Package: InterMineR

Version: 1.8.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings InterMineR_1.8.1.tar.gz

StartedAt: 2020-04-15 05:05:05 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:10:05 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 300.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: InterMineR.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings InterMineR_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/InterMineR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.1’
* 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 ... 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 or elapsed time > 5s
                                      user system elapsed
convertToGeneAnswers                16.700  0.160  29.436
simplifyResult                      12.516  0.048  18.811
doEnrichment                         7.116  0.068  39.093
runQuery                             3.896  0.016   7.231
convertToRangedSummarizedExperiment  3.500  0.008   8.333
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/InterMineR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL InterMineR
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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	0.376	0.004	1.033
PL_DiabetesGenes	0.000	0.000	0.003
PL_FlyTF_site_specific_TFs	0.000	0.000	0.001
convertToGRanges	0.884	0.008	1.522
convertToGeneAnswers	16.700	0.160	29.436
convertToRangedSummarizedExperiment	3.500	0.008	8.333
doEnrichment	7.116	0.068	39.093
getDatasets	0.152	0.000	0.995
getGeneIds	0.564	0.000	3.016
getModel	0	0	0
getRelease	0.032	0.000	0.299
getTemplateQuery	0.028	0.000	0.308
getTemplates	0.032	0.004	0.493
getVersion	0.032	0.000	0.294
getWidgets	0.060	0.000	0.609
initInterMine	0.012	0.004	0.206
listDatasets	0	0	0
listMines	0.020	0.000	0.205
newQuery	0	0	0
runQuery	3.896	0.016	7.231
setConstraints	0.044	0.000	0.571
setQuery	0.044	0.004	0.517
simplifyResult	12.516	0.048	18.811
summary	0.036	0.000	0.321