Package: TargetScore

Version: 1.16.0

Command: rm -rf TargetScore.buildbin-libdir TargetScore.Rcheck && mkdir TargetScore.buildbin-libdir TargetScore.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TargetScore.buildbin-libdir TargetScore_1.16.0.tar.gz >TargetScore.Rcheck\00install.out 2>&1 && cp TargetScore.Rcheck\00install.out TargetScore-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TargetScore.buildbin-libdir --install="check:TargetScore-install.out" --force-multiarch --no-vignettes --timings TargetScore_1.16.0.tar.gz

StartedAt: 2018-04-12 03:32:28 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:33:31 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 63.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TargetScore.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf TargetScore.buildbin-libdir TargetScore.Rcheck && mkdir TargetScore.buildbin-libdir TargetScore.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TargetScore.buildbin-libdir TargetScore_1.16.0.tar.gz >TargetScore.Rcheck\00install.out 2>&1 && cp TargetScore.Rcheck\00install.out TargetScore-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TargetScore.buildbin-libdir --install="check:TargetScore-install.out" --force-multiarch --no-vignettes --timings TargetScore_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TargetScore.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 'TargetScore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TargetScore' version '1.16.0'
* 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-3.6-bioc/tmpdir/RtmpQZ7gcd/R.INSTALL3fc0722d74ca/TargetScore/man/logmvgamma.Rd:44: missing file link 'lgamma'
See 'C:/Users/biocbuild/bbs-3.6-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
** 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 ... 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 installed files from 'inst/doc' ... 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-3.6-bioc/meat/TargetScore.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'TargetScore' ...
** R
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpQZ7gcd/R.INSTALL3fc0722d74ca/TargetScore/man/logmvgamma.Rd:44: missing file link 'lgamma'
    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
In R CMD INSTALL

install for x64

* installing *source* package 'TargetScore' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TargetScore' as TargetScore_1.16.0.zip
* DONE (TargetScore)
In R CMD INSTALL
In R CMD INSTALL