Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:17:14 -0400 (Thu, 12 Apr 2018).
Package 17/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
affycomp 1.54.0 Rafael A. Irizarry
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: affycomp |
Version: 1.54.0 |
Command: rm -rf affycomp.buildbin-libdir affycomp.Rcheck && mkdir affycomp.buildbin-libdir affycomp.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affycomp.buildbin-libdir affycomp_1.54.0.tar.gz >affycomp.Rcheck\00install.out 2>&1 && cp affycomp.Rcheck\00install.out affycomp-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=affycomp.buildbin-libdir --install="check:affycomp-install.out" --force-multiarch --no-vignettes --timings affycomp_1.54.0.tar.gz |
StartedAt: 2018-04-11 22:04:49 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 22:07:36 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 167.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: affycomp.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf affycomp.buildbin-libdir affycomp.Rcheck && mkdir affycomp.buildbin-libdir affycomp.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affycomp.buildbin-libdir affycomp_1.54.0.tar.gz >affycomp.Rcheck\00install.out 2>&1 && cp affycomp.Rcheck\00install.out affycomp-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=affycomp.buildbin-libdir --install="check:affycomp-install.out" --force-multiarch --no-vignettes --timings affycomp_1.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/affycomp.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'affycomp/DESCRIPTION' ... OK * this is package 'affycomp' version '1.54.0' * checking package namespace information ... OK * checking package dependencies ... OK * 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 'affycomp' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWeePbB/R.INSTALL24a0eaf33b1/affycomp/man/mas5.assessment.Rd:10: missing file link 'ExpressionSet' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/affycomp.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 8.2Mb sub-directories of 1Mb or more: data 7.0Mb * 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 ... NOTE 'library' or 'require' call to 'splines' in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: 'Biobase' 'methods' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE affycomp.figure2b: warning in affycomp.compfig2b(list(l), method.name = l$method.name, add.legend = FALSE, main = main): partial argument match of 'method.name' to 'method.names' affycompPlot: warning in vector(mode = "character", len = N): partial argument match of 'len' to 'length' tableAll: warning in vector(mode = "character", len = N): partial argument match of 'len' to 'length' tableOverallSNR: warning in vector(mode = "character", len = N): partial argument match of 'len' to 'length' tableRanks: warning in vector(mode = "character", len = N): partial argument match of 'len' to 'length' .onAttach: no visible global function definition for 'addVigs2WinMenu' affycomp.compfig2: no visible global function definition for 'plot' affycomp.compfig2: no visible global function definition for 'lines' affycomp.compfig2: no visible global function definition for 'legend' affycomp.compfig2b: no visible global function definition for 'plot' affycomp.compfig2b: no visible global function definition for 'lines' affycomp.compfig2b: no visible global function definition for 'legend' affycomp.compfig3: no visible global function definition for 'boxplot' affycomp.compfig4a: no visible global function definition for 'plot' affycomp.compfig4a: no visible global function definition for 'lines' affycomp.compfig4a: no visible global function definition for 'legend' affycomp.compfig4b: no visible global function definition for 'plot' affycomp.compfig4b: no visible global function definition for 'lines' affycomp.compfig4b: no visible global function definition for 'legend' affycomp.compfig4b: no visible global function definition for 'abline' affycomp.compfig4c: no visible global function definition for 'plot' affycomp.compfig4c: no visible global function definition for 'lines' affycomp.compfig4c: no visible global function definition for 'legend' affycomp.compfig4c: no visible global function definition for 'abline' affycomp.compfig5a: no visible global function definition for 'plot' affycomp.compfig5a: no visible global function definition for 'lines' affycomp.compfig5a: no visible global function definition for 'legend' affycomp.compfig5b: no visible global function definition for 'plot' affycomp.compfig5b: no visible global function definition for 'lines' affycomp.compfig5b: no visible global function definition for 'legend' affycomp.compfig5cde: no visible global function definition for 'plot' affycomp.compfig5cde: no visible global function definition for 'lines' affycomp.compfig5cde: no visible global function definition for 'legend' affycomp.compfig7: no visible global function definition for 'boxplot' affycomp.compfigs: no visible global function definition for 'par' affycomp.compfigs: no visible global function definition for 'dev.interactive' affycomp.figure1: no visible global function definition for 'topo.colors' affycomp.figure1: no visible global function definition for 'heat.colors' affycomp.figure1: no visible global function definition for 'plot' affycomp.figure1: no visible global function definition for 'points' affycomp.figure1: no visible global function definition for 'text' affycomp.figure1b: no visible global function definition for 'topo.colors' affycomp.figure1b: no visible global function definition for 'heat.colors' affycomp.figure1b: no visible global function definition for 'plot' affycomp.figure1b: no visible global function definition for 'points' affycomp.figure1b: no visible global function definition for 'text' affycomp.figure2: no visible global function definition for 'plot' affycomp.figure3: no visible global function definition for 'plot' affycomp.figure3: no visible global function definition for 'abline' affycomp.figure3: no visible global function definition for 'points' affycomp.figure4a: no visible global function definition for 'plot' affycomp.figure4a: no visible global function definition for 'lines' affycomp.figure4b: no visible global function definition for 'plot' affycomp.figure4b: no visible global function definition for 'abline' affycomp.figure5a: no visible global function definition for 