Package: rgsepd

Version: 1.16.0

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_1.16.0.tar.gz

StartedAt: 2019-10-16 06:14:34 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:26:50 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 736.7 seconds

RetCode: 0

Status:  OK

CheckDir: rgsepd.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:rgsepd.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rgsepd_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/rgsepd.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.16.0’
* 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
ExtractProjection 127.633  8.141 139.030
GSEPD_DEGHeatmap    6.217  0.119   6.341
* 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 rgsepd
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘rgsepd’ ...
** 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
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
** testing if installed package can be loaded from final location
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
** testing if installed package keeps a record of temporary installation path
* DONE (rgsepd)

name	user	system	elapsed
DisplayName	0.008	0.000	0.008
ExtractProjection	127.633	8.141	139.030
GSEPD_ChangeConditions	0.581	0.030	0.613
GSEPD_ChangeOutput	0.616	0.041	0.657
GSEPD_DEGHeatmap	6.217	0.119	6.341
GSEPD_Export_DESeq	0.658	0.031	0.690
GSEPD_Heatmap	4.073	0.077	4.151
GSEPD_INIT	0.530	0.036	0.567
GSEPD_PCA_Plot	4.042	0.103	4.148
GSEPD_PCA_Spec	4.220	0.081	4.303
GSEPD_Process	0.556	0.035	0.592
GSEPD_ProcessAll	0.518	0.035	0.553
GSEPD_PullDEG	4.034	0.101	4.136
IlluminaBodymap	0.572	0.030	0.602
IlluminaBodymapMeta	0.017	0.006	0.023
Name_to_RefSeq	0.001	0.001	0.002
rgsepd-package	0.608	0.036	0.644