Package: InterMineR

Version: 1.9.2

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_1.9.2.tar.gz

StartedAt: 2020-01-07 05:13:31 -0500 (Tue, 07 Jan 2020)

EndedAt: 2020-01-07 05:20:10 -0500 (Tue, 07 Jan 2020)

EllapsedTime: 398.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: InterMineR.Rcheck

Warnings: 1

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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_1.9.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/InterMineR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.9.2’
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
* 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 (user + system) or elapsed time > 5s
                                      user system elapsed
convertToGeneAnswers                24.175  0.575  35.768
simplifyResult                      14.381  0.459  17.000
doEnrichment                         7.691  0.165  39.415
runQuery                             6.688  0.129   8.681
convertToRangedSummarizedExperiment  5.292  0.131   9.179
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/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	0.293	0.046	1.040
PL_DiabetesGenes	0.004	0.003	0.007
PL_FlyTF_site_specific_TFs	0.002	0.002	0.004
convertToGRanges	1.473	0.089	2.127
convertToGeneAnswers	24.175	0.575	35.768
convertToRangedSummarizedExperiment	5.292	0.131	9.179
doEnrichment	7.691	0.165	39.415
getDatasets	0.155	0.004	0.854
getGeneIds	0.601	0.013	2.968
getModel	0.000	0.001	0.001
getRelease	0.023	0.001	0.296
getTemplateQuery	0.021	0.001	0.291
getTemplates	0.033	0.004	0.502
getVersion	0.022	0.001	0.292
getWidgets	0.055	0.002	0.596
initInterMine	0.013	0.001	0.195
listDatasets	0.001	0.001	0.001
listMines	0.016	0.003	0.190
newQuery	0.001	0.001	0.001
runQuery	6.688	0.129	8.681
setConstraints	0.042	0.005	0.486
setQuery	0.048	0.006	0.494
simplifyResult	14.381	0.459	17.000
summary	0.034	0.011	0.337