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CHECK report for InterMineR on merida1

This page was generated on 2019-04-16 12:00:58 -0400 (Tue, 16 Apr 2019).

Package 785/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InterMineR 1.4.1
InterMine Team
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/InterMineR
Branch: RELEASE_3_8
Last Commit: 1fdb15b
Last Changed Date: 2018-12-06 07:14:37 -0400 (Thu, 06 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: InterMineR
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings InterMineR_1.4.1.tar.gz
StartedAt: 2019-04-16 00:43:45 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:48:35 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 289.2 seconds
RetCode: 0
Status:  OK 
CheckDir: InterMineR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings InterMineR_1.4.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/InterMineR.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 ‘InterMineR/DESCRIPTION’ ... OK
* this is package ‘InterMineR’ version ‘1.4.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘InterMineR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convertToGeneAnswers: no visible binding for global variable
  ‘geneExpProfile’
convertToRangedSummarizedExperiment: no visible global function
  definition for ‘reshape’
doEnrichment: no visible global function definition for ‘URLencode’
listDatasets: no visible binding for global variable ‘child_name’
runQuery,ANY-InterMineR: no visible global function definition for
  ‘URLencode’
runQuery,ANY-list: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode child_name geneExpProfile reshape
Consider adding
  importFrom("stats", "reshape")
  importFrom("utils", "URLencode")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
convertToGeneAnswers                17.460  0.288  26.932
simplifyResult                      13.911  1.026  15.926
runQuery                             5.580  0.410   7.126
doEnrichment                         5.557  0.077  47.736
listDatasets                         4.735  0.436   6.658
convertToRangedSummarizedExperiment  3.771  0.037   7.844
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/InterMineR.Rcheck/00check.log’
for details.



Installation output

InterMineR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL InterMineR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘InterMineR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (InterMineR)

Tests output


Example timings

InterMineR.Rcheck/InterMineR-Ex.timings

nameusersystemelapsed
InterMineR-methods0.5580.0111.060
PL_DiabetesGenes0.0030.0010.004
PL_FlyTF_site_specific_TFs0.0010.0000.002
convertToGRanges0.8290.0801.379
convertToGeneAnswers17.460 0.28826.932
convertToRangedSummarizedExperiment3.7710.0377.844
doEnrichment 5.557 0.07747.736
getDatasets0.1120.0021.233
getGeneIds0.4130.0063.117
getModel1.4090.0292.147
getRelease0.0220.0020.321
getTemplateQuery0.0250.0020.342
getTemplates0.0320.0030.338
getVersion0.0230.0020.344
getWidgets0.0540.0050.641
initInterMine0.0130.0020.207
listDatasets4.7350.4366.658
listMines0.0150.0020.213
newQuery0.0000.0000.001
runQuery5.5800.4107.126
setConstraints0.0380.0040.538
setQuery0.0410.0060.528
simplifyResult13.911 1.02615.926
summary0.0300.0030.330