Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:18:23 -0400 (Tue, 09 Apr 2019).
Package 256/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ChIPQC 1.19.2 Tom Carroll
| 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 | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: ChIPQC |
Version: 1.19.2 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChIPQC_1.19.2.tar.gz |
StartedAt: 2019-04-09 01:43:28 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 01:52:30 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 542.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChIPQC.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChIPQC_1.19.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPQC.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ChIPQC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ChIPQC' version '1.19.2' * 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 'ChIPQC' 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 Unexported object imported by a ':::' call: 'S4Vectors:::tabulate2' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .Call("rle_sum_any", ..., PACKAGE = "chipseq") See chapter 'System and foreign language interfaces' in the 'Writing R Extensions' manual. * checking R code for possible problems ... NOTE GetGRanges: no visible global function definition for 'seqlevels<-' findCovMaxPos: no visible global function definition for 'seqlengths' findCovMaxPos: no visible global function definition for 'seqlengths<-' getAnnotation: no visible binding for global variable 'TxDb.Hsapiens.UCSC.hg38.knownGene' getAnnotation: no visible global function definition for 'seqlengths' makeCCplot: no visible binding for global variable 'Shift_Size' makeCCplot: no visible binding for global variable 'CC_Score' makeCoveragePlot: no visible binding for global variable 'Depth' makeCoveragePlot: no visible binding for global variable 'log10_bp' makeCoveragePlot: no visible binding for global variable 'Sample' makeFriblPlot: no visible binding for global variable 'Sample' makeFriblPlot: no visible binding for global variable 'FRIBL' makeFriblPlot: no visible binding for global variable 'Reads' makeFripPlot: no visible binding for global variable 'Sample' makeFripPlot: no visible binding for global variable 'FRIP' makeFripPlot: no visible binding for global variable 'Reads' makePeakProfilePlot: no visible binding for global variable 'Distance' makePeakProfilePlot: no visible binding for global variable 'Signal' makeRapPlot: no visible binding for global variable 'Sample' makeRapPlot: no visible binding for global variable 'CountsInPeaks' makeRegiPlot: no visible binding for global variable 'Sample' makeRegiPlot: no visible binding for global variable 'GenomicIntervals' makeRegiPlot: no visible binding for global variable 'log2_Enrichment' makeSSDPlot: no visible binding for global variable 'Sample' makeSSDPlot: no visible binding for global variable 'SSD' makeSSDPlot: no visible global function definition for 'geom_point' sampleQC: no visible global function definition for 'seqlevels<-' plotCC,ChIPQCexperiment: no visible binding for global variable 'Sample' plotCC,list: no visible binding for global variable 'Sample' plotPeakProfile,ChIPQCexperiment: no visible binding for global variable 'Sample' plotPeakProfile,list: no visible binding for global variable 'Sample' Undefined global functions or variables: CC_Score CountsInPeaks Depth Distance FRIBL FRIP GenomicIntervals Reads SSD Sample Shift_Size Signal TxDb.Hsapiens.UCSC.hg38.knownGene geom_point log10_bp log2_Enrichment seqlengths seqlengths<- seqlevels<- Consider adding importFrom("stats", "SSD") 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 ... NOTE Output for data("tamoxifen_QC", package = "ChIPQC"): * checking data for non-ASCII characters ... WARNING Error loading dataset 'exampleExp': Error in .requirePackage(package) : unable to find required package 'ChIPQC' Error loading dataset 'tamoxifen': Error in .requirePackage(package) : unable to find required package 'ChIPQC' The dataset(s) may use package(s) not declared in the DESCRIPTION file. * 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 Examples with CPU or elapsed time > 5s user system elapsed ChIPQCreport 28.63 3.83 32.53 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed ChIPQCreport 24.9 2.88 28.34 * 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, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPQC.Rcheck/00check.log' for details.
ChIPQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ChIPQC_1.19.2.tar.gz && rm -rf ChIPQC.buildbin-libdir && mkdir ChIPQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPQC.buildbin-libdir ChIPQC_1.19.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ChIPQC_1.19.2.zip && rm ChIPQC_1.19.2.tar.gz ChIPQC_1.19.2.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 1073k 100 1073k 0 0 15.5M 0 --:--:-- --:--:-- --:--:-- 17.4M install for i386 * installing *source* package 'ChIPQC' ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ChIPQC' finding HTML links ... done ChIPQC-data html finding level-2 HTML links ... done ChIPQC-package html ChIPQC html ChIPQCexperiment-class html ChIPQCreport html ChIPQCsample-class html FragmentLengthCrossCoverage-methods html Normalisedaveragepeaksignal-methods html QCannotation-methods html QCcontrol-methods html QCdba-methods html QCmetadata-methods html QCmetrics-methods html QCsample-methods html ReadLengthCrossCoverage-methods html RelativeCrossCoverage-methods html averagepeaksignal-methods html coveragehistogram-methods html crosscoverage-methods html duplicateRate-methods html duplicates-methods html flagtagcounts-methods html fragmentlength-methods html frip-methods html mapped-methods html peaks-methods html plotCC-methods html plotCorHeatmap-methods html plotCoverageHist-methods html plotFribl-methods html plotFrip-methods html plotPeakProfile-methods html plotPrincomp-methods html plotRap-methods html plotRegi-methods html plotSSD-methods html readlength-methods html reads-methods html regi-methods html ribl-methods html rip-methods html ssd-methods html ** building package indices ** installing vignettes 'ChIPQC.Rnw' ** 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 'ChIPQC' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'ChIPQC' as ChIPQC_1.19.2.zip * DONE (ChIPQC) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'ChIPQC' successfully unpacked and MD5 sums checked
ChIPQC.Rcheck/examples_i386/ChIPQC-Ex.timings
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ChIPQC.Rcheck/examples_x64/ChIPQC-Ex.timings
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