Package: InterMineR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings InterMineR_1.0.0.tar.gz

StartedAt: 2018-04-12 05:19:23 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 05:23:46 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 263.4 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 --no-vignettes --timings InterMineR_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/InterMineR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.0’
* 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 ... 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
convertToGeneAnswers                17.070  0.149  26.072
simplifyResult                      11.988  0.844  13.801
doEnrichment                         5.518  0.068  37.192
runQuery                             4.298  0.316   5.636
convertToRangedSummarizedExperiment  3.787  0.016   7.463
* 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-3.6-bioc/meat/InterMineR.Rcheck/00check.log’
for details.

* installing *source* package ‘InterMineR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (InterMineR)

name	user	system	elapsed
InterMineR-methods	0.72	0.03	1.18
PL_DiabetesGenes	0.003	0.001	0.004
PL_FlyTF_site_specific_TFs	0.001	0.001	0.003
convertToGRanges	0.938	0.009	1.356
convertToGeneAnswers	17.070	0.149	26.072
convertToRangedSummarizedExperiment	3.787	0.016	7.463
doEnrichment	5.518	0.068	37.192
getDatasets	0.095	0.002	0.788
getGeneIds	0.383	0.005	2.926
getModel	1.130	0.041	1.914
getRelease	0.014	0.001	0.297
getTemplateQuery	0.012	0.001	0.295
getTemplates	0.021	0.002	0.317
getVersion	0.014	0.001	0.295
getWidgets	0.034	0.004	0.600
initInterMine	0.008	0.001	0.191
listDatasets	2.800	0.231	4.410
listMines	0.009	0.002	0.187
newQuery	0.000	0.000	0.001
runQuery	4.298	0.316	5.636
setConstraints	0.025	0.003	0.505
setQuery	0.032	0.004	0.500
simplifyResult	11.988	0.844	13.801
summary	0.023	0.002	0.308