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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:divergence.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings divergence_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/divergence.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'divergence/DESCRIPTION' ... OK
* this is package 'divergence' version '1.10.0'
* package encoding: UTF-8
* 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 'divergence' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
check_SE: no visible binding for global variable 'data'
computeSingleFeaturesetBinaryVector: no visible global function
  definition for 'dist'
computeSingleFeaturesetSupport: no visible global function definition
  for 'dist'
computeSingleFeaturesetSupport: no visible global function definition
  for 'quantile'
computeSingleRange: no visible global function definition for
  'quantile'
getRangesBySections: no visible global function definition for
  'detectCores'
rowChiSq: no visible global function definition for 'chisq.test'
rowChiSq: no visible global function definition for 'xtabs'
Undefined global functions or variables:
  chisq.test data detectCores dist quantile xtabs
Consider adding
  importFrom("stats", "chisq.test", "dist", "quantile", "xtabs")
  importFrom("utils", "data")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
computeChiSquaredTest          14.22   0.18   14.39
computeUnivariateDigitization  13.96   0.11   14.07
findUnivariateGammaWithSupport 12.93   0.03   12.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
computeChiSquaredTest          16.14   0.06   16.20
computeUnivariateDigitization  15.39   0.05   15.44
findUnivariateGammaWithSupport 14.75   0.00   14.75
* 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-3.14-bioc/meat/divergence.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/divergence_1.10.0.tar.gz && rm -rf divergence.buildbin-libdir && mkdir divergence.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=divergence.buildbin-libdir divergence_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL divergence_1.10.0.zip && rm divergence_1.10.0.tar.gz divergence_1.10.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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 13 1917k   13  262k    0     0   735k      0  0:00:02 --:--:--  0:00:02  734k
100 1917k  100 1917k    0     0  1415k      0  0:00:01  0:00:01 --:--:-- 1415k
100 1917k  100 1917k    0     0  1415k      0  0:00:01  0:00:01 --:--:-- 1415k

install for i386

* installing *source* package 'divergence' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'divergence'
    finding HTML links ... done
    breastTCGA_ER                           html  
    breastTCGA_Group                        html  
    breastTCGA_Mat                          html  
    computeChiSquaredTest                   html  
    computeMultivariateBinaryMatrix         html  
    computeMultivariateDigitization         html  
    computeMultivariateSupport              html  
    computeQuantileMatrix                   html  
    computeUnivariateDigitization           html  
    computeUnivariateSupport                html  
    computeUnivariateTernaryMatrix          html  
    findMultivariateGammaWithSupport        html  
    findUnivariateGammaWithSupport          html  
    msigdb_Hallmarks                        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 'divergence' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'divergence' as divergence_1.10.0.zip
* DONE (divergence)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'divergence' successfully unpacked and MD5 sums checked