Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:21:13 -0400 (Thu, 12 Apr 2018).
Package 30/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
AGDEX 1.26.0 Cuilan lani Gao
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: AGDEX |
Version: 1.26.0 |
Command: rm -rf AGDEX.buildbin-libdir AGDEX.Rcheck && mkdir AGDEX.buildbin-libdir AGDEX.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AGDEX.buildbin-libdir AGDEX_1.26.0.tar.gz >AGDEX.Rcheck\00install.out 2>&1 && cp AGDEX.Rcheck\00install.out AGDEX-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AGDEX.buildbin-libdir --install="check:AGDEX-install.out" --force-multiarch --no-vignettes --timings AGDEX_1.26.0.tar.gz |
StartedAt: 2018-04-11 22:08:39 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 22:10:33 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 113.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: AGDEX.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf AGDEX.buildbin-libdir AGDEX.Rcheck && mkdir AGDEX.buildbin-libdir AGDEX.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AGDEX.buildbin-libdir AGDEX_1.26.0.tar.gz >AGDEX.Rcheck\00install.out 2>&1 && cp AGDEX.Rcheck\00install.out AGDEX-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AGDEX.buildbin-libdir --install="check:AGDEX-install.out" --force-multiarch --no-vignettes --timings AGDEX_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AGDEX.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 'AGDEX/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'AGDEX' version '1.26.0' * 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 'AGDEX' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/agdex.Rd:91: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/agdex.Rd:93: missing file link 'GeneSetCollection' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/gset.data.Rd:24: missing file link 'GeneSetCollection' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/human.data.Rd:35: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/make.dex.set.object.Rd:37: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/make.dex.set.object.Rd:39: missing file link 'GeneSetCollection' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/mouse.data.Rd:35: missing file link 'ExpressionSet' See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AGDEX.Rcheck/00install.out' for details. * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Non-standard license specification: GPL Version 2 or later Standardizable: TRUE Standardized license specification: GPL (>= 2) * 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 ** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: 'Biobase' 'GSEABase' 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 agdex: no visible global function definition for 'exprs' agdex: no visible global function definition for 'qnorm' agdex: no visible global function definition for 'pnorm' agdex: no visible global function definition for 'sampleNames' agdex: no visible global function definition for 'pData' agdex.scatterplot: no visible global function definition for 'plot' agdex.scatterplot: no visible global function definition for 'points' agdex.scatterplot: no visible global function definition for 'lines' agdex.scatterplot: no visible global function definition for 'prcomp' agdex.scatterplot: no visible global function definition for 'abline' gsc.to.index.list: no visible global function definition for 'geneIds' prep.dex.set: no visible global function definition for 'exprs' prep.dex.set: no visible global function definition for 'pData' read.agdex.gset.details: no visible global function definition for 'read.table' read.agdex.gset.list: no visible global function definition for 'read.table' read.agdex.result: no visible global function definition for 'read.table' read.enrich.gset.list: no visible global function definition for 'read.table' read.gset.collection: no visible global function definition for 'read.table' read.gset.collection: no visible global function definition for 'GeneSet' read.gset.collection: no visible global function definition for 'geneIds<-' read.gset.collection: no visible global function definition for 'GeneSetCollection' write.agdex.gset.details: no visible global function definition for 'write.table' write.agdex.result: no visible global function definition for 'write.table' write.gset.list.result: no visible global function definition for 'write.table' Undefined global functions or variables: GeneSet GeneSetCollection abline exprs geneIds geneIds<- lines pData plot pnorm points prcomp qnorm read.table sampleNames write.table Consider adding importFrom("graphics", "abline", "lines", "plot", "points") importFrom("stats", "pnorm", "prcomp", "qnorm") importFrom("utils", "read.table", "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 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/AGDEX.Rcheck/00check.log' for details.
AGDEX.Rcheck/00install.out
install for i386 * installing *source* package 'AGDEX' ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'AGDEX' finding HTML links ... done AGDEX-package html agdex html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/agdex.Rd:91: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/agdex.Rd:93: missing file link 'GeneSetCollection' agdex.res html agdex.scatterplot html get.gset.result.details html gset.data html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/gset.data.Rd:24: missing file link 'GeneSetCollection' human.data html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/human.data.Rd:35: missing file link 'ExpressionSet' make.dex.set.object html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/make.dex.set.object.Rd:37: missing file link 'ExpressionSet' Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/make.dex.set.object.Rd:39: missing file link 'GeneSetCollection' map.data html mouse.data html Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiyHvTu/R.INSTALL1704327c6ae9/AGDEX/man/mouse.data.Rd:35: missing file link 'ExpressionSet' read.agdex.gset.details html read.agdex.result html write.agdex.gset.details html write.agdex.result html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'AGDEX' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'AGDEX' as AGDEX_1.26.0.zip * DONE (AGDEX) In R CMD INSTALL In R CMD INSTALL
AGDEX.Rcheck/examples_i386/AGDEX-Ex.timings
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AGDEX.Rcheck/examples_x64/AGDEX-Ex.timings
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