definition for 'p.adjust' methodANOTA: no visible global function definition for 'p.adjust' methodEdgeR: no visible global function definition for 'p.adjust' methodLimma: no visible global function definition for 'model.matrix' methodLimma: no visible global function definition for 'lmFit' methodLimma: no visible global function definition for 'p.adjust' methodTTest: no visible global function definition for 'p.adjust' CVplot,DEGs: no visible global function definition for 'pdf' CVplot,DEGs: no visible global function definition for 'postscript' CVplot,DEGs: no visible global function definition for 'jpeg' CVplot,DEGs: no visible global function definition for 'par' CVplot,DEGs: no visible global function definition for 'layout' CVplot,DEGs: no visible global function definition for 'points' CVplot,DEGs: no visible global function definition for 'abline' CVplot,DEGs: no visible global function definition for 'legend' CVplot,DEGs: no visible global function definition for 'text' CVplot,DEGs: no visible global function definition for 'dev.off' GOEnrichment,DEGs: no visible global function definition for 'toTable' Heatmap,EnrichedSets: no visible global function definition for 'pdf' Heatmap,EnrichedSets: no visible global function definition for 'postscript' Heatmap,EnrichedSets: no visible global function definition for 'jpeg' Heatmap,EnrichedSets: no visible global function definition for 'png' Heatmap,EnrichedSets: no visible global function definition for 'dev.off' Heatmap,GOsets: no visible global function definition for 'pdf' Heatmap,GOsets: no visible global function definition for 'postscript' Heatmap,GOsets: no visible global function definition for 'jpeg' Heatmap,GOsets: no visible global function definition for 'png' Heatmap,GOsets: no visible global function definition for 'dev.off' Histogram,DEGs: no visible global function definition for 'pdf' Histogram,DEGs: no visible global function definition for 'postscript' Histogram,DEGs: no visible global function definition for 'jpeg' Histogram,DEGs: no visible global function definition for 'par' Histogram,DEGs: no visible global function definition for 'barplot' Histogram,DEGs: no visible global function definition for 'legend' Histogram,DEGs: no visible global function definition for 'mtext' Histogram,DEGs: no visible global function definition for 'dev.off' IdentityPlot,GOsims: no visible global function definition for 'pdf' IdentityPlot,GOsims: no visible global function definition for 'postscript' IdentityPlot,GOsims: no visible global function definition for 'jpeg' IdentityPlot,GOsims: no visible global function definition for 'barplot' IdentityPlot,GOsims: no visible global function definition for 'dev.off' MAplot,DEGs: no visible global function definition for 'pdf' MAplot,DEGs: no visible global function definition for 'postscript' MAplot,DEGs: no visible global function definition for 'jpeg' MAplot,DEGs: no visible global function definition for 'par' MAplot,DEGs: no visible global function definition for 'layout' MAplot,DEGs: no visible global function definition for 'points' MAplot,DEGs: no visible global function definition for 'abline' MAplot,DEGs: no visible global function definition for 'legend' MAplot,DEGs: no visible global function definition for 'text' MAplot,DEGs: no visible global function definition for 'dev.off' Radar,EnrichedSets: no visible global function definition for 'pdf' Radar,EnrichedSets: no visible global function definition for 'postscript' Radar,EnrichedSets: no visible global function definition for 'jpeg' Radar,EnrichedSets: no visible global function definition for 'png' Radar,EnrichedSets: no visible global function definition for 'par' Radar,EnrichedSets: no visible global function definition for 'legend' Radar,EnrichedSets: no visible global function definition for 'dev.off' Radar,GOsets: no visible global function definition for 'pdf' Radar,GOsets: no visible global function definition for 'postscript' Radar,GOsets: no visible global function definition for 'jpeg' Radar,GOsets: no visible global function definition for 'png' Radar,GOsets: no visible global function definition for 'par' Radar,GOsets: no visible global function definition for 'legend' Radar,GOsets: no visible global function definition for 'dev.off' SDplot,DEGs: no visible global function definition for 'pdf' SDplot,DEGs: no visible global function definition for 'postscript' SDplot,DEGs: no visible global function definition for 'jpeg' SDplot,DEGs: no visible global function definition for 'par' SDplot,DEGs: no visible global function definition for 'layout' SDplot,DEGs: no visible global function definition for 'points' SDplot,DEGs: no visible global function definition for 'abline' SDplot,DEGs: no visible global function definition for 'legend' SDplot,DEGs: