Package: CoCiteStats

Version: 1.54.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CoCiteStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CoCiteStats_1.54.0.tar.gz

StartedAt: 2019-04-15 23:07:56 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:11:33 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 217.6 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 --install=check:CoCiteStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CoCiteStats_1.54.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CoCiteStats.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.54.0’
* 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 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            22.231  3.488  26.174
gene.geneslist.sig       22.966  0.794  23.875
gene.geneslist.statistic 17.375  0.308  17.954
gene.gene.statistic      15.874  0.208  16.226
twTStats                 15.769  0.175  16.063
twowayTable              15.363  0.181  15.671
paperLen                 14.972  0.199  15.343
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/CoCiteStats.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CoCiteStats
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CoCiteStats’ ...
** R
** byte-compile and prepare 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	22.231	3.488	26.174
gene.gene.statistic	15.874	0.208	16.226
gene.geneslist.sig	22.966	0.794	23.875
gene.geneslist.statistic	17.375	0.308	17.954
paperLen	14.972	0.199	15.343
twTStats	15.769	0.175	16.063
twowayTable	15.363	0.181	15.671