Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-13 11:20:31 -0400 (Sat, 13 Apr 2019).
Package 25/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
AffyExpress 1.48.0 Xuejun Arthur Li
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: AffyExpress |
Version: 1.48.0 |
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AffyExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings AffyExpress_1.48.0.tar.gz |
StartedAt: 2019-04-13 00:23:52 -0400 (Sat, 13 Apr 2019) |
EndedAt: 2019-04-13 00:27:14 -0400 (Sat, 13 Apr 2019) |
EllapsedTime: 202.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AffyExpress.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AffyExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings AffyExpress_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/AffyExpress.Rcheck' * using R version 3.5.3 (2019-03-11) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'AffyExpress/DESCRIPTION' ... OK * this is package 'AffyExpress' version '1.48.0' * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 'AffyExpress' 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 ... NOTE 'library' or 'require' calls in package code: 'R2HTML' 'affyPLM' 'annaffy' 'gcrma' 'genefilter' 'simpleaffy' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: 'affy' 'limma' 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 AffyQA: warning in matrix(c(1, 3, 5, 7, 2, 4, 6, 7), nr = 4, ncol = 2): partial argument match of 'nr' to 'nrow' AffyInteraction: no visible global function definition for 'pData' AffyInteraction: no visible global function definition for 'annotation' AffyInteraction: no visible global function definition for 'exprs' AffyQA: no visible global function definition for 'pData' AffyQA: no visible global function definition for 'cdfName' AffyQA: no visible global function definition for 'cleancdfname' AffyQA: no visible global function definition for 'setQCEnvironment' AffyQA: no visible global function definition for 'qc.get.alpha1' AffyQA: no visible global function definition for 'HTMLStart' AffyQA: no visible global function definition for 'HTML' AffyQA: no visible global function definition for 'as.title' AffyQA: no visible global function definition for 'png' AffyQA: no visible global function definition for 'plot' AffyQA: no visible global function definition for 'text' AffyQA: no visible global function definition for 'HTMLInsertGraph' AffyQA: no visible global function definition for 'dev.off' AffyQA: no visible global function definition for 'call.exprs' AffyQA: no visible global function definition for 'layout' AffyQA: no visible global function definition for 'par' AffyQA: no visible global function definition for 'description' AffyQA: no visible global function definition for 'description<-' AffyQA: no visible global function definition for 'boxplot' AffyQA: no visible global function definition for 'barplot' AffyQA: no visible global function definition for 'avbg' AffyQA: no visible global function definition for 'percent.present' AffyQA: no visible global function definition for 'sfs' AffyQA: no visible global function definition for 'spikeInProbes' AffyQA: no visible global function definition for 'legend' AffyQA: no visible global function definition for 'ratios' AffyQA: no visible global function definition for 'AffyRNAdeg' AffyQA: no visible global function definition for 'summaryAffyRNAdeg' AffyQA: no visible global function definition for 'plotAffyRNAdeg' AffyQA: no visible global function definition for 'rma' AffyQA: no visible global function definition for 'cor' AffyQA: no visible global function definition for 'exprs' AffyQA: no visible global function definition for 'hclust' AffyQA: no visible global function definition for 'as.dist' AffyQA: no visible global function definition for 'sampleNames<-' AffyQA: no visible global function definition for 'fitPLM' AffyQA: no visible global function definition for 'image' AffyQA: no visible global function definition for 'Mbox' AffyQA: no visible global function definition for 'package.version' AffyQA: no visible global function definition for 'HTMLStop' AffyRegress: no visible global function definition for 'annotation' AffyRegress: no visible global function definition for 'pData' Filter: no visible global function definition for 'exprs' Filter: no visible global function definition for 'kOverA' Filter: no visible global function definition for 'filterfun' Filter: no visible global function definition for 'genefilter' Filter: no visible binding for global variable 'IQR' Filter: no visible global function definition for 'quantile' f.test: no visible global function definition for 'classifyTestsF' f.test: no visible