Package: CoCiteStats

Version: 1.55.0

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_1.55.0.tar.gz

StartedAt: 2019-04-09 00:02:06 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:05:38 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 211.8 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 --install=check:CoCiteStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CoCiteStats_1.55.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CoCiteStats.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.55.0’
* 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            21.492  3.552  25.487
gene.geneslist.sig       21.159  0.702  22.020
gene.geneslist.statistic 16.873  0.246  17.277
twowayTable              16.383  0.187  16.713
gene.gene.statistic      15.565  0.164  15.886
twTStats                 14.867  0.127  15.125
paperLen                 14.330  0.186  14.637
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-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/3.6/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	21.492	3.552	25.487
gene.gene.statistic	15.565	0.164	15.886
gene.geneslist.sig	21.159	0.702	22.020
gene.geneslist.statistic	16.873	0.246	17.277
paperLen	14.330	0.186	14.637
twTStats	14.867	0.127	15.125
twowayTable	16.383	0.187	16.713