Sarah Bonnin
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/TEQC |
| git_branch: RELEASE_3_20 |
| git_last_commit: 10faa27 |
| git_last_commit_date: 2024-10-29 09:35:28 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 2131/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TEQC 4.28.0 (landing page) Sarah Bonnin
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
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. |
| Package: TEQC |
| Version: 4.28.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TEQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TEQC_4.28.0.tar.gz |
| StartedAt: 2024-12-21 11:43:55 -0500 (Sat, 21 Dec 2024) |
| EndedAt: 2024-12-21 11:45:58 -0500 (Sat, 21 Dec 2024) |
| EllapsedTime: 123.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TEQC.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TEQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TEQC_4.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TEQC.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TEQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TEQC’ version ‘4.28.0’
* 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 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 or links in Rd file 'TEQCreport.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'chrom.barplot.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'coverage.GC.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'coverage.plot.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'coverage.target.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'coverage.targetlength.plot.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'duplicates.barplot.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'fraction.reads.target.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'fraction.target.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'get.baits.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'get.reads.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'get.targets.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'insert.size.hist.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links in Rd file 'reads2pairs.Rd':
‘[IRanges:RangedData-class]{RangedData}’
Missing link or links 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 sizes of PDF files under ‘inst/doc’ ... 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
‘/Users/biocbuild/bbs-3.20-bioc/meat/TEQC.Rcheck/00check.log’
for details.
TEQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TEQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 | 0.001 | 0.001 | 0.001 | |
| chrom.barplot | 0.307 | 0.020 | 0.330 | |
| coverage.GC | 1.134 | 0.012 | 1.158 | |
| coverage.correlation | 1.427 | 0.015 | 1.466 | |
| coverage.density | 0.747 | 0.009 | 0.783 | |
| coverage.hist | 0.686 | 0.009 | 0.703 | |
| coverage.plot | 0.694 | 0.008 | 0.714 | |
| coverage.target | 0.672 | 0.007 | 0.694 | |
| coverage.targetlength.plot | 0.765 | 0.009 | 0.785 | |
| coverage.uniformity | 0.683 | 0.007 | 0.698 | |
| covered.k | 0.670 | 0.006 | 0.688 | |
| duplicates.barplot | 0.406 | 0.010 | 0.422 | |
| fraction.reads.target | 0.138 | 0.003 | 0.143 | |
| fraction.target | 0.032 | 0.001 | 0.033 | |
| get.baits | 0.022 | 0.001 | 0.023 | |
| get.reads | 0.088 | 0.004 | 0.093 | |
| get.targets | 0.031 | 0.000 | 0.032 | |
| insert.size.hist | 0.254 | 0.005 | 0.262 | |
| make.wigfiles | 0.772 | 0.013 | 0.803 | |
| multiTEQCreport | 0.127 | 0.003 | 0.133 | |
| reads2pairs | 0.218 | 0.004 | 0.229 | |
| readsPerTarget | 0.192 | 0.005 | 0.204 | |