Package: pvac

Version: 1.32.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pvac.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pvac_1.32.0.tar.gz

StartedAt: 2019-10-16 06:13:15 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:14:33 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 78.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pvac.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pvac.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pvac_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/pvac.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.32.0'
* 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-3.9-bioc/tmpdir/Rtmp4W0bk6/R.INSTALL14c047533761/pvac/man/pvacFilter.Rd:16: file link 'ReadAffy' in package 'affy' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
pvacFilter 17.78   0.51    18.3
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
pvacFilter 13.2   0.26   13.47
* 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-3.9-bioc/meat/pvac.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/pvac_1.32.0.tar.gz && rm -rf pvac.buildbin-libdir && mkdir pvac.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pvac.buildbin-libdir pvac_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL pvac_1.32.0.zip && rm pvac_1.32.0.tar.gz pvac_1.32.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 16149  100 16149    0     0  86327      0 --:--:-- --:--:-- --:--:-- 89716

install for i386

* installing *source* package 'pvac' ...
** using staged installation
** R
** byte-compile and prepare 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-3.9-bioc/tmpdir/Rtmp4W0bk6/R.INSTALL14c047533761/pvac/man/pvacFilter.Rd:16: file link 'ReadAffy' in package 'affy' does not exist and so has been treated as a topic
** 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 'pvac' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pvac' as pvac_1.32.0.zip
* DONE (pvac)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'pvac' successfully unpacked and MD5 sums checked