Package: GenomicScores

Version: 1.2.2

Command: rm -rf GenomicScores.buildbin-libdir GenomicScores.Rcheck && mkdir GenomicScores.buildbin-libdir GenomicScores.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicScores.buildbin-libdir GenomicScores_1.2.2.tar.gz >GenomicScores.Rcheck\00install.out 2>&1 && cp GenomicScores.Rcheck\00install.out GenomicScores-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicScores.buildbin-libdir --install="check:GenomicScores-install.out" --force-multiarch --no-vignettes --timings GenomicScores_1.2.2.tar.gz

StartedAt: 2018-04-12 00:18:44 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:23:45 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 300.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GenomicScores.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf GenomicScores.buildbin-libdir GenomicScores.Rcheck && mkdir GenomicScores.buildbin-libdir GenomicScores.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicScores.buildbin-libdir GenomicScores_1.2.2.tar.gz >GenomicScores.Rcheck\00install.out 2>&1 && cp GenomicScores.Rcheck\00install.out GenomicScores-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicScores.buildbin-libdir --install="check:GenomicScores-install.out" --force-multiarch --no-vignettes --timings GenomicScores_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicScores.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 'GenomicScores/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicScores' version '1.2.2'
* 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 ... NOTE
Found the following hidden files and directories:
  inst/gscores-template/inst/extdata/.gitkeep
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'GenomicScores' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpikOQQ6/R.INSTALL18e4141e5146/GenomicScores/man/GScores-class.Rd:176: missing file link 'phastCons100way.UCSC.hg19'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpikOQQ6/R.INSTALL18e4141e5146/GenomicScores/man/scores.Rd:62: missing file link 'phastCons100way.UCSC.hg19'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicScores.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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'phastCons100way.UCSC.hg38'
* 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
Examples with CPU or elapsed time > 5s
              user system elapsed
GScores-class 4.59    0.3    9.85
** 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicScores.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GenomicScores' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicScores'
    finding HTML links ... done
    GScores-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpikOQQ6/R.INSTALL18e4141e5146/GenomicScores/man/GScores-class.Rd:176: missing file link 'phastCons100way.UCSC.hg19'
    MafDb-class                             html  
    scores                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpikOQQ6/R.INSTALL18e4141e5146/GenomicScores/man/scores.Rd:62: missing file link 'phastCons100way.UCSC.hg19'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GenomicScores' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicScores' as GenomicScores_1.2.2.zip
* DONE (GenomicScores)
In R CMD INSTALL
In R CMD INSTALL