global function definition for 'pf' get.f: no visible global function definition for 'classifyTestsF' import.data: no visible global function definition for 'read.AnnotatedDataFrame' import.data: no visible global function definition for 'ReadAffy' import.data: no visible global function definition for 'pData' interaction.result2html: no visible global function definition for 'aaf.handler' interaction.result2html: no visible global function definition for 'aafTableAnn' interaction.result2html: no visible global function definition for 'aafTable' interaction.result2html: no visible global function definition for 'saveHTML' make.design: no visible global function definition for 'model.matrix' make.design: no visible global function definition for 'as.formula' permute.1: no visible global function definition for 'lmFit' permute.1: no visible global function definition for 'contrasts.fit' post.interaction: no visible global function definition for 'pData' pre.process: no visible global function definition for 'gcrma' pre.process: no visible global function definition for 'rma' pre.process: no visible global function definition for 'exprs' pre.process: no visible global function definition for 'par' pre.process: no visible global function definition for 'hist' pre.process: no visible global function definition for 'write.table' regress: no visible global function definition for 'lmFit' regress: no visible global function definition for 'contrasts.fit' regress: no visible global function definition for 'eBayes' regress: no visible global function definition for 'p.adjust' result2html: no visible global function definition for 'aaf.handler' result2html: no visible global function definition for 'aafTableAnn' result2html: no visible global function definition for 'aafTable' result2html: no visible global function definition for 'saveHTML' Undefined global functions or variables: AffyRNAdeg HTML HTMLInsertGraph HTMLStart HTMLStop IQR Mbox ReadAffy aaf.handler aafTable aafTableAnn annotation as.dist as.formula as.title avbg barplot boxplot call.exprs cdfName classifyTestsF cleancdfname contrasts.fit cor description description<- dev.off eBayes exprs filterfun fitPLM gcrma genefilter hclust hist image kOverA layout legend lmFit model.matrix p.adjust pData package.version par percent.present pf plot plotAffyRNAdeg png qc.get.alpha1 quantile ratios read.AnnotatedDataFrame rma sampleNames<- saveHTML setQCEnvironment sfs spikeInProbes summaryAffyRNAdeg text write.table Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "barplot", "boxplot", "hist", "image", "layout", "legend", "par", "plot", "text") importFrom("stats", "IQR", "as.dist", "as.formula", "cor", "hclust", "model.matrix", "p.adjust", "pf", "quantile") importFrom("utils", "write.table") 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' ... OK Examples with CPU or elapsed time > 5s user system elapsed AffyInteraction 6.72 0.25 7.43 Filter 6.47 0.11 6.58 interaction.result2html 5.28 0.05 5.33 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed AffyInteraction 6.80 0.11 6.91 Filter 5.44 0.06 5.50 * 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 NOTEs See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/AffyExpress.Rcheck/00check.log' for details.
AffyExpress.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/AffyExpress_1.48.0.tar.gz && rm -rf AffyExpress.buildbin-libdir && mkdir AffyExpress.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AffyExpress.buildbin-libdir AffyExpress_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL AffyExpress_1.48.0.zip && rm AffyExpress_1.48.0.tar.gz AffyExpress_1.48.0.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 465k 100 465k 0 0 7778k 0 --:--:-- --:--:-- --:--:-- 8308k install for i386 * installing *source* package 'AffyExpress' ... ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'AffyExpress' finding HTML links ... done AffyInteraction html AffyQA html AffyRegress html Filter html import.data html interaction.result2html html make.contrast html make.design html post.interaction html pre.process html regress html result2html html select.sig.gene html testData html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'AffyExpress' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'AffyExpress' as AffyExpress_1.48.0.zip * DONE (AffyExpress) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library' package 'AffyExpress' successfully unpacked and MD5 sums checked In R CMD INSTALL
AffyExpress.Rcheck/examples_i386/AffyExpress-Ex.timings
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AffyExpress.Rcheck/examples_x64/AffyExpress-Ex.timings
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