Package: chroGPS

Version: 2.2.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chroGPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings chroGPS_2.2.0.tar.gz

StartedAt: 2019-10-16 02:38:48 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:45:14 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 386.0 seconds

RetCode: 0

Status:  OK

CheckDir: chroGPS.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chroGPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings chroGPS_2.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/chroGPS.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chroGPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chroGPS' version '2.2.0'
* 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 'chroGPS' 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
* 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
chisqdist : : no visible global function definition for
  'RleList'
chisqdist :  : : no visible global function
  definition for 'Rle'
Undefined global functions or variables:
  Rle RleList
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
rankFactorsbyProfile 100.45   0.35   100.8
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
rankFactorsbyProfile 88.01   0.17   88.20
procrustesAdj         4.70   0.32    5.02
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'gtools'
* 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/chroGPS.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/chroGPS_2.2.0.tar.gz && rm -rf chroGPS.buildbin-libdir && mkdir chroGPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chroGPS.buildbin-libdir chroGPS_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL chroGPS_2.2.0.zip && rm chroGPS_2.2.0.tar.gz chroGPS_2.2.0.zip
###
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install for i386

* installing *source* package 'chroGPS' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'chroGPS'
    finding HTML links ... done
    addVar                                  html  
    adjustPeaks                             html  
    bg3                                     html  
    boostMDS                                html  
    clusGPS-class                           html  
    clusGPS                                 html  
    combineGenesMatrix                      html  
    diffFactors                             html  
    diffGenes                               html  
    distGPS-class                           html  
    distGPS                                 html  
    domainDist                              html  
    geneSetGPS                              html  
    getURL                                  html  
    gff2RDList                              html  
    gps2xgmml                               html  
    mds-class                               html  
    mds                                     html  
    mergeClusters                           html  
    mergeReplicates                         html  
    procrustesAdj                           html  
    profileClusters                         html  
    rankFactorsbyDomain                     html  
    rankFactorsbyProfile                    html  
    s2                                      html  
    splitDistGPS-class                      html  
** building package indices
** installing vignettes
   'chroGPS.Rnw' 
** 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 'chroGPS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chroGPS' as chroGPS_2.2.0.zip
* DONE (chroGPS)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'chroGPS' successfully unpacked and MD5 sums checked