Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:22:44 -0400 (Wed, 16 Oct 2019).
Package 263/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
chipseq 1.34.0 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: chipseq |
Version: 1.34.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings chipseq_1.34.0.tar.gz |
StartedAt: 2019-10-16 02:37:16 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 02:42:06 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 289.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: chipseq.Rcheck |
Warnings: 4 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings chipseq_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/chipseq.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'chipseq/DESCRIPTION' ... OK * this is package 'chipseq' version '1.34.0' * 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 'chipseq' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIVkXSd/R.INSTALLe4435e57660/chipseq/man/estimate.mean.fraglen.Rd:48: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIVkXSd/R.INSTALLe4435e57660/chipseq/man/islandDepthPlot.Rd:17: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIVkXSd/R.INSTALLe4435e57660/chipseq/man/peakCutoff.Rd:17: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/chipseq.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. Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'methods' 'BiocGenerics' 'IRanges' 'GenomicRanges' 'ShortRead' A package should be listed in only one of these fields. * 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 .genomicContext: no visible global function definition for 'transcripts' .genomicContext: no visible global function definition for 'cdsBy' .genomicContext: no visible global function definition for 'threeUTRsByTranscript' .genomicContext: no visible global function definition for 'fiveUTRsByTranscript' .genomicContext: no visible global function definition for 'intronsByTranscript' .nearestTss: no visible global function definition for 'transcripts' .nearestTss: no visible global function definition for 'seqlevels<-' .nearestTss: no visible global function definition for 'seqlevels' applyPosByChrAndStrand: no visible global function definition for 'seqnames' correlation.estimate: no visible binding for global variable 'mu' correlation.estimate: no visible binding for global variable 'corr' correlationProfile :: no visible global function definition for 'subseq' coverage.estimate: no visible binding for global variable 'mu' coverage.estimate: no visible binding for global variable 'covered' islandDepthPlot: no visible binding for global variable 'depth' islandDepthPlot : : no visible global function definition for 'panel.lines' islandDepthPlot : : no visible global function definition for 'panel.xyplot' laneSubsample: no visible global function definition for 'seqnames' laneSubsample: no visible global function definition for 'GRangesList' subsetSummary: no visible global function definition for 'seqlengths' subsetSummary: no visible global function definition for 'GRanges' subsetSummary: no visible global function definition for 'seqnames' subsetSummary: no visible global function definition for 'seqlengths<-' diffPeakSummary,RleViewsList-RleViewsList: no visible global function definition for 'GRanges' estimate.mean.fraglen,GRanges: no visible global function definition for 'seqnames' peakSummary,RleViewsList: no visible global function definition for 'GRanges' Undefined global functions or variables: GRanges GRangesList cdsBy corr covered depth fiveUTRsByTranscript intronsByTranscript mu panel.lines panel.xyplot seqlengths seqlengths<- seqlevels seqlevels<- seqnames subseq threeUTRsByTranscript transcripts * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'densityCorr' and siglist 'GenomicRanges' generic 'densityCorr' and siglist 'list' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'estimate.mean.fraglen': densityCorr Code: function(x, ...) Docs: function(x, shift = seq(0, 500, 5), center = FALSE, width = seqLen * 2L, seqLen = 100L, maxDist = 500L, ...) Argument names in docs not in code: shift center width seqLen maxDist Mismatches in argument names: Position: 2 Code: ... Docs: shift * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... WARNING 'library' or 'require' call not declared from: 'BSgenome.Mmusculus.UCSC.mm9' * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/chipseq/libs/i386/chipseq.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/chipseq/libs/x64/chipseq.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) 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. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * 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: 4 WARNINGs, 3 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/chipseq.Rcheck/00check.log' for details.
chipseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/chipseq_1.34.0.tar.gz && rm -rf chipseq.buildbin-libdir && mkdir chipseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chipseq.buildbin-libdir chipseq_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL chipseq_1.34.0.zip && rm chipseq_1.34.0.tar.gz chipseq_1.34.0.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 1705k 100 1705k 0 0 5965k 0 --:--:-- --:--:-- --:--:-- 6112k install for i386 * installing *source* package 'chipseq' ... ** using staged installation ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c rlesumprod.c -o rlesumprod.o C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o chipseq.dll tmp.def rlesumprod.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/chipseq.buildbin-libdir/00LOCK-chipseq/00new/chipseq/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'chipseq' finding HTML links ... done chipseqFilter html coverageplot html cstest html diffPeakSummary html estimate.mean.fraglen html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIVkXSd/R.INSTALLe4435e57660/chipseq/man/estimate.mean.fraglen.Rd:48: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic islandDepthPlot html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIVkXSd/R.INSTALLe4435e57660/chipseq/man/islandDepthPlot.Rd:17: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic laneSubsample html peakCutoff html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIVkXSd/R.INSTALLe4435e57660/chipseq/man/peakCutoff.Rd:17: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic peakSummary-methods html subsetSummary html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'chipseq' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c rlesumprod.c -o rlesumprod.o C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o chipseq.dll tmp.def rlesumprod.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/chipseq.buildbin-libdir/chipseq/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'chipseq' as chipseq_1.34.0.zip * DONE (chipseq) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'chipseq' successfully unpacked and MD5 sums checked
chipseq.Rcheck/examples_i386/chipseq-Ex.timings
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chipseq.Rcheck/examples_x64/chipseq-Ex.timings
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