Package: InterMineR

Version: 1.6.1

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_1.6.1.tar.gz

StartedAt: 2019-10-15 03:33:20 -0400 (Tue, 15 Oct 2019)

EndedAt: 2019-10-15 03:39:24 -0400 (Tue, 15 Oct 2019)

EllapsedTime: 364.1 seconds

RetCode: 0

Status:  OK

CheckDir: InterMineR.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:InterMineR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings InterMineR_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/InterMineR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.1’
* 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                25.508  0.584  37.302
simplifyResult                      15.404  0.438  18.084
doEnrichment                         7.559  0.150  39.813
runQuery                             5.675  0.046   7.622
convertToRangedSummarizedExperiment  4.975  0.162   9.135
* 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-3.9-bioc/meat/InterMineR.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 InterMineR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘InterMineR’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (InterMineR)

name	user	system	elapsed
InterMineR-methods	0.198	0.034	0.968
PL_DiabetesGenes	0.004	0.002	0.006
PL_FlyTF_site_specific_TFs	0.001	0.002	0.003
convertToGRanges	1.155	0.029	1.751
convertToGeneAnswers	25.508	0.584	37.302
convertToRangedSummarizedExperiment	4.975	0.162	9.135
doEnrichment	7.559	0.150	39.813
getDatasets	0.147	0.004	0.821
getGeneIds	0.591	0.013	2.986
getModel	0	0	0
getRelease	0.024	0.001	0.303
getTemplateQuery	0.025	0.001	0.295
getTemplates	0.039	0.004	0.509
getVersion	0.024	0.002	0.285
getWidgets	0.055	0.004	0.588
initInterMine	0.014	0.001	0.187
listDatasets	0.001	0.000	0.000
listMines	0.013	0.002	0.183
newQuery	0.001	0.000	0.001
runQuery	5.675	0.046	7.622
setConstraints	0.041	0.003	0.543
setQuery	0.049	0.006	0.580
simplifyResult	15.404	0.438	18.084
summary	0.033	0.002	0.297