BioC 3.3: CHECK report for paxtoolsr on zin2

Package: paxtoolsr

Version: 1.6.3

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings paxtoolsr_1.6.3.tar.gz

StartedAt: 2016-10-13 05:05:42 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:06:42 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 59.5 seconds

RetCode: 0

Status:  OK

CheckDir: paxtoolsr.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings paxtoolsr_1.6.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/paxtoolsr.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.3’
* 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 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
.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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-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	0.031	0.000	0.160
downloadPc2	0.001	0.000	0.000
downloadSignedPC	0.000	0.000	0.001
extractIds	0.031	0.000	0.031
fetch	2.725	0.028	1.612
filterSif	0.253	0.004	0.224
getCacheFiles	0.001	0.000	0.001
getErrorMessage	0.001	0.000	0.001
getNeighbors	0.514	0.016	0.287
getPc	0.001	0.000	0.001
getPcUrl	0.000	0.000	0.001
getSifInteractionCategories	0.001	0.000	0.001
graphPc	0	0	0
idMapping	0.001	0.000	0.000
integrateBiopax	2.019	0.012	1.142
loadSifInIgraph	0.007	0.000	0.007
mapValues	0.000	0.004	0.001
mergeBiopax	0.707	0.024	0.524
pcDirections	0	0	0
pcFormats	0.001	0.000	0.001
pcGraphQueries	0	0	0
processPcRequest	0.005	0.000	0.004
readBiopax	0.002	0.000	0.002
readGmt	0.045	0.000	0.044
readSbgn	0.001	0.000	0.002
readSif	0.002	0.000	0.002
readSifnx	0.023	0.004	0.027
searchListOfVectors	0.001	0.004	0.002
searchPc	0.000	0.000	0.001
summarize	0.093	0.004	0.071
summarizeSif	0.003	0.000	0.003
toGSEA	0.038	0.000	0.044
toLevel3	0.202	0.000	0.105
toSBGN	0.851	0.004	0.613
toSif	1.640	0.012	0.799
toSifnx	0.922	0.000	0.451
topPathways	0	0	0
traverse	0.001	0.000	0.000
validate	0.627	0.001	1.535