BioC 3.1: CHECK report for CoCiteStats on petty

Package: CoCiteStats

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CoCiteStats_1.40.0.tar.gz

StartedAt: 2015-10-08 22:14:20 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:22:09 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 468.7 seconds

RetCode: 0

Status:  OK

CheckDir: CoCiteStats.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CoCiteStats_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.40.0’
* 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 ... [12s/13s] 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 ... [334s/344s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
actorAdjTable            53.397  0.835  54.677
gene.geneslist.sig       52.440  0.829  54.838
twowayTable              45.595  0.336  45.965
gene.geneslist.statistic 45.112  0.326  48.689
gene.gene.statistic      42.990  0.312  43.326
twTStats                 42.509  0.272  45.005
paperLen                 42.333  0.337  45.379
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/CoCiteStats.Rcheck/00check.log’
for details.

* installing *source* package ‘CoCiteStats’ ...
** R
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (CoCiteStats)

name	user	system	elapsed
actorAdjTable	53.397	0.835	54.677
gene.gene.statistic	42.990	0.312	43.326
gene.geneslist.sig	52.440	0.829	54.838
gene.geneslist.statistic	45.112	0.326	48.689
paperLen	42.333	0.337	45.379
twTStats	42.509	0.272	45.005
twowayTable	45.595	0.336	45.965