BioC 3.2: CHECK report for systemPipeR on moscato1

Package: systemPipeR

Version: 1.4.8

Command: rm -rf systemPipeR.buildbin-libdir systemPipeR.Rcheck && mkdir systemPipeR.buildbin-libdir systemPipeR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=systemPipeR.buildbin-libdir systemPipeR_1.4.8.tar.gz >systemPipeR.Rcheck\00install.out 2>&1 && cp systemPipeR.Rcheck\00install.out systemPipeR-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=systemPipeR.buildbin-libdir --install="check:systemPipeR-install.out" --force-multiarch --no-vignettes --timings systemPipeR_1.4.8.tar.gz

StartedAt: 2016-04-23 08:06:58 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 08:18:26 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 687.3 seconds

RetCode: 0

Status:  OK

CheckDir: systemPipeR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf systemPipeR.buildbin-libdir systemPipeR.Rcheck && mkdir systemPipeR.buildbin-libdir systemPipeR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=systemPipeR.buildbin-libdir systemPipeR_1.4.8.tar.gz >systemPipeR.Rcheck\00install.out 2>&1 && cp systemPipeR.Rcheck\00install.out systemPipeR-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=systemPipeR.buildbin-libdir --install="check:systemPipeR-install.out" --force-multiarch --no-vignettes --timings systemPipeR_1.4.8.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/systemPipeR.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'systemPipeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'systemPipeR' version '1.4.8'
* 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 whether package 'systemPipeR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.7Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
.resizeFeature: no visible global function definition for 'DataFrame'
.subsetReadsByMappingRegion: no visible global function definition for
  'IRanges'
.subsetReadsByMappingRegion: no visible global function definition for
  'seqlengths'
.subsetReadsByMappingRegion: no visible global function definition for
  'readGAlignments'
GOHyperGAll_Subset: no visible binding for global variable
  'test_sample'
clusterRun: no visible global function definition for 'chunk'
countRangeset: no visible global function definition for 'import.bed'
countRangeset: no visible global function definition for
  'summarizeOverlaps'
featureCoverage: no visible global function definition for
  'readGAlignments'
featureCoverage: no visible global function definition for 'qwidth'
featureCoverage: no visible global function definition for 'Rle'
featuretypeCounts: no visible global function definition for
  'readGAlignments'
featuretypeCounts: no visible global function definition for
  'readGAlignmentPairs'
featuretypeCounts: no visible global function definition for 'qwidth'
featuretypeCounts: no visible global function definition for 'last'
featuretypeCounts: no visible global function definition for 'first'
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'
genFeatures: no visible global function definition for 'DataFrame'
genFeatures: no visible global function definition for 'seqlengths<-'
getQsubargs: no visible binding for global variable 'tophatargs'
goBarplot: no visible binding for global variable 'SampleMatch'
goBarplot: no visible binding for global variable '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'
plotfeatureCoverage: no visible binding for global variable 'Coverage'
plotfeatureCoverage: no visible binding for global variable 'Strand'
plotfeaturetypeCounts: no visible binding for global variable 'Feature'
plotfeaturetypeCounts: no visible binding for global variable 'Counts'
plotfeaturetypeCounts: no visible binding for global variable 'Strand'
plotfeaturetypeCounts: no visible binding for global variable 'Length'
predORF : .predORF: no visible global function definition for 'IRanges'
scaleRanges : .scaleRanges: no visible global function definition for
  'IRanges'
scaleRanges: no visible global function definition for 'DataFrame'
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [63s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
genFeatures 20.30   0.59   21.22
run_edgeR    6.69   0.04    6.73
run_DESeq2   5.90   0.06    5.96
filterDEGs   5.38   0.00    5.38
** running examples for arch 'x64' ... [63s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
genFeatures 20.07   0.60   20.73
run_DESeq2   7.03   0.01    7.05
filterDEGs   6.00   0.00    6.01
run_edgeR    5.59   0.03    5.62
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [17s]
 [17s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [22s]
 [22s] 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: 4 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/systemPipeR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'systemPipeR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'systemPipeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'systemPipeR' as systemPipeR_1.4.8.zip
* DONE (systemPipeR)

name	user	system	elapsed
GOHyperGAll	0	0	0
INTERSECTset-class	0.03	0.00	0.03
SYSargs-class	0.07	0.00	0.06
VENNset-class	0.00	0.02	0.02
alignStats	0.03	0.00	0.03
catDB-class	0	0	0
catmap	0	0	0
clusterRun	0.03	0.00	0.03
countRangeset	0.11	0.00	0.11
featureCoverage	0.00	0.02	0.01
featuretypeCounts	0.03	0.00	0.04
filterDEGs	5.38	0.00	5.38
filterVars	0.03	0.00	0.03
genFeatures	20.30	0.59	21.22
getQsubargs	0.02	0.00	0.33
mergeBamByFactor	0.01	0.00	0.01
moduleload	0	0	0
olBarplot	0.83	0.01	0.85
overLapper	1.15	0.04	1.19
plotfeatureCoverage	0.02	0.00	0.01
plotfeaturetypeCounts	0.01	0.00	0.02
predORF	0.35	0.00	0.34
preprocessReads	0.04	0.00	0.05
qsubRun	0.02	0.00	0.01
readComp	0.03	0.00	0.04
returnRPKM	0	0	0
runCommandline	0.03	0.00	0.03
runDiff	0.09	0.00	0.09
run_DESeq2	5.90	0.06	5.96
run_edgeR	6.69	0.04	6.73
scaleRanges	0.3	0.0	0.3
seeFastq	0	0	0
symLink2bam	0.03	0.00	0.03
sysargs	0.03	0.00	0.03
systemArgs	0.03	0.00	0.03
variantReport	0.04	0.00	0.03
vennPlot	1.32	0.02	1.34
writeTargetsRef	0	0	0
writeTargetsout	0.03	0.00	0.03

name	user	system	elapsed
GOHyperGAll	0	0	0
INTERSECTset-class	0.03	0.00	0.03
SYSargs-class	0.08	0.00	0.07
VENNset-class	0.01	0.00	0.02
alignStats	0.05	0.00	0.05
catDB-class	0	0	0
catmap	0	0	0
clusterRun	0.03	0.00	0.03
countRangeset	0.12	0.01	0.14
featureCoverage	0.04	0.00	0.03
featuretypeCounts	0.03	0.00	0.03
filterDEGs	6.00	0.00	6.01
filterVars	0.03	0.00	0.03
genFeatures	20.07	0.60	20.73
getQsubargs	0.02	0.00	0.01
mergeBamByFactor	0.01	0.01	0.03
moduleload	0	0	0
olBarplot	0.94	0.02	0.95
overLapper	0.86	0.00	0.86
plotfeatureCoverage	0.01	0.00	0.02
plotfeaturetypeCounts	0.01	0.00	0.02
predORF	0.83	0.00	0.83
preprocessReads	0.06	0.00	0.06
qsubRun	0.03	0.00	0.03
readComp	0.05	0.00	0.05
returnRPKM	0	0	0
runCommandline	0.03	0.00	0.03
runDiff	0.10	0.00	0.09
run_DESeq2	7.03	0.01	7.05
run_edgeR	5.59	0.03	5.62
scaleRanges	0.31	0.00	0.31
seeFastq	0	0	0
symLink2bam	0.01	0.02	0.03
sysargs	0.03	0.00	0.03
systemArgs	0.04	0.00	0.03
variantReport	0.01	0.02	0.04
vennPlot	1.02	0.03	1.04
writeTargetsRef	0	0	0
writeTargetsout	0.03	0.00	0.03