BioC 3.1: CHECK report for systemPipeR on petty

Package: systemPipeR

Version: 1.2.23

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings systemPipeR_1.2.23.tar.gz

StartedAt: 2015-10-09 02:18:52 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:25:58 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 426.0 seconds

RetCode: 0

Status:  OK

CheckDir: systemPipeR.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 systemPipeR_1.2.23.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/systemPipeR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘systemPipeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘systemPipeR’ version ‘1.2.23’
* 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 ... NOTE
Found the following hidden files and directories:
  inst/extdata/.BatchJobs.R
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘systemPipeR’ can be installed ... [38s/38s] 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘VariantAnnotation’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
countRangeset: warning in read.delim(infile1(args)[i], comment = "#"):
  partial argument match of 'comment' to 'comment.char'
vennPlot : ellipseVenn: warning in close.screen(all = TRUE): partial
  argument match of 'all' to 'all.screens'
writeTargetsRef: warning in read.delim(infile, comment = "#"): partial
  argument match of 'comment' to 'comment.char'
.codingReport: no visible global function definition for ‘transcripts’
.subsetReadsByMappingRegion: no visible global function definition for
  ‘IRanges’
.subsetReadsByMappingRegion: no visible global function definition for
  ‘seqlengths’
clusterRun: no visible global function definition for ‘chunk’
countRangeset: no visible global function definition for ‘import.bed’
filterDEGs: no visible binding for global variable ‘Comparisons’
filterDEGs: no visible binding for global variable ‘Counts’
filterDEGs: no visible binding for global variable ‘Type’
filterVars: no visible global function definition for ‘readVcf’
filterVars: no visible global function definition for ‘totalDepth<-’
filterVars: no visible global function definition for ‘refDepth<-’
filterVars: no visible global function definition for ‘altDepth<-’
filterVars: no visible global function definition for ‘asVCF’
filterVars: no visible global function definition for ‘writeVcf’
getQsubargs: no visible binding for global variable ‘tophatargs’
goBarplot: no visible binding for global variable ‘SampleMatch’
goBarplot: no visible binding for global variable ‘Sample’
GOHyperGAll_Subset: no visible binding for global variable
  ‘test_sample’
olBarplot: no visible binding for global variable ‘Intersect_Sets’
olBarplot: no visible binding for global variable ‘Counts’
olBarplot: no visible binding for global variable ‘Level’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Cycle’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘low’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘mid’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘top’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Frequency’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘Base’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Quality’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘RelDiv’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Method’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘minQuality’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Percent’
seeFastqPlot : fastqPlot: no visible binding for global variable
  ‘Outliers’
variantReport: no visible global function definition for ‘readVcf’
variantReport: no visible global function definition for
  ‘locateVariants’
variantReport: no visible global function definition for ‘AllVariants’
variantReport: no visible global function definition for
  ‘predictCoding’
variantReport: no visible global function definition for ‘ref’
variantReport: no visible global function definition for ‘alt’
show,INTERSECTset: no visible binding for global variable ‘vennset’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
filterDEGs 5.723  0.043   5.771
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [20s/20s]
 [20s/20s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.

* installing *source* package ‘systemPipeR’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (systemPipeR)

name	user	system	elapsed
GOHyperGAll	0.004	0.001	0.004
INTERSECTset-class	0.023	0.007	0.030
SYSargs-class	0.082	0.006	0.088
VENNset-class	0.013	0.004	0.017
alignStats	0.035	0.003	0.038
catDB-class	0.003	0.001	0.003
catmap	0.002	0.000	0.002
clusterRun	0.036	0.003	0.350
countRangeset	0.103	0.003	0.106
filterDEGs	5.723	0.043	5.771
filterVars	0.029	0.003	0.032
getQsubargs	0.048	0.004	0.052
mergeBamByFactor	0.024	0.002	0.026
moduleload	0.001	0.001	0.001
olBarplot	0.737	0.026	0.766
overLapper	0.734	0.081	0.821
preprocessReads	0.053	0.005	0.059
qsubRun	0.034	0.002	0.036
readComp	0.040	0.003	0.043
returnRPKM	0.001	0.001	0.001
runCommandline	0.036	0.003	0.039
runDiff	0.095	0.002	0.097
run_DESeq2	4.607	0.037	4.653
run_edgeR	4.742	0.026	4.771
seeFastq	0.000	0.000	0.001
symLink2bam	0.018	0.002	0.019
sysargs	0.034	0.003	0.038
systemArgs	0.030	0.003	0.034
variantReport	0.022	0.002	0.024
vennPlot	0.593	0.020	0.615
writeTargetsRef	0.003	0.001	0.003
writeTargetsout	0.026	0.002	0.027