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CHECK report for REMP on malbec1

This page was generated on 2018-04-12 13:15:54 -0400 (Thu, 12 Apr 2018).

Package 1158/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REMP 1.2.5
Yinan Zheng
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/REMP
Branch: RELEASE_3_6
Last Commit: e2dcb7b
Last Changed Date: 2017-12-01 18:41:57 -0400 (Fri, 01 Dec 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: REMP
Version: 1.2.5
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings REMP_1.2.5.tar.gz
StartedAt: 2018-04-12 02:18:58 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:42:17 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 1399.2 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-3.6-bioc/R/bin/R CMD check --no-vignettes --timings REMP_1.2.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/REMP.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.2.5’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
GRannot         14.676  0.288  16.364
remp            11.548  0.784  12.087
initREMP        11.348  0.648  13.771
remprofile      10.084  0.604  12.704
fetchRMSK        6.428  0.336   8.716
grooMethy        6.248  0.064   8.378
fetchRefSeqGene  3.248  0.080   5.332
* 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

* installing *source* package ‘REMP’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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
GRannot14.676 0.28816.364
REMParcel-class0.0000.0000.001
REMProduct-class0.0000.0000.002
fetchRMSK6.4280.3368.716
fetchRefSeqGene3.2480.0805.332
findRECpG2.1640.2962.487
getBackend0.9240.6921.648
getGM128783.0360.2283.585
grooMethy6.2480.0648.378
initREMP11.348 0.64813.771
options0.0000.0000.002
remp11.548 0.78412.087
remprofile10.084 0.60412.704