BioC 3.5: CHECK report for paxtoolsr on toluca2

Package: paxtoolsr

Version: 1.9.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings paxtoolsr_1.9.1.tar.gz

StartedAt: 2017-04-23 07:46:24 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 07:47:50 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 86.7 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_1.9.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/paxtoolsr.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.9.1’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 30.9Mb
  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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.5-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	0.677	0.006	0.860
downloadPc2	0.001	0.000	0.001
downloadSignedPC	0.000	0.000	0.001
extractIds	0.034	0.001	0.037
fetch	3.156	0.167	1.327
filterSif	0.857	0.015	0.417
getCacheFiles	0.001	0.000	0.001
getErrorMessage	0.001	0.000	0.001
getNeighbors	0.935	0.040	0.413
getPc	0	0	0
getPcUrl	0.000	0.001	0.000
getSifInteractionCategories	0.001	0.000	0.001
graphPc	0.001	0.000	0.000
integrateBiopax	3.013	0.132	1.121
loadSifInIgraph	0.054	0.004	0.054
mapValues	0.001	0.000	0.002
mergeBiopax	1.289	0.056	0.616
pcDirections	0	0	0
pcFormats	0.001	0.000	0.001
pcGraphQueries	0.001	0.000	0.001
processPcRequest	0.007	0.001	0.008
readBiopax	0.003	0.001	0.002
readGmt	0.013	0.001	0.014
readSbgn	0.002	0.000	0.002
readSif	0.002	0.001	0.003
readSifnx	0.025	0.000	0.026
searchListOfVectors	0.003	0.000	0.003
searchPc	0	0	0
summarize	0.167	0.012	0.137
summarizeSif	0.003	0.001	0.004
toGSEA	0.225	0.012	0.131
toLevel3	0.243	0.009	0.084
toSBGN	1.392	0.076	0.809
toSif	1.841	0.046	0.666
toSifnx	1.022	0.023	0.324
topPathways	0.001	0.000	0.001
traverse	0.003	0.000	0.001
validate	0.966	0.052	2.333