Package: loci2path

Version: 1.3.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:loci2path.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings loci2path_1.3.0.tar.gz

StartedAt: 2019-04-09 01:36:00 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:37:53 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 112.9 seconds

RetCode: 0

Status:  OK

CheckDir: loci2path.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:loci2path.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings loci2path_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/loci2path.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘loci2path/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘loci2path’ version ‘1.3.0’
* package encoding: UTF-8
* 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 ‘loci2path’ 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
query-methods              22.349  0.149   4.238
getHeatmap-methods         18.506  0.115   3.515
getPathDescription-methods 17.884  0.068   3.063
getWordcloud-methods       17.735  0.084   3.189
loci2pathResult-class      17.297  0.065   3.092
getMat-methods             17.132  0.084   3.260
getPval-methods            16.750  0.085   3.131
getTissueDegree-methods    16.416  0.047   3.192
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL loci2path
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘loci2path’ ...
** 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 (loci2path)

name	user	system	elapsed
biocarta	0.015	0.004	0.018
check.geneid	0.018	0.000	0.018
eqtlSet-class	0.187	0.023	0.556
eset.list	0.001	0.000	0.001
geneSet-class	0.013	0.001	0.040
getHeatmap-methods	18.506	0.115	3.515
getMat-methods	17.132	0.084	3.260
getPathDescription-methods	17.884	0.068	3.063
getPval-methods	16.750	0.085	3.131
getTissueDegree-methods	16.416	0.047	3.192
getWordcloud-methods	17.735	0.084	3.189
loci2pathResult-class	17.297	0.065	3.092
query-methods	22.349	0.149	4.238
query.gr	0.001	0.000	0.002