BioC 3.2: CHECK report for paxtoolsr on oaxaca

Package: paxtoolsr

Version: 1.4.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings paxtoolsr_1.4.6.tar.gz

StartedAt: 2016-04-23 02:55:17 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:56:35 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 78.4 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_1.4.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/paxtoolsr.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.6’
* 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 ... [4s/6s] OK
* checking installed package size ... NOTE
  installed size is 30.1Mb
  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 ... [14s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [14s/19s]
 [14s/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	0.037	0.005	0.242
downloadPc2	0.001	0.000	0.001
downloadSignedPC	0.001	0.000	0.001
extractIds	0.036	0.001	0.038
fetch	2.902	0.072	1.454
filterSif	0.002	0.000	0.003
getCacheFiles	0.001	0.000	0.001
getErrorMessage	0.002	0.000	0.002
getNeighbors	0.508	0.010	0.215
getPc	0.000	0.001	0.000
getPcUrl	0.001	0.000	0.000
getSifInteractionCategories	0.001	0.000	0.001
graphPc	0	0	0
idMapping	0.000	0.000	0.001
integrateBiopax	1.805	0.048	0.997
loadSifInIgraph	0.007	0.001	0.008
mapValues	0.002	0.000	0.001
mergeBiopax	0.998	0.045	0.595
pcDirections	0.000	0.000	0.001
pcFormats	0.000	0.000	0.001
pcGraphQueries	0.001	0.000	0.001
processPcRequest	0.007	0.001	0.009
readBiopax	0.002	0.001	0.003
readGmt	0.015	0.000	0.015
readSbgn	0.002	0.001	0.002
readSif	0.002	0.000	0.003
readSifnx	0.032	0.001	0.033
searchListOfVectors	0.004	0.000	0.003
searchPc	0.001	0.000	0.001
summarize	0.099	0.003	0.078
summarizeSif	0.002	0.000	0.002
toGSEA	0.032	0.003	0.064
toLevel3	0.115	0.004	0.082
toSBGN	1.085	0.036	0.769
toSif	1.740	0.030	0.762
toSifnx	1.033	0.024	0.392
topPathways	0.001	0.000	0.000
traverse	0.002	0.000	0.000
validate	0.937	0.038	1.620