Package: ChIPsim

Version: 1.37.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPsim.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChIPsim_1.37.0.tar.gz

StartedAt: 2019-04-09 01:43:51 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:47:57 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 246.1 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPsim.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChIPsim.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ChIPsim_1.37.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ChIPsim.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.37.0'
* 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
* 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 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 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-3.9-bioc/meat/ChIPsim.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ChIPsim_1.37.0.tar.gz && rm -rf ChIPsim.buildbin-libdir && mkdir ChIPsim.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChIPsim.buildbin-libdir ChIPsim_1.37.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ChIPsim_1.37.0.zip && rm ChIPsim_1.37.0.tar.gz ChIPsim_1.37.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 39323  100 39323    0     0   253k      0 --:--:-- --:--:-- --:--:--  264k

install for i386

* installing *source* package 'ChIPsim' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ChIPsim'
    finding HTML links ... done
    ChIPsim-package                         html  
    bindDens2readDens                       html  
    decodeQuality                           html  
    defaultControl                          html  
    defaultErrorProb                        html  
    defaultFunctions                        html  
    defaultGenerator                        html  
    distDens                                html  
    extractQuality                          html  
    feat2dens                               html  
    featureDensity                          html  
    internal                                html  
    joinRegion                              html  
    makeFeatures                            html  
    placeFeatures                           html  
    pos2fastq                               html  
    readError                               html  
    readQualitySample                       html  
    readSequence                            html  
    reconcileFeatures                       html  
    sampleReads                             html  
    simChIP                                 html  
    simpleNames                             html  
    stableFeature                           html  
    writeFASTQ                              html  
    writeReads                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ChIPsim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChIPsim' as ChIPsim_1.37.0.zip
* DONE (ChIPsim)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ChIPsim' successfully unpacked and MD5 sums checked