Package: piano

Version: 2.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:piano.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings piano_2.3.0.tar.gz

StartedAt: 2020-01-16 07:27:00 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:30:50 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 229.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: piano.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:piano.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings piano_2.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/piano.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 ‘piano/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘piano’ version ‘2.3.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘piano’ 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 ... OK
* 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 ... NOTE
Missing or unexported object: ‘rsbml::species’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Unknown package ‘HTSanalyzeR’ in Rd xrefs
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
diffExp         8.664  0.467   9.282
networkPlot2    6.999  0.484   7.527
GSAheatmap      6.830  0.574   7.412
networkPlot     6.641  0.361   7.007
exploreGSAres   6.524  0.434   6.966
runGSA          6.499  0.382   6.883
geneSetSummary  6.402  0.356   6.760
GSAsummaryTable 5.850  0.229   6.082
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/piano.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 piano
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘piano’ ...
** using staged installation
** R
** data
** 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 (piano)

name	user	system	elapsed
GSAheatmap	6.830	0.574	7.412
GSAsummaryTable	5.850	0.229	6.082
consensusHeatmap	1.279	0.123	1.405
consensusScores	0.219	0.024	0.342
diffExp	8.664	0.467	9.282
exploreGSAres	6.524	0.434	6.966
extractFactors	0.319	0.021	0.340
geneSetSummary	6.402	0.356	6.760
loadGSC	0.022	0.000	0.022
loadMAdata	0.305	0.012	0.318
networkPlot	6.641	0.361	7.007
networkPlot2	6.999	0.484	7.527
polarPlot	3.883	0.103	3.986
runGSA	6.499	0.382	6.883
runGSAhyper	0.418	0.033	0.452
runQC	1.575	0.102	1.678
writeFilesForKiwi	0.283	0.015	0.299