Package: KEGGprofile

Version: 1.26.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:KEGGprofile.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings KEGGprofile_1.26.0.tar.gz

StartedAt: 2019-07-03 03:03:11 -0400 (Wed, 03 Jul 2019)

EndedAt: 2019-07-03 03:06:53 -0400 (Wed, 03 Jul 2019)

EllapsedTime: 221.9 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGprofile.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:KEGGprofile.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings KEGGprofile_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/KEGGprofile.Rcheck’
* using R version 3.6.0 (2019-04-26)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGprofile/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGprofile’ version ‘1.26.0’
* 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 ‘KEGGprofile’ 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 ... OK
* 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 ... 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
plot_pathway 6.137  0.060   6.230
convertId    0.248  0.016 109.722
* 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: OK

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL KEGGprofile
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘KEGGprofile’ ...
** 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 (KEGGprofile)

name	user	system	elapsed
col_by_value	0.010	0.004	0.013
convertId	0.248	0.016	109.722
download_KEGGfile	0.207	0.016	4.417
download_latest_pathway	0	0	0
find_enriched_pathway	3.184	0.016	3.211
newIdMatrix	0.001	0.000	0.001
parse_XMLfile	0.044	0.000	0.139
plot_pathway	6.137	0.060	6.230
plot_pathway_cor	3.261	0.004	3.264
plot_profile	1.345	0.028	1.374