Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 2131/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TEQC 4.28.0  (landing page)
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)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for TEQC on nebbiolo2

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.

raw results


Summary

Package: TEQC
Version: 4.28.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:TEQC.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings TEQC_4.28.0.tar.gz
StartedAt: 2024-12-20 06:06:49 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:08:33 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 104.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TEQC.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:TEQC.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings TEQC_4.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/TEQC.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/TEQC.Rcheck/00check.log’
for details.


Installation output

TEQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL TEQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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)

Tests output


Example timings

TEQC.Rcheck/TEQC-Ex.timings

nameusersystemelapsed
TEQCreport0.0010.0010.000
chrom.barplot0.2440.0290.275
coverage.GC0.9900.0030.993
coverage.correlation1.2380.0001.238
coverage.density0.6320.0000.631
coverage.hist0.6020.0000.601
coverage.plot0.5850.0010.586
coverage.target0.5810.0010.583
coverage.targetlength.plot0.6330.0010.634
coverage.uniformity0.5710.0020.572
covered.k0.5820.0010.584
duplicates.barplot0.3320.0040.335
fraction.reads.target0.1190.0010.119
fraction.target0.0280.0000.028
get.baits0.0180.0000.019
get.reads0.0700.0000.069
get.targets0.0270.0000.028
insert.size.hist0.1980.0010.199
make.wigfiles0.6270.0010.629
multiTEQCreport0.1000.0000.101
reads2pairs0.1810.0000.181
readsPerTarget0.1580.0000.159