BioC 3.5: CHECK report for paxtoolsr on tokay2

Package: paxtoolsr

Version: 1.10.0

Command: rm -rf paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && mkdir paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=paxtoolsr.buildbin-libdir paxtoolsr_1.10.0.tar.gz >paxtoolsr.Rcheck\00install.out 2>&1 && cp paxtoolsr.Rcheck\00install.out paxtoolsr-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=paxtoolsr.buildbin-libdir --install="check:paxtoolsr-install.out" --force-multiarch --no-vignettes --timings paxtoolsr_1.10.0.tar.gz

StartedAt: 2017-08-16 01:49:24 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:52:00 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 156.0 seconds

RetCode: 0

Status:  OK

CheckDir: paxtoolsr.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && mkdir paxtoolsr.buildbin-libdir paxtoolsr.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=paxtoolsr.buildbin-libdir paxtoolsr_1.10.0.tar.gz >paxtoolsr.Rcheck\00install.out 2>&1 && cp paxtoolsr.Rcheck\00install.out paxtoolsr-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=paxtoolsr.buildbin-libdir --install="check:paxtoolsr-install.out" --force-multiarch --no-vignettes --timings paxtoolsr_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/paxtoolsr.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.10.0'
* 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 30.7Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    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
* 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
Namespace in Imports field not imported from: 'jsonlite'
  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
.onLoad: no visible global function definition for 'write.table'
downloadFile: no visible global function definition for 'URLencode'
downloadFile: no visible global function definition for 'read.table'
downloadFile: no visible global function definition for 'write.table'
downloadPc2: no visible global function definition for 'select.list'
downloadSignedPC: no visible global function definition for
  'read.table'
getPcRequest: no visible global function definition for 'URLencode'
readSifnx: no visible global function definition for 'read.table'
splitSifnxByPathway: no visible global function definition for
  'txtProgressBar'
splitSifnxByPathway: no visible global function definition for
  '%dopar%'
splitSifnxByPathway: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  %dopar% URLencode read.table select.list setTxtProgressBar
  txtProgressBar write.table
Consider adding
  importFrom("utils", "URLencode", "read.table", "select.list",
             "setTxtProgressBar", "txtProgressBar", "write.table")
to your NAMESPACE file.
* 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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-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_1.10.0.zip
* DONE (paxtoolsr)

name	user	system	elapsed
downloadFile	0.20	0.03	0.56
downloadPc2	0	0	0
downloadSignedPC	0	0	0
extractIds	0.02	0.00	0.02
fetch	1.14	0.13	1.54
filterSif	0.23	0.00	0.24
getCacheFiles	0	0	0
getErrorMessage	0	0	0
getNeighbors	0.25	0.00	0.25
getPc	0	0	0
getPcUrl	0	0	0
getSifInteractionCategories	0	0	0
graphPc	0	0	0
integrateBiopax	1.23	0.03	1.27
loadSifInIgraph	0.08	0.00	0.08
mapValues	0	0	0
mergeBiopax	1.08	0.01	1.03
pcDirections	0	0	0
pcFormats	0	0	0
pcGraphQueries	0	0	0
processPcRequest	0.00	0.02	0.08
readBiopax	0	0	0
readGmt	0.01	0.00	0.01
readSbgn	0.00	0.02	0.02
readSif	0	0	0
readSifnx	0.02	0.00	0.01
searchListOfVectors	0.01	0.00	0.02
searchPc	0	0	0
summarize	0.11	0.00	0.15
summarizeSif	0	0	0
toGSEA	0.07	0.00	0.49
toLevel3	0.09	0.00	0.14
toSBGN	0.83	0.09	3.92
toSif	0.79	0.00	0.92
toSifnx	0.46	0.00	0.58
topPathways	0	0	0
traverse	0	0	0
validate	0.33	0.16	4.72

name	user	system	elapsed
downloadFile	0.26	0.01	0.54
downloadPc2	0	0	0
downloadSignedPC	0	0	0
extractIds	0.03	0.00	0.03
fetch	4.44	0.27	1.28
filterSif	0.62	0.00	0.30
getCacheFiles	0	0	0
getErrorMessage	0	0	0
getNeighbors	1.00	0.03	0.25
getPc	0	0	0
getPcUrl	0	0	0
getSifInteractionCategories	0	0	0
graphPc	0	0	0
integrateBiopax	3.13	0.12	0.80
loadSifInIgraph	0.12	0.00	0.06
mapValues	0	0	0
mergeBiopax	1.21	0.03	0.42
pcDirections	0	0	0
pcFormats	0	0	0
pcGraphQueries	0	0	0
processPcRequest	0.09	0.00	0.08
readBiopax	0	0	0
readGmt	0.03	0.00	0.02
readSbgn	0	0	0
readSif	0.02	0.00	0.01
readSifnx	0.01	0.00	0.02
searchListOfVectors	0	0	0
searchPc	0	0	0
summarize	0.21	0.00	0.09
summarizeSif	0	0	0
toGSEA	0.18	0.04	0.19
toLevel3	0.49	0.01	0.13
toSBGN	1.78	0.10	1.96
toSif	3.09	0.09	1.43
toSifnx	1.63	0.03	0.78
topPathways	0	0	0
traverse	0	0	0
validate	1.22	0.20	3.08