BioC 3.2: CHECK report for CoCiteStats on perceval

Package: CoCiteStats

Version: 1.41.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CoCiteStats_1.41.0.tar.gz

StartedAt: 2015-08-23 23:25:38 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:32:48 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 429.7 seconds

RetCode: 0

Status:  OK

CheckDir: CoCiteStats.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 CoCiteStats_1.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CoCiteStats.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoCiteStats/DESCRIPTION’ ... OK
* this is package ‘CoCiteStats’ version ‘1.41.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CoCiteStats’ can be installed ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
Package in Depends field not imported from: ‘org.Hs.eg.db’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gene.geneslist.sig: no visible global function definition for ‘Lkeys’
gene.geneslist.sig: no visible binding for global variable
  ‘org.Hs.egPMID’
paperLen: no visible global function definition for ‘toTable’
paperLen: no visible binding for global variable ‘org.Hs.egPMID’
paperLen: no visible global function definition for ‘nhit’
paperLen: no visible global function definition for ‘revmap’
* checking Rd files ... NOTE
prepare_Rd: gene.geneslist.statistic.Rd:19-21: Dropping empty section \details
* 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 examples ... [309s/334s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
gene.geneslist.sig       54.746  0.995  55.916
actorAdjTable            52.143  0.928  53.217
gene.geneslist.statistic 42.166  0.507  47.972
twowayTable              38.865  0.388  42.704
gene.gene.statistic      38.616  0.363  39.074
paperLen                 37.043  0.446  46.952
twTStats                 36.822  0.347  42.616
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/CoCiteStats.Rcheck/00check.log’
for details.

* installing *source* package ‘CoCiteStats’ ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (CoCiteStats)

name	user	system	elapsed
actorAdjTable	52.143	0.928	53.217
gene.gene.statistic	38.616	0.363	39.074
gene.geneslist.sig	54.746	0.995	55.916
gene.geneslist.statistic	42.166	0.507	47.972
paperLen	37.043	0.446	46.952
twTStats	36.822	0.347	42.616
twowayTable	38.865	0.388	42.704