Package: rgsepd

Version: 1.18.0

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_1.18.0.tar.gz

StartedAt: 2020-04-15 05:09:34 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:19:25 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 591.8 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_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/rgsepd.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.18.0’
* 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 105.539  4.568 112.184
GSEPD_DEGHeatmap    5.729  0.080   5.858
* 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	0.004	0.001	0.004
ExtractProjection	105.539	4.568	112.184
GSEPD_ChangeConditions	0.463	0.015	0.479
GSEPD_ChangeOutput	0.448	0.019	0.469
GSEPD_DEGHeatmap	5.729	0.080	5.858
GSEPD_Export_DESeq	0.805	0.017	0.826
GSEPD_Heatmap	3.894	0.060	3.986
GSEPD_INIT	0.516	0.018	0.541
GSEPD_PCA_Plot	3.921	0.055	3.996
GSEPD_PCA_Spec	3.684	0.048	3.759
GSEPD_Process	0.429	0.015	0.445
GSEPD_ProcessAll	0.490	0.021	0.515
GSEPD_PullDEG	3.820	0.063	3.912
IlluminaBodymap	0.472	0.016	0.496
IlluminaBodymapMeta	0.009	0.002	0.010
Name_to_RefSeq	0.000	0.000	0.001
rgsepd-package	0.525	0.018	0.549