Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:28 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the TEQC package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/TEQC.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1943/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TEQC 4.16.0 (landing page) Sarah Bonnin
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: TEQC |
Version: 4.16.0 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TEQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings TEQC_4.16.0.tar.gz |
StartedAt: 2022-04-13 03:57:28 -0400 (Wed, 13 Apr 2022) |
EndedAt: 2022-04-13 04:00:01 -0400 (Wed, 13 Apr 2022) |
EllapsedTime: 153.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TEQC.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TEQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings TEQC_4.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/TEQC.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'TEQC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'TEQC' version '4.16.0' * 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 'TEQC' 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 .coverage.hist: no visible global function definition for 'par' .coverage.hist: no visible global function definition for 'boxplot.stats' .coverage.hist: no visible global function definition for 'hist' .coverage.hist: no visible global function definition for 'lines' .coverage.hist: no visible global function definition for 'axis' .coverage.hist: no visible global function definition for 'mtext' .coverage.hist: no visible global function definition for 'legend' Rlepairs : localAxis: no visible global function definition for 'Axis' Rlepairs : localUpperPanel: no visible global function definition for 'text' Rlepairs : localLowerPanel: no visible global function definition for 'points' Rlepairs : localLowerPanel: no visible global function definition for 'abline' Rlepairs: no visible global function definition for 'par' Rlepairs: no visible global function definition for 'box' Rlepairs: no visible global function definition for 'strwidth' Rlepairs: no visible global function definition for 'text' Rlepairs: no visible global function definition for 'mtext' TEQCreport: no visible global function definition for 'write.table' chrom.barplot: no visible global function definition for 'seqnames' chrom.barplot: no visible global function definition for 'barplot' chrom.barplot: no visible global function definition for 'text' chrom.barplot: no visible global function definition for 'par' chrom.barplot: no visible global function definition for 'legend' cortext: no visible global function definition for 'text' covBoxplot: no visible global function definition for 'par' covBoxplot: no visible global function definition for 'points' covBoxplot: no visible global function definition for 'legend' covcorplot: no visible global function definition for 'pairs' coverage.GC: no visible global function definition for 'values' coverage.GC: no visible global function definition for 'seqnames' coverage.GC: no visible global function definition for 'lines' coverage.GC: no visible global function definition for 'smooth.spline' coverage.density: no visible global function definition for 'lines' coverage.hist: no visible global function definition for 'par' coverage.hist: no visible global function definition for 'boxplot.stats' coverage.hist: no visible global function definition for 'hist' coverage.hist: no visible global function definition for 'lines' coverage.hist: no visible global function definition for 'axis' coverage.hist: no visible global function definition for 'mtext' coverage.hist: no visible global function definition for 'legend' coverage.plot: no visible global function definition for 'Rle' coverage.plot: no visible global function definition for 'abline' coverage.plot: no visible global function definition for 'lines' coverage.plot: no visible global function definition for 'seqnames' coverage.plot: no visible global function definition for 'par' coverage.plot: no visible global function definition for 'rect' coverage.target: no visible global function definition for 'seqnames' coverage.target: no visible global function definition for 'Rle' coverage.targetlength.plot: no visible global function definition for 'mcols' coverage.targetlength.plot: no visible global function definition for 'lines' coverage.targetlength.plot: no visible global function definition for 'smooth.spline' coverage.uniformity: no visible global function definition for 'lines' covplot: no visible global function definition for 'par' covplot: no visible global function definition for 'points' covplot: no visible global function definition for 'axis' covplot: no visible global function definition for 'legend' duplicates.barplot: no visible global function definition for 'barplot' duplicates.barplot: no visible global function definition for 'legend' duplicates.barplot: no visible global function definition for 'text' get.baits: no visible global function definition for 'read.delim' get.baits: no visible global function definition for 'GRanges' get.baits: no visible global function definition for 'sortSeqlevels' get.reads: no visible global function definition for 'count.fields' get.reads: no visible global function definition for 'read.delim' get.reads: