Ashley Sawle
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/qPLEXanalyzer |
| Branch: RELEASE_3_10 |
| Last Commit: dd19a73 |
| Last Changed Date: 2019-10-29 13:11:14 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:30:45 -0400 (Wed, 15 Apr 2020).
| Package 1342/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| qPLEXanalyzer 1.4.0 Ashley Sawle
| malbec1 | Linux (Ubuntu 18.04.4 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: qPLEXanalyzer |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.4.0.tar.gz |
| StartedAt: 2020-04-15 05:47:37 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:51:34 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 237.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qPLEXanalyzer.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qPLEXanalyzer.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings qPLEXanalyzer_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/qPLEXanalyzer.Rcheck' * using R version 3.6.3 (2020-02-29) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'qPLEXanalyzer/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'qPLEXanalyzer' version '1.4.0' * 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 'qPLEXanalyzer' 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE convertToMSnset: no visible binding for global variable '.' corrPlot: no visible binding for global variable 'Cor' corrPlot: no visible binding for global variable 'X' corrPlot: no visible binding for global variable 'Y' corrPlot: no visible binding for global variable 'CorTxt' coveragePlot: no visible binding for global variable 'Accessions' coveragePlot: no visible binding for global variable 'Sequence' coveragePlot: no visible binding for global variable '.' getContrastResults: no visible binding for global variable 'B' getContrastResults: no visible binding for global variable '.' getContrastResults: no visible binding for global variable 'AveExpr' getContrastResults: no visible binding for global variable 'logFC' groupScaling: no visible binding for global variable 'PeptideID' groupScaling: no visible binding for global variable 'SampleName' groupScaling: no visible binding for global variable 'RawIntensity' groupScaling: no visible binding for global variable 'Grouping_column' groupScaling: no visible binding for global variable 'scaledIntensity' groupScaling: no visible binding for global variable 'meanscaledIntensity' groupScaling: no visible binding for global variable 'scalingFactors' groupScaling: no visible binding for global variable 'normalizedIntensities' hierarchicalPlot: no visible binding for global variable 'x' hierarchicalPlot: no visible binding for global variable 'y' hierarchicalPlot: no visible binding for global variable 'xend' hierarchicalPlot: no visible binding for global variable 'yend' intensityBoxplot: no visible binding for global variable 'Intensity' intensityBoxplot: no visible binding for global variable 'logInt' intensityPlot: no visible binding for global variable 'SampleName' intensityPlot: no visible binding for global variable 'Intensity' maVolPlot: no visible binding for global variable 'controlLogFoldChange' maVolPlot: no visible binding for global variable '.' maVolPlot: no visible binding for global variable 'Accessions' maVolPlot: no visible binding for global variable 'group' maVolPlot: no visible binding for global variable 'adj.P.Val' maVolPlot: no visible binding for global variable 'GeneSymbol' mergePeptides: no visible binding for global variable 'Accessions' mergePeptides: no visible binding for global variable 'Sequences' mergePeptides: no visible binding for global variable 'phosseqid' mergePeptides: no visible binding for global variable 'Count' peptideIntensityPlot: no visible binding for global variable 'SampleName' peptideIntensityPlot: no visible binding for global variable 'Intensity' peptideIntensityPlot: no visible binding for global variable 'PeptideID' peptideIntensityPlot: no visible binding for global variable 'Accessions' peptideIntensityPlot: no visible binding for global variable 'Sequences' peptideIntensityPlot: no visible binding for global variable 'Modifications' peptideIntensityPlot: no visible binding for global variable 'logIntensity' plotMeanVar: no visible binding for global variable 'x' plotMeanVar: no visible binding for global variable 'y' plotMeanVar: no visible binding for global variable 'Mean' plotMeanVar: no visible binding for global variable 'Variance' rliPlot: no visible binding for global variable 'RowID' rliPlot: no visible binding for global variable 'Intensity' rliPlot: no visible binding for global variable 'logInt' rliPlot: no visible binding for global variable 'medianLogInt' summarizeIntensities: no visible binding for global variable 'Accessions' summarizeIntensities: no visible binding for global variable 'Sequences' summarizeIntensities: no visible binding for global variable 'Count' Undefined global functions or variables: . Accessions AveExpr B Cor CorTxt Count GeneSymbol Grouping_column Intensity Mean Modifications PeptideID RawIntensity RowID SampleName Sequence Sequences Variance X Y adj.P.Val controlLogFoldChange group logFC logInt logIntensity meanscaledIntensity medianLogInt normalizedIntensities phosseqid scaledIntensity scalingFactors x xend y yend * 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 ** 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 NOTE See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/qPLEXanalyzer.Rcheck/00check.log' for details.
qPLEXanalyzer.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/qPLEXanalyzer_1.4.0.tar.gz && rm -rf qPLEXanalyzer.buildbin-libdir && mkdir qPLEXanalyzer.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qPLEXanalyzer.buildbin-libdir qPLEXanalyzer_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL qPLEXanalyzer_1.4.0.zip && rm qPLEXanalyzer_1.4.0.tar.gz qPLEXanalyzer_1.4.0.zip
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install for i386
* installing *source* package 'qPLEXanalyzer' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'qPLEXanalyzer'
finding HTML links ... done
assignColours html
computeDiffStats html
finding level-2 HTML links ... done
convertToMSnset html
corrPlot html
coveragePlot html
exp2_Xlink html
exp3_OHT_ESR1 html
getContrastResults html
groupScaling html
hierarchicalPlot html
human_anno html
intensityBoxplot html
intensityPlot html
maVolPlot html
mergePeptides html
normalizeQuantiles html
normalizeScaling html
pcaPlot html
peptideIntensityPlot html
plotMeanVar html
qPLEXanalyzer-package html
regressIntensity html
rliPlot html
rowScaling html
summarizeIntensities 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 'qPLEXanalyzer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qPLEXanalyzer' as qPLEXanalyzer_1.4.0.zip
* DONE (qPLEXanalyzer)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'qPLEXanalyzer' successfully unpacked and MD5 sums checked
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qPLEXanalyzer.Rcheck/examples_i386/qPLEXanalyzer-Ex.timings
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qPLEXanalyzer.Rcheck/examples_x64/qPLEXanalyzer-Ex.timings
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