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CHECK report for motifbreakR on malbec2

This page was generated on 2018-10-17 08:28:00 -0400 (Wed, 17 Oct 2018).

Package 938/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifbreakR 1.10.0
Simon Gert Coetzee
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/motifbreakR
Branch: RELEASE_3_7
Last Commit: fe4d25a
Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: motifbreakR
Version: 1.10.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings motifbreakR_1.10.0.tar.gz
StartedAt: 2018-10-16 02:08:10 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:13:56 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 346.1 seconds
RetCode: 0
Status:  OK 
CheckDir: motifbreakR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings motifbreakR_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/motifbreakR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifbreakR/DESCRIPTION’ ... OK
* this is package ‘motifbreakR’ version ‘1.10.0’
* 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 ‘motifbreakR’ 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 ... NOTE
Packages in Depends field not imported from:
  'MotifDb' 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotMotifLogoStack.2: no visible global function definition for 'par'
snps.from.file: no visible global function definition for 'info'
snps.from.file: no visible global function definition for 'rowRanges'
snps.from.rsid: no visible global function definition for 'snpsById'
Undefined global functions or variables:
  info par rowRanges snpsById
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
* 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
snps.from.rsid 48.144  1.044  49.372
motifbreakR     6.252  0.120   6.389
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/motifbreakR.Rcheck/00check.log’
for details.



Installation output

motifbreakR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL motifbreakR
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘motifbreakR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
See system.file("LICENSE", package="MotifDb") for use restrictions.
* DONE (motifbreakR)

Tests output


Example timings

motifbreakR.Rcheck/motifbreakR-Ex.timings

nameusersystemelapsed
calculatePvalue0.2280.0080.233
encodemotif0.0280.0000.028
example.results0.0800.0040.082
factorbook0.0080.0000.007
hocomoco0.0080.0040.010
homer0.0080.0000.010
motifbreakR6.2520.1206.389
motifbreakR_motif0.0320.0000.030
plotMB0.0560.0000.056
snps.from.file0.5320.0080.715
snps.from.rsid48.144 1.04449.372