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CHECK report for rgsepd on malbec2

This page was generated on 2019-10-16 12:05:56 -0400 (Wed, 16 Oct 2019).

Package 1370/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rgsepd 1.16.0
Karl Stamm
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/rgsepd
Branch: RELEASE_3_9
Last Commit: 178df72
Last Changed Date: 2019-05-02 11:53:52 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rgsepd
Version: 1.16.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rgsepd.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rgsepd_1.16.0.tar.gz
StartedAt: 2019-10-16 04:31:14 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:39:55 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 520.9 seconds
RetCode: 0
Status:  OK 
CheckDir: rgsepd.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rgsepd.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rgsepd_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rgsepd.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 ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ExtractProjection 79.489  1.601  138.27
* 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


Installation output

rgsepd.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rgsepd
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

Tests output


Example timings

rgsepd.Rcheck/rgsepd-Ex.timings

nameusersystemelapsed
DisplayName0.0040.0000.003
ExtractProjection 79.489 1.601138.270
GSEPD_ChangeConditions0.4640.0000.465
GSEPD_ChangeOutput0.4480.0040.453
GSEPD_DEGHeatmap4.7360.0044.740
GSEPD_Export_DESeq0.3590.0040.363
GSEPD_Heatmap2.0380.0002.038
GSEPD_INIT0.2490.0000.249
GSEPD_PCA_Plot2.0770.0002.077
GSEPD_PCA_Spec2.1510.0042.155
GSEPD_Process0.3310.0000.331
GSEPD_ProcessAll0.4680.0040.472
GSEPD_PullDEG2.0360.0002.036
IlluminaBodymap0.2510.0040.255
IlluminaBodymapMeta0.0070.0000.007
Name_to_RefSeq000
rgsepd-package0.2500.0040.254