BioC 3.3: CHECK report for paxtoolsr on windows2.bioconductor.org

Package: paxtoolsr

Version: 1.5.0

Command: rm -rf paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && mkdir paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=paxtoolsr.buildbin-libdir paxtoolsr_1.5.0.tar.gz >paxtoolsr.Rcheck\00install.out 2>&1 && cp paxtoolsr.Rcheck\00install.out paxtoolsr-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=paxtoolsr.buildbin-libdir --install="check:paxtoolsr-install.out" --force-multiarch --no-vignettes --timings paxtoolsr_1.5.0.tar.gz

StartedAt: 2015-10-27 04:51:59 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:53:50 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 110.6 seconds

RetCode: 0

Status:  OK

CheckDir: paxtoolsr.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && mkdir paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=paxtoolsr.buildbin-libdir paxtoolsr_1.5.0.tar.gz >paxtoolsr.Rcheck\00install.out 2>&1 && cp paxtoolsr.Rcheck\00install.out paxtoolsr-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=paxtoolsr.buildbin-libdir --install="check:paxtoolsr-install.out" --force-multiarch --no-vignettes --timings paxtoolsr_1.5.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/paxtoolsr.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'paxtoolsr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'paxtoolsr' version '1.5.0'
* 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 whether package 'paxtoolsr' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 29.9Mb
  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
* 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
** checking loading without being on the library search path ... 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 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%'
Undefined global functions or variables:
  %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 ...
** running examples for arch 'i386' ... [7s] OK
** running examples for arch 'x64' ... [8s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [13s]
 [13s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [13s]
 [14s] 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
  'c:/biocbld/bbs-3.3-bioc/meat/paxtoolsr.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'paxtoolsr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'paxtoolsr' as paxtoolsr_1.5.0.zip
* DONE (paxtoolsr)

name	user	system	elapsed
downloadFile	0.03	0.02	0.63
downloadPc	0	0	0
downloadPc2	0	0	0
extractIds	0.04	0.00	0.03
fetch	0.92	0.03	0.75
filterSif	0	0	0
getCacheFiles	0	0	0
getErrorMessage	0	0	0
getNeighbors	0.13	0.01	0.12
getPc	0	0	0
getPcUrl	0	0	0
getSifInteractionCategories	0	0	0
graphPc	0	0	0
idMapping	0	0	0
integrateBiopax	0.74	0.05	0.68
loadSifInIgraph	0	0	0
mapValues	0	0	0
mergeBiopax	0.73	0.03	0.75
pcDirections	0	0	0
pcFormats	0	0	0
pcGraphQueries	0	0	0
processPcRequest	0.00	0.00	0.06
readBiopax	0	0	0
readGmt	0.01	0.00	0.02
readSbgn	0	0	0
readSif	0	0	0
readSifnx	0.07	0.00	0.07
searchListOfVectors	0	0	0
searchPc	0	0	0
summarize	0.12	0.00	0.12
summarizeSif	0	0	0
toGSEA	0.03	0.00	0.05
toLevel3	0.13	0.00	0.11
toSBGN	0.42	0.06	0.48
toSif	0.51	0.00	0.44
toSifnx	0.19	0.02	0.26
topPathways	0	0	0
traverse	0	0	0
validate	0.41	0.06	1.26

name	user	system	elapsed
downloadFile	0.06	0.00	0.59
downloadPc	0	0	0
downloadPc2	0	0	0
extractIds	0.04	0.00	0.03
fetch	3.79	0.25	0.92
filterSif	0	0	0
getCacheFiles	0	0	0
getErrorMessage	0	0	0
getNeighbors	0.78	0.11	0.15
getPc	0	0	0
getPcUrl	0	0	0
getSifInteractionCategories	0	0	0
graphPc	0	0	0
idMapping	0	0	0
integrateBiopax	2.75	0.05	0.72
loadSifInIgraph	0.03	0.00	0.02
mapValues	0	0	0
mergeBiopax	0.89	0.09	0.42
pcDirections	0	0	0
pcFormats	0	0	0
pcGraphQueries	0	0	0
processPcRequest	0.00	0.00	0.08
readBiopax	0	0	0
readGmt	0	0	0
readSbgn	0.02	0.00	0.01
readSif	0	0	0
readSifnx	0.01	0.00	0.02
searchListOfVectors	0	0	0
searchPc	0	0	0
summarize	0.05	0.01	0.05
summarizeSif	0.02	0.00	0.01
toGSEA	0.09	0.02	0.03
toLevel3	0.31	0.02	0.09
toSBGN	0.94	0.06	0.49
toSif	1.96	0.05	0.51
toSifnx	1.40	0.06	0.35
topPathways	0	0	0
traverse	0.03	0.00	0.01
validate	0.81	0.19	1.77