BioC 3.0: CHECK report for systemPipeR on perceval

Package: systemPipeR

Version: 1.0.12

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch systemPipeR_1.0.12.tar.gz

StartedAt: 2015-04-10 06:54:28 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 07:04:29 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 601.3 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 --no-multiarch systemPipeR_1.0.12.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/systemPipeR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.0.12’
* 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 ... [55s/59s] 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 ... NOTE
Namespace in Imports field not imported from: ‘BiocGenerics’
  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
vennPlot : ellipseVenn: warning in close.screen(all = TRUE): partial
  argument match of 'all' to 'all.screens'
.subsetReadsByMappingRegion: no visible global function definition for
  ‘GRanges’
.subsetReadsByMappingRegion: no visible global function definition for
  ‘readGAlignments’
clusterRun: no visible global function definition for ‘chunk’
filterDEGs: no visible binding for global variable ‘Comparisons’
filterDEGs: no visible binding for global variable ‘Counts’
filterDEGs: no visible binding for global variable ‘Type’
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 ‘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’
show,INTERSECTset: no visible binding for global variable ‘vennset’
* checking Rd files ... NOTE
prepare_Rd: writeTargetsout.Rd:42-43: Dropping empty section \seealso
* 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 ... [41s/42s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
run_DESeq2 4.966  0.058   5.049
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [27s/28s]
 [27s/28s] 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.

* 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
* DONE (systemPipeR)

name	user	system	elapsed
GOHyperGAll	0.002	0.000	0.002
INTERSECTset-class	0.016	0.006	0.023
SYSargs-class	0.059	0.005	0.065
VENNset-class	0.011	0.003	0.015
alignStats	0.025	0.003	0.029
catDB-class	0.001	0.000	0.002
catmap	0.001	0.001	0.001
clusterRun	0.027	0.003	0.030
filterDEGs	4.271	0.049	4.324
getQsubargs	0.024	0.005	0.029
moduleload	0.001	0.000	0.001
olBarplot	0.533	0.028	0.631
overLapper	0.511	0.026	0.624
preprocessReads	0.021	0.003	0.025
qsubRun	0.027	0.004	0.031
readComp	0.034	0.004	0.039
returnRPKM	0.001	0.000	0.001
runCommandline	0.027	0.004	0.031
run_DESeq2	4.966	0.058	5.049
run_edgeR	3.868	0.034	3.909
seeFastq	0	0	0
symLink2bam	0.020	0.003	0.024
sysargs	0.024	0.003	0.027
systemArgs	0.025	0.003	0.028
vennPlot	0.523	0.024	0.630
writeTargetsout	0.018	0.002	0.020