no visible global function definition for 'GRanges' get.reads: no visible global function definition for 'keepSeqlevels' get.reads: no visible global function definition for 'seqlevelsInUse' get.reads: no visible global function definition for 'sortSeqlevels' get.targets: no visible global function definition for 'count.fields' get.targets: no visible global function definition for 'read.delim' get.targets: no visible global function definition for 'GRanges' get.targets: no visible global function definition for 'sortSeqlevels' htmlChromBarplot: no visible global function definition for 'jpeg' htmlChromBarplot: no visible global function definition for 'png' htmlChromBarplot: no visible global function definition for 'tiff' htmlChromBarplot: no visible global function definition for 'dev.off' htmlChromBarplot: no visible global function definition for 'pdf' htmlCovBoxplot: no visible global function definition for 'jpeg' htmlCovBoxplot: no visible global function definition for 'png' htmlCovBoxplot: no visible global function definition for 'tiff' htmlCovBoxplot: no visible global function definition for 'dev.off' htmlCovBoxplot: no visible global function definition for 'pdf' htmlCovCorrelationPlot: no visible global function definition for 'jpeg' htmlCovCorrelationPlot: no visible global function definition for 'png' htmlCovCorrelationPlot: no visible global function definition for 'tiff' htmlCovCorrelationPlot: no visible global function definition for 'dev.off' htmlCovCorrelationPlot: no visible global function definition for 'pdf' htmlCovGC: no visible global function definition for 'jpeg' htmlCovGC: no visible global function definition for 'png' htmlCovGC: no visible global function definition for 'tiff' htmlCovGC: no visible global function definition for 'dev.off' htmlCovGC: no visible global function definition for 'pdf' htmlCovTargetLength: no visible global function definition for 'jpeg' htmlCovTargetLength: no visible global function definition for 'png' htmlCovTargetLength: no visible global function definition for 'tiff' htmlCovTargetLength: no visible global function definition for 'par' htmlCovTargetLength: no visible global function definition for 'dev.off' htmlCovTargetLength: no visible global function definition for 'pdf' htmlCovUniformity: no visible global function definition for 'jpeg' htmlCovUniformity: no visible global function definition for 'png' htmlCovUniformity: no visible global function definition for 'tiff' htmlCovUniformity: no visible global function definition for 'dev.off' htmlCovUniformity: no visible global function definition for 'pdf' htmlCoverageHist: no visible global function definition for 'jpeg' htmlCoverageHist: no visible global function definition for 'png' htmlCoverageHist: no visible global function definition for 'tiff' htmlCoverageHist: no visible global function definition for 'dev.off' htmlCoverageHist: no visible global function definition for 'write.table' htmlCoverageHist: no visible global function definition for 'pdf' htmlDuplicatesBarplot: no visible global function definition for 'jpeg' htmlDuplicatesBarplot: no visible global function definition for 'png' htmlDuplicatesBarplot: no visible global function definition for 'tiff' htmlDuplicatesBarplot: no visible global function definition for 'dev.off' htmlDuplicatesBarplot: no visible global function definition for 'pdf' htmlInsertSizeHist: no visible global function definition for 'jpeg' htmlInsertSizeHist: no visible global function definition for 'png' htmlInsertSizeHist: no visible global function definition for 'tiff' htmlInsertSizeHist: no visible global function definition for 'dev.off' htmlInsertSizeHist: no visible global function definition for 'pdf' htmlSensiBarplot: no visible global function definition for 'jpeg' htmlSensiBarplot: no visible global function definition for 'png' htmlSensiBarplot: no visible global function definition for 'tiff' htmlSensiBarplot: no visible global function definition for 'dev.off' htmlSensiBarplot: no visible global function definition for 'pdf' htmlSpeciBarplot: no visible global function definition for 'jpeg' htmlSpeciBarplot: no visible global function definition for 'png' htmlSpeciBarplot: no visible global function definition for 'tiff' htmlSpeciBarplot: no visible global function definition for 'dev.off' htmlSpeciBarplot: no visible global function definition for 'pdf' htmlUniformityPlot: no visible global function definition for 'jpeg' htmlUniformityPlot: no visible global function definition for 'png' htmlUniformityPlot: no visible global function definition for 'tiff' htmlUniformityPlot: no visible global function definition for 'dev.off' htmlUniformityPlot: no visible global function definition for 'pdf' html_img: no visible global function definition for 'jpeg' html_img: no visible global function definition for 'png' html_img: no visible global function definition for 'tiff' html_img: no visible global function definition for 'dev.off' html_img: no visible global function definition for 'pdf' insert.size.hist: no visible global function definition for 'boxplot.stats' insert.size.hist: no visible global function definition for 'hist' insert.size.hist: no visible global function definition for 'abline' insert.size.hist: no visible global function definition for 'legend' insert.size.hist: no