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CHECK report for InterMineR on malbec2

This page was generated on 2018-10-17 08:30:40 -0400 (Wed, 17 Oct 2018).

Package 743/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InterMineR 1.2.1
InterMine Team
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/InterMineR
Branch: RELEASE_3_7
Last Commit: 978b6c2
Last Changed Date: 2018-08-21 16:01:13 -0400 (Tue, 21 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: InterMineR
Version: 1.2.1
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings InterMineR_1.2.1.tar.gz
StartedAt: 2018-10-16 01:20:17 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 01:24:12 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 234.3 seconds
RetCode: 0
Status:  OK 
CheckDir: InterMineR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings InterMineR_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/InterMineR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InterMineR/DESCRIPTION’ ... OK
* this is package ‘InterMineR’ version ‘1.2.1’
* 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                13.688  0.068  22.205
simplifyResult                       7.520  0.328   8.909
doEnrichment                         6.408  0.040  52.867
runQuery                             3.476  0.108   5.662
listDatasets                         3.204  0.172   6.230
convertToRangedSummarizedExperiment  2.648  0.008  10.236
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/InterMineR.Rcheck/00check.log’
for details.



Installation output

InterMineR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL InterMineR
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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-methods0.2280.0000.744
PL_DiabetesGenes0.0000.0000.004
PL_FlyTF_site_specific_TFs0.0000.0000.002
convertToGRanges1.0840.0281.718
convertToGeneAnswers13.688 0.06822.205
convertToRangedSummarizedExperiment 2.648 0.00810.236
doEnrichment 6.408 0.04052.867
getDatasets0.1480.0002.861
getGeneIds0.4880.0043.131
getModel1.3040.0082.270
getRelease0.0280.0000.340
getTemplateQuery0.0320.0000.388
getTemplates0.0400.0000.399
getVersion0.0320.0000.351
getWidgets0.0640.0000.709
initInterMine0.0160.0000.226
listDatasets3.2040.1726.230
listMines0.0080.0080.234
newQuery0.0000.0000.001
runQuery3.4760.1085.662
setConstraints0.0400.0080.640
setQuery0.0400.0120.717
simplifyResult7.5200.3288.909
summary0.0320.0000.387