Package: deco

Version: 0.99.56

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:deco.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings deco_0.99.56.tar.gz

StartedAt: 2019-04-09 02:10:30 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:15:07 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 276.6 seconds

RetCode: 0

Status:  OK

CheckDir: deco.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:deco.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings deco_0.99.56.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/deco.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 'deco/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'deco' version '0.99.56'
* 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 'deco' 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
plotAssociationH: no visible binding for global variable 'Subclasses'
plotAssociationH: no visible binding for global variable 'h.statistic'
plotAssociationH: no visible binding for global variable 'input.info'
plotAssociationH: no visible binding for global variable
  'DECO.subclasses'
plotAssociationH: no visible binding for global variable 'Samples'
plotAssociationH: no visible binding for global variable 'Features'
plotGainingH: no visible binding for global variable 'omic.data'
plotGainingH: no visible binding for global variable 'h.statistic'
plotGainingH: no visible binding for global variable 'ranking'
Undefined global functions or variables:
  DECO.subclasses Features Samples Subclasses h.statistic input.info
  omic.data ranking
* 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 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/deco.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/deco_0.99.56.tar.gz && rm -rf deco.buildbin-libdir && mkdir deco.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=deco.buildbin-libdir deco_0.99.56.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL deco_0.99.56.zip && rm deco_0.99.56.tar.gz deco_0.99.56.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2485k  100 2485k    0     0  17.2M      0 --:--:-- --:--:-- --:--:-- 18.1M

install for i386

* installing *source* package 'deco' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'deco'
    finding HTML links ... done
    ALCLdata                                html  
    AnnotateDECO                            html  
    NSCAcluster                             html  
    deco-class                              html  
    deco-package                            html  
    decoNSCA                                html  
    decoRDA                                 html  
    decoReport                              html  
    featureTable                            html  
    plotAssociationH                        html  
    plotDECOProfile                         html  
    plotGainingH                            html  
    plotHeatmapH                            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 'deco' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'deco' as deco_0.99.56.zip
* DONE (deco)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'deco' successfully unpacked and MD5 sums checked