BioC 3.2: CHECK report for paxtoolsr on perceval

Package: paxtoolsr

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings paxtoolsr_1.4.0.tar.gz

StartedAt: 2015-10-27 10:47:52 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 10:49:20 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 88.7 seconds

RetCode: 0

Status:  OK

CheckDir: paxtoolsr.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 paxtoolsr_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/paxtoolsr.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘paxtoolsr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘paxtoolsr’ version ‘1.4.0’
* 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 ‘paxtoolsr’ can be installed ... [5s/5s] OK
* checking installed package size ... NOTE
  installed size is 30.0Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
    java     24.5Mb
* 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
splitSifnxByPathway: no visible global function definition for
  ‘%dopar%’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [17s/19s]
 [17s/19s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/paxtoolsr.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
downloadFile	0.052	0.007	0.236
downloadPc	0.001	0.000	0.001
downloadPc2	0.001	0.000	0.001
extractIds	0.040	0.001	0.042
fetch	3.252	0.156	1.571
filterSif	0.002	0.000	0.003
getCacheFiles	0.000	0.001	0.000
getErrorMessage	0.001	0.000	0.001
getNeighbors	0.604	0.022	0.244
getPc	0.001	0.000	0.001
getPcUrl	0.000	0.000	0.001
getSifInteractionCategories	0.001	0.000	0.002
graphPc	0.000	0.000	0.001
idMapping	0.000	0.000	0.001
integrateBiopax	2.350	0.105	1.127
loadSifInIgraph	0.007	0.001	0.007
mapValues	0.002	0.000	0.001
mergeBiopax	1.356	0.102	0.695
pcDirections	0.000	0.000	0.001
pcFormats	0.001	0.000	0.001
pcGraphQueries	0.001	0.000	0.001
processPcRequest	0.006	0.002	0.008
readBiopax	0.002	0.000	0.003
readGmt	0.012	0.001	0.012
readSbgn	0.002	0.000	0.002
readSif	0.003	0.000	0.002
readSifnx	0.034	0.001	0.035
searchListOfVectors	0.001	0.000	0.001
searchPc	0.001	0.000	0.001
summarize	0.138	0.007	0.098
summarizeSif	0.004	0.000	0.004
toGSEA	0.039	0.007	0.072
toLevel3	0.153	0.011	0.099
toSBGN	1.259	0.062	1.030
toSif	2.116	0.059	0.834
toSifnx	1.261	0.073	0.459
topPathways	0.009	0.000	0.000
traverse	0.001	0.000	0.000
validate	0.909	0.054	2.081