'plot' affycomp.figure6a: no visible global function definition for 'matplot' affycomp.figure6a: no visible global function definition for 'lines' affycomp.figure6a: no visible global function definition for 'abline' affycomp.figure6b: no visible global function definition for 'plot' affycomp.figure6b: no visible global function definition for 'lines' affycomp.figure6b: no visible global function definition for 'abline' affycomp.figure7: no visible global function definition for 'lm' affycomp.figure7: no visible global function definition for 'plot' affycomp.figure7: no visible global function definition for 'lines' affycomp.figure7: no visible global function definition for 'abline' affycomp.figures: no visible global function definition for 'par' affycomp.figures: no visible global function definition for 'dev.interactive' assessDilution: no visible global function definition for 'exprs' assessDilution: no visible global function definition for 'pData' assessDilution : <anonymous>: no visible global function definition for 'cor' assessDilution : <anonymous>: no visible binding for global variable 'sd' assessDilution: no visible global function definition for 'lm' assessDilution: no visible global function definition for 'median' assessDilution: no visible global function definition for 'cor' assessFC: no visible global function definition for 'exprs' assessFC: no visible global function definition for 'pData' assessFC: no visible global function definition for 'quantile' assessFC: no visible global function definition for 'lm' assessFC2: no visible global function definition for 'exprs' assessFC2: no visible global function definition for 'pData' assessLS: no visible global function definition for 'exprs' assessLS: no visible global function definition for 'pData' assessLS: no visible global function definition for 'featureNames' assessLS: no visible global function definition for 'lm' assessLS: no visible global function definition for 'cor' assessMA: no visible global function definition for 'exprs' assessMA: no visible global function definition for 'pData' assessMA2: no visible global function definition for 'exprs' assessMA2: no visible global function definition for 'pData' assessMA2: no visible global function definition for 'featureNames' assessMA2: no visible binding for global variable 'median' assessSD: no visible global function definition for 'exprs' assessSD: no visible global function definition for 'assayDataElement' assessSD: no visible global function definition for 'pData' assessSD : <anonymous>: no visible binding for global variable 'sd' assessSD: no visible global function definition for 'cor' assessSignal: no visible global function definition for 'exprs' assessSignal: no visible global function definition for 'pData' assessSignal: no visible global function definition for 'featureNames' assessSignal: no visible global function definition for 'lm' assessSpikeIn2: no visible global function definition for 'exprs' assessSpikeInSD: no visible global function definition for 'pData' assessSpikeInSD: no visible global function definition for 'featureNames' assessSpikeInSD: no visible global function definition for 'esApply' assessSpikeInSD: no visible binding for global variable 'sd' assessSpikeInSD: no visible global function definition for 'loess' exprset.log: no visible global function definition for 'exprs' exprset.log: no visible global function definition for 'exprs<-' getData: no visible global function definition for 'data' read.dilution: no visible global function definition for 'read.csv' read.dilution: no visible global function definition for 'sampleNames' read.dilution: no visible global function definition for 'new' read.spikein: no visible global function definition for 'read.csv' read.spikein: no visible global function definition for 'sampleNames' read.spikein: no visible global function definition for 'new' remove.hgu133a.xhyb: no visible global function definition for 'featureNames' tableMA2 : myauc: no visible global function definition for 'approx' tableMA2: no visible global function definition for 'IQR' tableMA2: no visible global function definition for 'quantile' tableOverallSNR: no visible global function definition for 'median' tableOverallSNR: no visible global function definition for 'IQR' tableOverallSNR: no visible global function definition for 'quantile' tableSD: no visible global function definition for 'IQR' tableSpikeInSD: no visible global function definition for 'quantile' Undefined global functions or variables: IQR abline addVigs2WinMenu approx assayDataElement boxplot cor data dev.interactive esApply exprs exprs<- featureNames heat.colors legend lines lm loess matplot median new pData par plot points quantile read.csv sampleNames sd text topo.colors Consider adding importFrom("grDevices", "dev.interactive", "heat.colors", "topo.colors") importFrom("graphics", "abline", "boxplot", "legend", "lines", "matplot", "par", "plot", "points", "text") importFrom("methods", "new") importFrom("stats", "IQR", "approx", "cor", "lm", "loess", "median", "quantile", "sd") importFrom("utils", "data", "read.csv") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * 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: 1 WARNING, 3 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/affycomp.Rcheck/00check.log' for details.
affycomp.Rcheck/00install.out
install for i386 * installing *source* package 'affycomp' ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'affycomp' finding HTML links ... done SD html affycomp.compfigs.auxiliary html affycomp.figures.auxiliary html affycomp.table html affycompPlot html assessAll html assessDilution html assessSD html assessSpikeIn html assessSpikeIn2 html dilution.phenodata html exprset.log html hgu133a.spikein.phenodata html mas5.assessment html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWeePbB/R.INSTALL24a0eaf33b1/affycomp/man/mas5.assessment.Rd:10: missing file link 'ExpressionSet' readin html remove.hgu133a.xhyb html spikein.phenodata html xhyb html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'affycomp' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'affycomp' as affycomp_1.54.0.zip * DONE (affycomp) In R CMD INSTALL In R CMD INSTALL
affycomp.Rcheck/examples_i386/affycomp-Ex.timings
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affycomp.Rcheck/examples_x64/affycomp-Ex.timings
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