BioC 3.0: CHECK report for CoCiteStats on zin1

Package: CoCiteStats

Version: 1.38.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings CoCiteStats_1.38.0.tar.gz

StartedAt: 2015-04-09 22:48:35 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:52:18 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 223.1 seconds

RetCode: 0

Status:  OK

CheckDir: CoCiteStats.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings CoCiteStats_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/CoCiteStats.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoCiteStats/DESCRIPTION’ ... OK
* this is package ‘CoCiteStats’ version ‘1.38.0’
* 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 ... [9s/9s] OK
* checking installed package size ... OK
* checking package 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 ... 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 ... [136s/137s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
actorAdjTable            27.429  0.236  27.761
gene.geneslist.sig       22.409  0.016  22.484
twowayTable              17.057  0.000  17.913
twTStats                 16.565  0.004  16.598
gene.gene.statistic      16.242  0.044  16.330
gene.geneslist.statistic 16.273  0.000  16.391
paperLen                 14.933  0.004  15.013
* checking PDF version of manual ... OK
* DONE

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-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	27.429	0.236	27.761
gene.gene.statistic	16.242	0.044	16.330
gene.geneslist.sig	22.409	0.016	22.484
gene.geneslist.statistic	16.273	0.000	16.391
paperLen	14.933	0.004	15.013
twTStats	16.565	0.004	16.598
twowayTable	17.057	0.000	17.913