Sarah Bonnin
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/TEQC |
| git_branch: RELEASE_3_17 |
| git_last_commit: ece9a2f |
| git_last_commit_date: 2023-04-25 10:18:30 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 2084/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TEQC 4.22.0 (landing page) Sarah Bonnin
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the TEQC package: - 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: 4.22.0 |
| 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_4.22.0.tar.gz |
| StartedAt: 2023-10-19 06:33:03 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 06:36:49 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 225.9 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_4.22.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TEQC.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TEQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TEQC’ version ‘4.22.0’
* 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 R 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 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 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 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 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-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 | 0.000 | 0.004 | |
| chrom.barplot | 0.318 | 0.008 | 0.570 | |
| coverage.GC | 1.372 | 0.018 | 2.483 | |
| coverage.correlation | 1.532 | 0.018 | 2.786 | |
| coverage.density | 0.845 | 0.012 | 1.530 | |
| coverage.hist | 0.779 | 0.011 | 1.400 | |
| coverage.plot | 0.797 | 0.012 | 1.460 | |
| coverage.target | 0.767 | 0.011 | 1.389 | |
| coverage.targetlength.plot | 0.856 | 0.013 | 1.561 | |
| coverage.uniformity | 0.766 | 0.011 | 1.388 | |
| covered.k | 0.731 | 0.009 | 1.336 | |
| duplicates.barplot | 0.449 | 0.011 | 0.832 | |
| fraction.reads.target | 0.160 | 0.005 | 0.297 | |
| fraction.target | 0.037 | 0.001 | 0.067 | |
| get.baits | 0.026 | 0.000 | 0.046 | |
| get.reads | 0.096 | 0.003 | 0.176 | |
| get.targets | 0.034 | 0.001 | 0.063 | |
| insert.size.hist | 0.283 | 0.008 | 0.524 | |
| make.wigfiles | 0.864 | 0.018 | 1.574 | |
| multiTEQCreport | 0.149 | 0.004 | 0.274 | |
| reads2pairs | 0.229 | 0.004 | 0.416 | |
| readsPerTarget | 0.196 | 0.005 | 0.352 | |