Package: loci2path

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2019-10-16 02:45:05 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:46:54 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 108.7 seconds

RetCode: 0

Status:  OK

CheckDir: loci2path.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:loci2path.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings loci2path_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/loci2path.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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              23.205  0.104   4.206
getHeatmap-methods         18.030  0.084   3.652
getMat-methods             17.760  0.086   3.507
loci2pathResult-class      17.087  0.060   3.063
getTissueDegree-methods    16.948  0.048   3.152
getPathDescription-methods 16.553  0.071   3.312
getWordcloud-methods       16.492  0.068   3.088
getPval-methods            14.386  0.073   2.602
* 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 loci2path
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* 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	0.016	0.004	0.020
check.geneid	0.007	0.008	0.015
eqtlSet-class	0.138	0.012	0.175
eset.list	0.000	0.001	0.001
geneSet-class	0.010	0.000	0.016
getHeatmap-methods	18.030	0.084	3.652
getMat-methods	17.760	0.086	3.507
getPathDescription-methods	16.553	0.071	3.312
getPval-methods	14.386	0.073	2.602
getTissueDegree-methods	16.948	0.048	3.152
getWordcloud-methods	16.492	0.068	3.088
loci2pathResult-class	17.087	0.060	3.063
query-methods	23.205	0.104	4.206
query.gr	0.001	0.000	0.001