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CHECK report for REMP on malbec1

This page was generated on 2019-04-16 11:52:36 -0400 (Tue, 16 Apr 2019).

Package 1289/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REMP 1.6.1
Yinan Zheng
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/REMP
Branch: RELEASE_3_8
Last Commit: 4e47738
Last Changed Date: 2019-01-04 13:46:39 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: REMP
Version: 1.6.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:REMP.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings REMP_1.6.1.tar.gz
StartedAt: 2019-04-16 02:32:16 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:55:12 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 1376.7 seconds
RetCode: 0
Status:  OK 
CheckDir: REMP.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:REMP.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings REMP_1.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/REMP.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘REMP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘REMP’ version ‘1.6.1’
* package encoding: UTF-8
* 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 ‘REMP’ 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
GRannot    20.016  0.512  23.014
remp       12.432  1.248  13.343
remprofile 10.696  0.644  13.023
initREMP    7.628  0.600  10.018
fetchRMSK   6.932  0.372  10.024
grooMethy   7.036  0.128   9.344
getGM12878  5.392  0.280   6.035
* 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

REMP.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL REMP
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘REMP’ ...
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (REMP)

Tests output


Example timings

REMP.Rcheck/REMP-Ex.timings

nameusersystemelapsed
GRannot20.016 0.51223.014
REMParcel-class0.0000.0000.001
REMProduct-class0.0000.0000.002
fetchRMSK 6.932 0.37210.024
fetchRefSeqGene2.9600.1364.932
findRECpG0.9320.3241.262
getBackend0.0881.0361.149
getGM128785.3920.2806.035
grooMethy7.0360.1289.344
initREMP 7.628 0.60010.018
options0.0000.0000.003
remp12.432 1.24813.343
remprofile10.696 0.64413.023