Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:54 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

CHECK results for TEQC on machv2


To the developers/maintainers of the TEQC package:
- Please 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 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.

raw results

Package 1943/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TEQC 4.16.0  (landing page)
Sarah Bonnin
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/TEQC
git_branch: RELEASE_3_14
git_last_commit: 5854c95
git_last_commit_date: 2021-10-26 11:57:43 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: TEQC
Version: 4.16.0
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_4.16.0.tar.gz
StartedAt: 2022-04-12 19:18:33 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:21:14 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 160.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TEQC.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_4.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/TEQC.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TEQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TEQC’ version ‘4.16.0’
* 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 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 ... OK
* 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 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/TEQC.Rcheck/00check.log’
for details.



Installation output

TEQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TEQC
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output


Example timings

TEQC.Rcheck/TEQC-Ex.timings

nameusersystemelapsed
TEQCreport0.0010.0000.001
chrom.barplot0.5180.0060.525
coverage.GC1.9720.0292.002
coverage.correlation2.7120.0172.731
coverage.density1.4510.0091.475
coverage.hist1.2930.0081.302
coverage.plot1.3190.0071.327
coverage.target1.2430.0051.248
coverage.targetlength.plot1.2940.0091.304
coverage.uniformity1.3120.0121.325
covered.k1.3090.0151.325
duplicates.barplot0.6980.0080.708
fraction.reads.target0.2180.0040.222
fraction.target0.0630.0010.065
get.baits0.0520.0010.053
get.reads0.0990.0030.102
get.targets0.0480.0010.049
insert.size.hist0.4230.0050.429
make.wigfiles1.5660.0121.579
multiTEQCreport0.1560.0030.159
reads2pairs0.3270.0050.332
readsPerTarget0.3840.0060.389