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BioC 3.6: CHECK report for ChIPsim on tokay1

This page was generated on 2017-08-16 13:28:36 -0400 (Wed, 16 Aug 2017).

Package 215/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPsim 1.31.0
Peter Humburg
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPsim
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 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: ChIPsim
Version: 1.31.0
Command: rm -rf ChIPsim.buildbin-libdir ChIPsim.Rcheck && mkdir ChIPsim.buildbin-libdir ChIPsim.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPsim.buildbin-libdir ChIPsim_1.31.0.tar.gz >ChIPsim.Rcheck\00install.out 2>&1 && cp ChIPsim.Rcheck\00install.out ChIPsim-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ChIPsim.buildbin-libdir --install="check:ChIPsim-install.out" --force-multiarch --no-vignettes --timings ChIPsim_1.31.0.tar.gz
StartedAt: 2017-08-15 22:21:50 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:26:25 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 275.4 seconds
RetCode: 0
Status:  OK  
CheckDir: ChIPsim.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ChIPsim.buildbin-libdir ChIPsim.Rcheck && mkdir ChIPsim.buildbin-libdir ChIPsim.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPsim.buildbin-libdir ChIPsim_1.31.0.tar.gz >ChIPsim.Rcheck\00install.out 2>&1 && cp ChIPsim.Rcheck\00install.out ChIPsim-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ChIPsim.buildbin-libdir --install="check:ChIPsim-install.out" --force-multiarch --no-vignettes --timings ChIPsim_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPsim.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPsim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPsim' version '1.31.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/ChIPsim.Rcheck/00check.log'
for details.


ChIPsim.Rcheck/00install.out:


install for i386

* installing *source* package 'ChIPsim' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'ChIPsim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPsim' as ChIPsim_1.31.0.zip
* DONE (ChIPsim)

ChIPsim.Rcheck/examples_i386/ChIPsim-Ex.timings:

nameusersystemelapsed
ChIPsim-package000
bindDens2readDens1.880.041.91
decodeQuality0.020.000.01
defaultControl000
defaultErrorProb000
defaultFunctions000
defaultGenerator0.030.000.03
extractQuality000
feat2dens1.410.011.43
featureDensity000
makeFeatures0.040.000.04
placeFeatures0.060.000.06
pos2fastq0.10.00.1
readError000
reconcileFeatures0.120.000.12
sampleReads1.440.001.44
simChIP000
simpleNames000
stableFeature000
writeFASTQ000

ChIPsim.Rcheck/examples_x64/ChIPsim-Ex.timings:

nameusersystemelapsed
ChIPsim-package000
bindDens2readDens1.560.031.59
decodeQuality000
defaultControl0.020.000.01
defaultErrorProb000
defaultFunctions000
defaultGenerator0.050.000.05
extractQuality000
feat2dens1.560.001.56
featureDensity000
makeFeatures0.060.000.06
placeFeatures0.070.000.06
pos2fastq0.090.000.10
readError000
reconcileFeatures0.080.000.08
sampleReads1.290.021.31
simChIP000
simpleNames000
stableFeature000
writeFASTQ000