Package: rgsepd

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rgsepd.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rgsepd_1.12.0.tar.gz

StartedAt: 2018-10-16 23:41:21 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:50:23 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 542.7 seconds

RetCode: 0

Status:  OK

CheckDir: rgsepd.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rgsepd.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rgsepd_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/rgsepd.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rgsepd/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rgsepd’ version ‘1.12.0’
* 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 ‘rgsepd’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
GSEPD_DEGHeatmap 126.676  5.024 136.371
* 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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rgsepd
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘rgsepd’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
* DONE (rgsepd)

name	user	system	elapsed
DisplayName	0.004	0.000	0.004
GSEPD_ChangeConditions	0.481	0.024	0.508
GSEPD_ChangeOutput	0.486	0.020	0.509
GSEPD_DEGHeatmap	126.676	5.024	136.371
GSEPD_Export_DESeq	0.505	0.014	0.519
GSEPD_Heatmap	2.007	0.040	2.052
GSEPD_INIT	0.343	0.012	0.357
GSEPD_PCA_Plot	2.298	0.036	2.342
GSEPD_PCA_Spec	2.311	0.031	2.348
GSEPD_Process	0.374	0.015	0.390
GSEPD_ProcessAll	0.436	0.020	0.458
GSEPD_PullDEG	2.296	0.038	2.339
IlluminaBodymap	0.347	0.011	0.357
IlluminaBodymapMeta	0.009	0.002	0.010
Name_to_RefSeq	0.001	0.000	0.001
rgsepd-package	0.498	0.025	0.527