visible global function definition for 'values' make.multi.report: no visible global function definition for 'packageDescription' make.report: no visible global function definition for 'packageDescription' make.wigfiles: no visible global function definition for 'write.table' multiTEQCreport: no visible global function definition for 'read.table' multiTEQCreport: no visible global function definition for 'write.table' myreduce: no visible global function definition for 'isTRUEorFALSE' myreduce: no visible global function definition for 'isSingleNumber' myreduce : FUN: no visible global function definition for 'new2' myreduce: no visible global function definition for 'new2' myreduce: no visible global function definition for 'endoapply' plot.i: no visible global function definition for 'points' plot.i: no visible global function definition for 'abline' reads2pairs: no visible global function definition for 'seqnames' reads2pairs: no visible global function definition for 'Rle' reads2pairs: no visible global function definition for 'GRanges' readsPerTarget: no visible global function definition for 'queryHits' sensiBarplot: no visible global function definition for 'colorRampPalette' sensiBarplot: no visible global function definition for 'par' sensiBarplot: no visible global function definition for 'barplot' sensiBarplot: no visible global function definition for 'legend' speciBarplot: no visible global function definition for 'par' speciBarplot: no visible global function definition for 'barplot' unifplot: no visible global function definition for 'par' unifplot: no visible global function definition for 'lines' unifplot: no visible global function definition for 'legend' Undefined global functions or variables: Axis GRanges Rle abline axis barplot box boxplot.stats colorRampPalette count.fields dev.off endoapply hist isSingleNumber isTRUEorFALSE jpeg keepSeqlevels legend lines mcols mtext new2 packageDescription pairs par pdf png points queryHits read.delim read.table rect seqlevelsInUse seqnames smooth.spline sortSeqlevels strwidth text tiff values write.table Consider adding importFrom("grDevices", "boxplot.stats", "colorRampPalette", "dev.off", "jpeg", "pdf", "png", "tiff") importFrom("graphics", "Axis", "abline", "axis", "barplot", "box", "hist", "legend", "lines", "mtext", "pairs", "par", "points", "rect", "strwidth", "text") importFrom("stats", "smooth.spline") importFrom("utils", "count.fields", "packageDescription", "read.delim", "read.table", "write.table") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'TEQCreport.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'chrom.barplot.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'coverage.GC.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'coverage.plot.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'coverage.target.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'coverage.targetlength.plot.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'duplicates.barplot.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'fraction.reads.target.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'fraction.target.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'get.baits.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'get.reads.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'get.targets.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'insert.size.hist.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'reads2pairs.Rd': '[IRanges:RangedData-class]{RangedData}' Missing link or links in documentation object 'readsPerTarget.Rd': '[IRanges:RangedData-class]{RangedData}' See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 ** 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, 1 NOTE See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/TEQC.Rcheck/00check.log' for details.
TEQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/TEQC_4.16.0.tar.gz && rm -rf TEQC.buildbin-libdir && mkdir TEQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TEQC.buildbin-libdir TEQC_4.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL TEQC_4.16.0.zip && rm TEQC_4.16.0.tar.gz TEQC_4.16.0.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 33 273k 33 94289 0 0 446k 0 --:--:-- --:--:-- --:--:-- 446k 100 273k 100 273k 0 0 660k 0 --:--:-- --:--:-- --:--:-- 660k install for i386 * installing *source* package 'TEQC' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'TEQC' finding HTML links ... done TEQCreport html chrom.barplot html coverage.GC html coverage.correlation html coverage.density html coverage.hist html coverage.plot html coverage.target html coverage.targetlength.plot html coverage.uniformity html covered.k html duplicates.barplot html fraction.reads.target html fraction.target html get.baits html get.reads html get.targets html insert.size.hist html make.wigfiles html multiTEQCreport html reads2pairs html readsPerTarget 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 'TEQC' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'TEQC' as TEQC_4.16.0.zip * DONE (TEQC) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'TEQC' successfully unpacked and MD5 sums checked
TEQC.Rcheck/examples_i386/TEQC-Ex.timings
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TEQC.Rcheck/examples_x64/TEQC-Ex.timings
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