BioC 3.5: CHECK report for CoCiteStats on veracruz2

Package: CoCiteStats

Version: 1.48.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CoCiteStats_1.48.0.tar.gz

StartedAt: 2017-10-18 01:59:42 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:03:56 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 253.8 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_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CoCiteStats.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoCiteStats/DESCRIPTION’ ... OK
* this is package ‘CoCiteStats’ version ‘1.48.0’
* 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 ... 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’
Undefined global functions or variables:
  Lkeys nhit org.Hs.egPMID revmap toTable
* 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 ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
actorAdjTable            27.412  2.007  30.384
gene.geneslist.sig       25.390  0.449  26.657
gene.geneslist.statistic 21.644  0.303  24.817
twowayTable              21.201  0.235  23.054
paperLen                 20.447  0.207  27.018
twTStats                 19.928  0.248  23.095
gene.gene.statistic      19.951  0.191  20.796
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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	27.412	2.007	30.384
gene.gene.statistic	19.951	0.191	20.796
gene.geneslist.sig	25.390	0.449	26.657
gene.geneslist.statistic	21.644	0.303	24.817
paperLen	20.447	0.207	27.018
twTStats	19.928	0.248	23.095
twowayTable	21.201	0.235	23.054