BioC 3.3: CHECK report for TEQC on oaxaca

Package: TEQC

Version: 3.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TEQC_3.12.0.tar.gz

StartedAt: 2016-10-13 06:49:29 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:51:56 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 146.6 seconds

RetCode: 0

Status:  OK

CheckDir: TEQC.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TEQC_3.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/TEQC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘3.12.0’
* 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’
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 jpeg legend lines mtext 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
Examples with CPU or elapsed time > 5s
                    user system elapsed
duplicates.barplot 5.121  0.012   5.136
* 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-3.3-bioc/meat/TEQC.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
TEQCreport	0.002	0.000	0.002
chrom.barplot	0.742	0.018	0.759
coverage.GC	1.486	0.008	1.494
coverage.correlation	2.008	0.015	2.863
coverage.density	1.171	0.024	2.388
coverage.hist	1.039	0.006	1.872
coverage.plot	0.787	0.010	1.565
coverage.target	0.906	0.003	1.024
coverage.targetlength.plot	0.779	0.011	0.895
coverage.uniformity	0.933	0.012	0.951
covered.k	0.994	0.006	0.999
duplicates.barplot	5.121	0.012	5.136
fraction.reads.target	0.674	0.004	0.679
fraction.target	0.137	0.000	0.137
get.baits	0.022	0.001	0.021
get.reads	0.339	0.003	0.342
get.targets	0.142	0.001	0.143
insert.size.hist	2.212	0.012	2.225
make.wigfiles	1.098	0.008	1.106
multiTEQCreport	0.643	0.009	0.652
reads2pairs	2.269	0.013	2.288
readsPerTarget	0.865	0.009	0.877