Package: chroGPS

Version: 1.27.3

Command: rm -rf chroGPS.buildbin-libdir chroGPS.Rcheck && mkdir chroGPS.buildbin-libdir chroGPS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chroGPS.buildbin-libdir chroGPS_1.27.3.tar.gz >chroGPS.Rcheck\00install.out 2>&1 && cp chroGPS.Rcheck\00install.out chroGPS-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chroGPS.buildbin-libdir --install="check:chroGPS-install.out" --force-multiarch --no-vignettes --timings chroGPS_1.27.3.tar.gz

StartedAt: 2018-04-11 22:53:03 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:56:22 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 198.5 seconds

RetCode: 0

Status:  OK

CheckDir: chroGPS.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf chroGPS.buildbin-libdir chroGPS.Rcheck && mkdir chroGPS.buildbin-libdir chroGPS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chroGPS.buildbin-libdir chroGPS_1.27.3.tar.gz >chroGPS.Rcheck\00install.out 2>&1 && cp chroGPS.Rcheck\00install.out chroGPS-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chroGPS.buildbin-libdir --install="check:chroGPS-install.out" --force-multiarch --no-vignettes --timings chroGPS_1.27.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chroGPS.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.27.3'
* 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
** 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 ... NOTE
Missing or unexported object: 'changepoint::cpt.method'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
avgdistpair: no visible global function definition for '%over%'
chisqdist : <anonymous>: no visible global function definition for
  'RleList'
chisqdist : <anonymous> : <anonymous>: no visible global function
  definition for 'Rle'
chisqdist2: no visible global function definition for 'mclapply'
contour2dDP: no visible binding for global variable 'state'
gff2RDList: no visible global function definition for 'GenomicRanges'
gps2xgmml: no visible global function definition for 'col2hex'
realtanipair: no visible global function definition for '%over%'
uniqueCount: no visible binding for global variable 'u'
xgmml2d: no visible global function definition for 'xmlOutputDOM'
xgmml2d: no visible global function definition for 'saveXML'
xgmml3d: no visible global function definition for 'xmlOutputDOM'
xgmml3d: no visible global function definition for 'saveXML'
gps2xgmml,mds: no visible global function definition for 'col2hex'
plot,mds-ANY: no visible global function definition for 'plot3d'
plot,mds-ANY: no visible global function definition for 'text3d'
plot,mds-ANY: no visible global function definition for 'spheres3d'
Undefined global functions or variables:
  %over% GenomicRanges Rle RleList col2hex mclapply plot3d saveXML
  spheres3d state text3d u xmlOutputDOM
* 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
procrustesAdj 6.66   0.23    6.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
procrustesAdj 6.51   0.12    6.64
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'gplots'
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/chroGPS.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'chroGPS' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'chroGPS'
    finding HTML links ... done
    addVar                                  html  
    adjustPeaks                             html  
    boostMDS                                html  
    clusGPS-class                           html  
    clusGPS                                 html  
    distGPS-class                           html  
    distGPS                                 html  
    domainDist                              html  
    geneSetGPS                              html  
    getURL                                  html  
    gff2RDList                              html  
    gps2xgmml                               html  
    mds-class                               html  
    mds                                     html  
    mergeClusters                           html  
    procrustesAdj                           html  
    profileClusters                         html  
    s2                                      html  
    splitDistGPS-class                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'chroGPS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chroGPS' as chroGPS_1.27.3.zip
* DONE (chroGPS)
In R CMD INSTALL
In R CMD INSTALL