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CHECK report for rgsepd on malbec2

This page was generated on 2020-10-17 11:55:34 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE rgsepd PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1480/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rgsepd 1.20.2
Karl Stamm
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/rgsepd
Branch: RELEASE_3_11
Last Commit: ee961a0
Last Changed Date: 2020-06-04 10:25:45 -0400 (Thu, 04 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rgsepd
Version: 1.20.2
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:rgsepd.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings rgsepd_1.20.2.tar.gz
StartedAt: 2020-10-17 04:46:42 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:55:42 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 539.8 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-3.11-bioc/R/bin/R CMD check --install=check:rgsepd.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings rgsepd_1.20.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/rgsepd.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.20.2’
* 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 (user + system) or elapsed time > 5s
                   user system elapsed
ExtractProjection 83.59   1.54   92.23
* 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-3.11-bioc/R/bin/R CMD INSTALL rgsepd
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* installing to library ‘/home/biocbuild/bbs-3.11-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
DisplayName0.0050.0000.005
ExtractProjection83.59 1.5492.23
GSEPD_ChangeConditions0.2950.0000.296
GSEPD_ChangeOutput0.2990.0040.303
GSEPD_DEGHeatmap4.6150.0004.616
GSEPD_Export_DESeq0.5540.0000.554
GSEPD_Heatmap2.8350.0042.839
GSEPD_INIT0.2820.0000.282
GSEPD_PCA_Plot3.3720.0003.381
GSEPD_PCA_Spec3.510.003.51
GSEPD_Process0.2910.0000.291
GSEPD_ProcessAll0.3100.0000.311
GSEPD_PullDEG3.0880.0003.088
IlluminaBodymap0.2890.0000.290
IlluminaBodymapMeta0.0090.0000.008
Name_to_RefSeq0.0010.0000.000
rgsepd-package0.2840.0000.283