Package: pvac

Version: 1.26.0

Command: rm -rf pvac.buildbin-libdir pvac.Rcheck && mkdir pvac.buildbin-libdir pvac.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pvac.buildbin-libdir pvac_1.26.0.tar.gz >pvac.Rcheck\00install.out 2>&1 && cp pvac.Rcheck\00install.out pvac-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=pvac.buildbin-libdir --install="check:pvac-install.out" --force-multiarch --no-vignettes --timings pvac_1.26.0.tar.gz

StartedAt: 2018-04-12 02:20:08 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:21:23 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 74.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pvac.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf pvac.buildbin-libdir pvac.Rcheck && mkdir pvac.buildbin-libdir pvac.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pvac.buildbin-libdir pvac_1.26.0.tar.gz >pvac.Rcheck\00install.out 2>&1 && cp pvac.Rcheck\00install.out pvac-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=pvac.buildbin-libdir --install="check:pvac-install.out" --force-multiarch --no-vignettes --timings pvac_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/pvac.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 'pvac/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pvac' version '1.26.0'
* 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 'pvac' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpO0tg2C/R.INSTALL377c14425e71/pvac/man/pvacFilter.Rd:16: missing file link 'ReadAffy'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/pvac.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 ... NOTE
'library' or 'require' call to 'pbapply' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
pvacFilter: no visible global function definition for 'sampleNames'
pvacFilter: no visible global function definition for 'pbsapply'
Undefined global functions or variables:
  pbsapply sampleNames
* 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
Examples with CPU or elapsed time > 5s
            user system elapsed
pvacFilter 12.04   0.22   12.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
pvacFilter 14.28   0.28   14.56
* 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/pvac.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'pvac' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'pvac'
    finding HTML links ... done
    pvacFilter                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpO0tg2C/R.INSTALL377c14425e71/pvac/man/pvacFilter.Rd:16: missing file link 'ReadAffy'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'pvac' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pvac' as pvac_1.26.0.zip
* DONE (pvac)
In R CMD INSTALL
In R CMD INSTALL