Package: loci2path

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:loci2path.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings loci2path_1.2.0.tar.gz

StartedAt: 2019-04-16 00:54:27 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:55:58 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 91.3 seconds

RetCode: 0

Status:  OK

CheckDir: loci2path.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:loci2path.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings loci2path_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/loci2path.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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 3.64  1.723    0.58
* 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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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL loci2path
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘loci2path’ ...
** 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
* DONE (loci2path)

name	user	system	elapsed
biocarta	0.017	0.006	0.022
check.geneid	0.016	0.002	0.018
eqtlSet-class	0.202	0.024	0.228
eset.list	0.002	0.001	0.002
geneSet-class	0.013	0.002	0.016
getHeatmap-methods	2.227	2.122	0.930
getMat-methods	1.349	0.761	0.462
getPathDescription-methods	2.593	0.538	0.431
getPval-methods	1.332	1.182	0.361
getTissueDegree-methods	1.611	1.321	0.422
getWordcloud-methods	1.439	1.215	0.378
loci2pathResult-class	1.311	1.408	0.344
query-methods	3.640	1.723	0.580
query.gr	0.008	0.013	0.002