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BioC 3.5: CHECK report for TEQC on oaxaca

This page was generated on 2017-03-04 16:40:18 -0500 (Sat, 04 Mar 2017).

Package 1271/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TEQC 3.15.0
Manuela Hummel
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TEQC
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: TEQC
Version: 3.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TEQC_3.15.0.tar.gz
StartedAt: 2017-03-04 10:00:13 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 10:02:39 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 145.4 seconds
RetCode: 0
Status:  OK 
CheckDir: TEQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TEQC_3.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TEQC.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘3.15.0’
* 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 loading without being on the library search path ... 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 ‘plot’
.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 ‘plot’
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 ‘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 ‘plot’
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 ‘plot’
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 ‘plot’
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 ‘plot’
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 ‘par’
coverage.plot: no visible global function definition for ‘rect’
coverage.target: no visible global function definition for ‘Rle’
coverage.targetlength.plot: no visible global function definition for
  ‘plot’
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 ‘plot’
coverage.uniformity: no visible global function definition for ‘lines’
covplot: no visible global function definition for ‘par’
covplot: no visible global function definition for ‘plot’
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.reads: no visible binding for global variable ‘pos’
get.reads: no visible binding for global variable ‘qwidth’
get.reads: no visible binding for global variable ‘qname’
get.reads: no visible binding for global variable ‘rname’
get.reads: no visible global function definition for ‘count.fields’
get.reads: no visible global function definition for ‘read.delim’
get.targets: no visible global function definition for ‘count.fields’
get.targets: no visible global function definition for ‘read.delim’
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’
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’
multfun: no visible global function definition for ‘Rle’
multfun: no visible global function definition for ‘runValue’
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’
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 ‘Rle’
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 ‘plot’
unifplot: no visible global function definition for ‘lines’
unifplot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  Axis Rle abline axis barplot box boxplot.stats colorRampPalette
  count.fields dev.off hist isSingleNumber isTRUEorFALSE jpeg legend
  lines mtext new2 packageDescription pairs par pdf plot png points pos
  qname queryHits qwidth read.delim read.table rect rname runValue
  smooth.spline strwidth text tiff 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", "plot",
             "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 ... OK
* 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 installed files from ‘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 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/TEQC.Rcheck/00check.log’
for details.


TEQC.Rcheck/00install.out:

* installing *source* package ‘TEQC’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TEQC)

TEQC.Rcheck/TEQC-Ex.timings:

nameusersystemelapsed
TEQCreport0.0010.0010.001
chrom.barplot0.9080.0040.913
coverage.GC2.0710.0222.093
coverage.correlation2.2500.0162.268
coverage.density1.1150.0071.124
coverage.hist0.9840.0090.993
coverage.plot1.0200.0061.027
coverage.target0.8560.0030.859
coverage.targetlength.plot1.0030.0041.008
coverage.uniformity0.9190.0040.924
covered.k0.9960.0051.001
duplicates.barplot4.6250.0104.638
fraction.reads.target0.6230.0040.628
fraction.target0.1510.0010.153
get.baits0.0450.0000.046
get.reads0.3870.0030.391
get.targets0.1070.0010.108
insert.size.hist2.0120.0052.018
make.wigfiles1.0490.0091.059
multiTEQCreport0.5310.0060.536
reads2pairs1.7210.0041.724
readsPerTarget0.7430.0050.748