Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 |
Package 2115/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TEQC 4.29.0 (landing page) Sarah Bonnin
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the TEQC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TEQC.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: TEQC |
Version: 4.29.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:TEQC.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TEQC_4.29.0.tar.gz |
StartedAt: 2024-12-24 12:00:28 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 12:02:54 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 146.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TEQC.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:TEQC.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TEQC_4.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/TEQC.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TEQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TEQC’ version ‘4.29.0’ * 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 for sufficient/correct file permissions ... 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: fixed problem with IRanges version >=2.13.28 in coverage.target() * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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(s) in Rd file 'TEQCreport.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'chrom.barplot.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'coverage.GC.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'coverage.plot.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'coverage.target.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'coverage.targetlength.plot.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'duplicates.barplot.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'fraction.reads.target.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'fraction.target.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'get.baits.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'get.reads.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'get.targets.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'insert.size.hist.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file 'reads2pairs.Rd': ‘[IRanges:RangedData-class]{RangedData}’ Missing link(s) in Rd file '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 ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/TEQC.Rcheck/00check.log’ for details.
TEQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL TEQC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘TEQC’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (TEQC)
TEQC.Rcheck/TEQC-Ex.timings
name | user | system | elapsed | |
TEQCreport | 0 | 0 | 0 | |
chrom.barplot | 0.310 | 0.013 | 0.348 | |
coverage.GC | 1.504 | 0.004 | 1.519 | |
coverage.correlation | 1.693 | 0.000 | 1.767 | |
coverage.density | 0.930 | 0.004 | 0.944 | |
coverage.hist | 0.842 | 0.000 | 0.912 | |
coverage.plot | 0.838 | 0.000 | 0.928 | |
coverage.target | 0.826 | 0.000 | 1.247 | |
coverage.targetlength.plot | 0.947 | 0.000 | 1.301 | |
coverage.uniformity | 0.831 | 0.000 | 1.011 | |
covered.k | 0.843 | 0.000 | 1.689 | |
duplicates.barplot | 0.459 | 0.012 | 0.941 | |
fraction.reads.target | 0.153 | 0.000 | 0.306 | |
fraction.target | 0.041 | 0.000 | 0.086 | |
get.baits | 0.027 | 0.000 | 0.050 | |
get.reads | 0.083 | 0.000 | 0.167 | |
get.targets | 0.042 | 0.000 | 0.082 | |
insert.size.hist | 0.290 | 0.004 | 0.587 | |
make.wigfiles | 0.939 | 0.000 | 1.596 | |
multiTEQCreport | 0.13 | 0.00 | 0.13 | |
reads2pairs | 0.234 | 0.000 | 0.235 | |
readsPerTarget | 0.201 | 0.004 | 0.206 | |