BioC 3.1: CHECK report for paxtoolsr on zin2

Package: paxtoolsr

Version: 1.2.1

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings paxtoolsr_1.2.1.tar.gz

StartedAt: 2015-10-09 04:11:46 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:12:37 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 51.0 seconds

RetCode: 0

Status:  OK

CheckDir: paxtoolsr.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings paxtoolsr_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/paxtoolsr.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.1’
* 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 ... [2s/2s] OK
* checking installed package size ... NOTE
  installed size is 26.8Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
    java     21.3Mb
* 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 ... OK
* 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/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [13s/10s]
 [13s/10s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.1-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
downloadPc	0.001	0.000	0.001
fetch	3.117	0.048	1.756
fromPsimi	1.595	0.040	0.903
getNeighbors	0.585	0.000	0.259
getPc	0.002	0.000	0.000
getPcUrl	0.043	0.004	0.617
graphPc	0.000	0.000	0.001
idMapping	0	0	0
integrateBiopax	1.918	0.028	1.137
mergeBiopax	0.790	0.020	0.591
pcDirections	0.001	0.000	0.000
pcFormats	0.000	0.000	0.001
pcGraphQueries	0.001	0.000	0.000
readGmt	0.008	0.000	0.008
searchPc	0	0	0
splitSifnx	0.012	0.000	0.012
summarize	0.092	0.000	0.076
toGSEA	0.074	0.004	0.056
toLevel3	0.128	0.000	0.077
toSBGN	0.724	0.004	0.399
toSif	1.805	0.020	0.890
toSifnx	0.280	0.000	0.113
topPathways	0.001	0.000	0.000
traverse	0.002	0.000	0.001
validate	1.312	0.020	2.271