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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TargetScore.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings TargetScore_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/TargetScore.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TargetScore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TargetScore' version '1.28.0'
* 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 'TargetScore' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqoW0Ip/R.INSTALLcd462fd3816/TargetScore/man/logmvgamma.Rd:44: file link 'lgamma' in package 'base' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/TargetScore.Rcheck/00install.out' for details.
* 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
dot.ext: no visible global function definition for 'size'
getTargetScores: no visible global function definition for
  'get_TargetScanHuman_contextScore'
getTargetScores: no visible global function definition for
  'get_TargetScanHuman_PCT'
getTargetScores: no visible global function definition for
  'get_validated_targets'
getTargetScores: no visible global function definition for
  'get_miRNA_family_info'
getTargetScores: no visible binding for global variable 'logFC.imputed'
getTargetScores : <anonymous>: no visible global function definition
  for 'cor'
getTargetScores: no visible global function definition for 'aggregate'
logmvgamma: no visible global function definition for 'size'
targetScore: no visible global function definition for 'as.roman'
targetScore : <anonymous>: no visible global function definition for
  'as.roman'
targetScore: no visible global function definition for 'sigmoid'
Undefined global functions or variables:
  aggregate as.roman cor get_TargetScanHuman_PCT
  get_TargetScanHuman_contextScore get_miRNA_family_info
  get_validated_targets logFC.imputed sigmoid size
Consider adding
  importFrom("stats", "aggregate", "cor")
  importFrom("utils", "as.roman")
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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/TargetScore.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/TargetScore_1.28.0.tar.gz && rm -rf TargetScore.buildbin-libdir && mkdir TargetScore.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TargetScore.buildbin-libdir TargetScore_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL TargetScore_1.28.0.zip && rm TargetScore_1.28.0.tar.gz TargetScore_1.28.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  420k  100  420k    0     0  16.9M      0 --:--:-- --:--:-- --:--:-- 17.8M

install for i386

* installing *source* package 'TargetScore' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TargetScore'
    finding HTML links ... done
    TargetScore-package                     html  
    bsxfun.se                               html  
    dot.ext                                 html  
    getTargetScores                         html  
    initialization                          html  
    logmvgamma                              html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqoW0Ip/R.INSTALLcd462fd3816/TargetScore/man/logmvgamma.Rd:44: file link 'lgamma' in package 'base' does not exist and so has been treated as a topic
    logsumexp                               html  
    sort_components                         html  
    targetScore                             html  
    vbgmm                                   html  
    vbound                                  html  
    vexp                                    html  
    vmax                                    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 'TargetScore' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TargetScore' as TargetScore_1.28.0.zip
* DONE (TargetScore)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'TargetScore' successfully unpacked and MD5 sums checked