no visible global function definition for 'text' SDplot,DEGs: no visible global function definition for 'dev.off' Scatterplot,DEGs: no visible global function definition for 'pdf' Scatterplot,DEGs: no visible global function definition for 'postscript' Scatterplot,DEGs: no visible global function definition for 'jpeg' Scatterplot,DEGs: no visible global function definition for 'mtext' Scatterplot,DEGs: no visible global function definition for 'cor.test' Scatterplot,DEGs: no visible global function definition for 'points' Scatterplot,DEGs: no visible global function definition for 'abline' Scatterplot,DEGs: no visible global function definition for 'legend' Scatterplot,DEGs: no visible global function definition for 'text' Scatterplot,DEGs: no visible global function definition for 'dev.off' SimilarityPlot,GOsims: no visible global function definition for 'pdf' SimilarityPlot,GOsims: no visible global function definition for 'postscript' SimilarityPlot,GOsims: no visible global function definition for 'jpeg' SimilarityPlot,GOsims: no visible global function definition for 'barplot' SimilarityPlot,GOsims: no visible global function definition for 'legend' SimilarityPlot,GOsims: no visible global function definition for 'dev.off' computeDEGs,TranslatomeDataset : <anonymous>: no visible global function definition for 'sd' show,DEGs: no visible global function definition for 'head' show,GOsims: no visible global function definition for 'head' show,TranslatomeDataset: no visible global function definition for 'head' Undefined global functions or variables: abline barplot cor.test data dev.off fisher.test head jpeg layout legend lmFit model.matrix mtext p.adjust par pdf png points postscript sd str tRanslatomeSampleData text toTable Consider adding importFrom("grDevices", "dev.off", "jpeg", "pdf", "png", "postscript") importFrom("graphics", "abline", "barplot", "layout", "legend", "mtext", "par", "points", "text") importFrom("stats", "cor.test", "fisher.test", "model.matrix", "p.adjust", "sd") importFrom("utils", "data", "head", "str") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... WARNING Found the following significant warnings: Warning: 'RGBColVec' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed GOEnrichment 19.03 0.70 24.42 GOComparison 14.23 1.25 15.54 ** running examples for arch 'x64' ... WARNING Found the following significant warnings: Warning: 'RGBColVec' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed GOEnrichment 12.43 0.06 12.5 GOComparison 10.86 0.64 11.5 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/tRanslatome.Rcheck/00check.log' for details.
tRanslatome.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/tRanslatome_1.30.0.tar.gz && rm -rf tRanslatome.buildbin-libdir && mkdir tRanslatome.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tRanslatome.buildbin-libdir tRanslatome_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL tRanslatome_1.30.0.zip && rm tRanslatome_1.30.0.tar.gz tRanslatome_1.30.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 623k 100 623k 0 0 1812k 0 --:--:-- --:--:-- --:--:-- 1818k install for i386 * installing *source* package 'tRanslatome' ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** help *** installing help indices converting help for package 'tRanslatome' finding HTML links ... done CVplot html DEGs html DEGs.table html EnrichedSets html FC.threshold html GOComparison html GOEnrichment html GOsets html GOsims html Heatmap html Histogram html IdentityPlot html MAplot html Radar html RegulatoryEnrichment html SDplot html Scatterplot html SimilarityPlot html TranslatomeDataset html average.similarity.scores html computeDEGs html enriched.table html getConditionA html getConditionB html getConditionC html getConditionD html getConditionLabels html getDEGs html getDEGsMethod html getDataType html getExprMatrix html getLevelLabels html identity.matrix html label.condition html label.level.DEGs html label.level.enriched html newTranslatomeDataset html significance.threshold html similarity.matrix html tRanslatome-package html tRanslatomeSampleData html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package can be loaded from final location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'tRanslatome' ... ** testing if installed package can be loaded groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. * MD5 sums packaged installation of 'tRanslatome' as tRanslatome_1.30.0.zip * DONE (tRanslatome) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'tRanslatome' successfully unpacked and MD5 sums checked
tRanslatome.Rcheck/examples_i386/tRanslatome-Ex.timings
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tRanslatome.Rcheck/examples_x64/tRanslatome-Ex.timings
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