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CHECK report for ChIPsim on merida2

This page was generated on 2018-10-17 08:48:16 -0400 (Wed, 17 Oct 2018).

Package 237/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPsim 1.34.0
Peter Humburg
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ChIPsim
Branch: RELEASE_3_7
Last Commit: e141408
Last Changed Date: 2018-04-30 10:35:11 -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  OK  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: ChIPsim
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPsim.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPsim_1.34.0.tar.gz
StartedAt: 2018-10-16 20:25:26 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:28:40 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 194.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ChIPsim.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPsim.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPsim_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ChIPsim.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPsim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPsim’ version ‘1.34.0’
* 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 ‘ChIPsim’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biostrings’
A package should be listed in only one of these fields.
* 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 ... NOTE
print.SimulatedFeature: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/ChIPsim.Rcheck/00check.log’
for details.



Installation output

ChIPsim.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPsim
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ChIPsim’ ...
** R
** 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 (ChIPsim)

Tests output


Example timings

ChIPsim.Rcheck/ChIPsim-Ex.timings

nameusersystemelapsed
ChIPsim-package0.0010.0000.001
bindDens2readDens2.0020.2292.257
decodeQuality0.0040.0010.004
defaultControl0.0040.0000.005
defaultErrorProb0.0010.0000.002
defaultFunctions0.0060.0010.007
defaultGenerator0.0700.0010.070
extractQuality0.0020.0000.003
feat2dens1.6990.1551.891
featureDensity0.0020.0000.002
makeFeatures0.0900.0060.099
placeFeatures0.0980.0010.100
pos2fastq0.0720.0020.076
readError0.0040.0000.003
reconcileFeatures0.1170.0020.119
sampleReads1.2150.2041.437
simChIP0.0020.0010.002
simpleNames0.0020.0000.002
stableFeature0.0010.0000.001
writeFASTQ0.0040.0000.005