Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-02-09 13:56:54 -0500 (Sat, 09 Feb 2019).
Package 109/1659 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
BBCAnalyzer 1.13.0 Sarah Sandmann
| malbec2 | Linux (Ubuntu 18.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: BBCAnalyzer |
Version: 1.13.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BBCAnalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BBCAnalyzer_1.13.0.tar.gz |
StartedAt: 2019-02-09 01:15:56 -0500 (Sat, 09 Feb 2019) |
EndedAt: 2019-02-09 01:22:07 -0500 (Sat, 09 Feb 2019) |
EllapsedTime: 371.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BBCAnalyzer.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BBCAnalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BBCAnalyzer_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BBCAnalyzer.Rcheck' * using R Under development (unstable) (2019-01-10 r75962) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'BBCAnalyzer/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BBCAnalyzer' version '1.13.0' * 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 'BBCAnalyzer' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer' See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BBCAnalyzer.Rcheck/00install.out' for details. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE analyzeBases: no visible global function definition for 'read.table' analyzeBasesPlotOnly: no visible global function definition for 'read.table' analyzeReads: no visible global function definition for 'path' analyzeReads: no visible global function definition for 'write.table' checkBamInput: no visible global function definition for 'path' checkVcfInput: no visible global function definition for 'path' frequencyAnalysis: no visible global function definition for 'write.table' frequencyAnalysisVcf: no visible global function definition for 'read.table' frequencyAnalysisVcf: no visible global function definition for 'path' frequencyAnalysisVcf: no visible global function definition for 'write.table' plotCountsPerSampleRelativeVcf_plot: no visible global function definition for 'par' plotCountsPerSampleRelativeVcf_plot: no visible global function definition for 'barplot' plotCountsPerSampleRelativeVcf_plot: no visible global function definition for 'rect' plotCountsPerSampleRelativeVcf_plot: no visible global function definition for 'lines' plotCountsPerSampleRelativeVcf_plot: no visible global function definition for 'text' plotCountsPerSampleRelative_plot: no visible global function definition for 'par' plotCountsPerSampleRelative_plot: no visible global function definition for 'barplot' plotCountsPerSampleRelative_plot: no visible global function definition for 'rect' plotCountsPerSampleRelative_plot: no visible global function definition for 'lines' plotCountsPerSampleRelative_plot: no visible global function definition for 'text' plotCountsPerSampleVcf_plot: no visible global function definition for 'par' plotCountsPerSampleVcf_plot: no visible global function definition for 'barplot' plotCountsPerSampleVcf_plot: no visible global function definition for 'rect' plotCountsPerSampleVcf_plot: no visible global function definition for 'lines' plotCountsPerSampleVcf_plot: no visible global function definition for 'text' plotCountsPerSample_plot: no visible global function definition for 'par' plotCountsPerSample_plot: no visible global function definition for 'barplot' plotCountsPerSample_plot: no visible global function definition for 'rect' plotCountsPerSample_plot: no visible global function definition for 'lines' plotCountsPerSample_plot: no visible global function definition for 'text' plotCountsPerTargetRelativeVcf_plot: no visible global function definition for 'par' plotCountsPerTargetRelativeVcf_plot: no visible global function definition for 'barplot' plotCountsPerTargetRelativeVcf_plot: no visible global function definition for 'rect' plotCountsPerTargetRelativeVcf_plot: no visible global function definition for 'lines' plotCountsPerTargetRelativeVcf_plot: no visible global function definition for 'text' plotCountsPerTargetRelative_plot: no visible global function definition for 'par' plotCountsPerTargetRelative_plot: no visible global function definition for 'barplot' plotCountsPerTargetRelative_plot: no visible global function definition for 'rect' plotCountsPerTargetRelative_plot: no visible global function definition for 'lines' plotCountsPerTargetRelative_plot: no visible global function definition for 'text' plotCountsPerTargetVcf_plot: no visible global function definition for 'par' plotCountsPerTargetVcf_plot: no visible global function definition for 'barplot' plotCountsPerTargetVcf_plot: no visible global function definition for 'rect' plotCountsPerTargetVcf_plot: no visible global function definition for 'lines' plotCountsPerTargetVcf_plot: no visible global function definition for 'text' plotCountsPerTarget_plot: no visible global function definition for 'par' plotCountsPerTarget_plot: no visible global function definition for 'barplot' plotCountsPerTarget_plot: no visible global function definition for 'rect' plotCountsPerTarget_plot: no visible global function definition for 'lines' plotCountsPerTarget_plot: no visible global function definition for 'text' processVcfFile: no visible global function definition for 'read.table' reportVariants: no visible global function definition for 'write.table' reportVariantsVcf: no visible global function definition for 'write.table' Undefined global functions or variables: barplot lines par path read.table rect text write.table Consider adding importFrom("graphics", "barplot", "lines", "par", "rect", "text") 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed analyzeBasesPlotOnly 24.95 0.69 25.75 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed analyzeBasesPlotOnly 31.97 0.36 32.36 * 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, 1 NOTE See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BBCAnalyzer.Rcheck/00check.log' for details.
BBCAnalyzer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/BBCAnalyzer_1.13.0.tar.gz && rm -rf BBCAnalyzer.buildbin-libdir && mkdir BBCAnalyzer.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BBCAnalyzer.buildbin-libdir BBCAnalyzer_1.13.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL BBCAnalyzer_1.13.0.zip && rm BBCAnalyzer_1.13.0.tar.gz BBCAnalyzer_1.13.0.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 1798k 100 1798k 0 0 15.2M 0 --:--:-- --:--:-- --:--:-- 16.1M install for i386 * installing *source* package 'BBCAnalyzer' ... ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer' ** help *** installing help indices converting help for package 'BBCAnalyzer' finding HTML links ... done BBCAnalyzer-package html analyzeBases html analyzeBasesPlotOnly html ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer' install for x64 * installing *source* package 'BBCAnalyzer' ... ** testing if installed package can be loaded Warning: replacing previous import 'grDevices::windows' by 'GenomicRanges::windows' when loading 'BBCAnalyzer' * MD5 sums packaged installation of 'BBCAnalyzer' as BBCAnalyzer_1.13.0.zip * DONE (BBCAnalyzer) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'BBCAnalyzer' successfully unpacked and MD5 sums checked
BBCAnalyzer.Rcheck/examples_i386/BBCAnalyzer-Ex.timings
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BBCAnalyzer.Rcheck/examples_x64/BBCAnalyzer-Ex.timings
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