BioC 3.5: CHECK report for pvca on tokay2

Package: pvca

Version: 1.16.0

Command: rm -rf pvca.buildbin-libdir pvca.Rcheck && mkdir pvca.buildbin-libdir pvca.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pvca.buildbin-libdir pvca_1.16.0.tar.gz >pvca.Rcheck\00install.out 2>&1 && cp pvca.Rcheck\00install.out pvca-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=pvca.buildbin-libdir --install="check:pvca-install.out" --force-multiarch --no-vignettes --timings pvca_1.16.0.tar.gz

StartedAt: 2017-08-16 02:07:13 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:09:36 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 142.0 seconds

RetCode: 0

Status:  OK

CheckDir: pvca.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf pvca.buildbin-libdir pvca.Rcheck && mkdir pvca.buildbin-libdir pvca.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pvca.buildbin-libdir pvca_1.16.0.tar.gz >pvca.Rcheck\00install.out 2>&1 && cp pvca.Rcheck\00install.out pvca-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=pvca.buildbin-libdir --install="check:pvca-install.out" --force-multiarch --no-vignettes --timings pvca_1.16.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/pvca.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pvca/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pvca' 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 'pvca' can be installed ... OK
* 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
pvcaBatchAssess: no visible global function definition for 'cor'
pvcaBatchAssess: no visible binding for global variable 'na.omit'
Undefined global functions or variables:
  cor na.omit
Consider adding
  importFrom("stats", "cor", "na.omit")
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
Examples with CPU or elapsed time > 5s
                 user system elapsed
pvcaBatchAssess 10.53   0.22   10.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
pvcaBatchAssess 11.5   0.06   11.56
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/pvca.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'pvca' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'pvca' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pvca' as pvca_1.16.0.zip
* DONE (pvca)

name	user	system	elapsed
pvcaBatchAssess	10.53	0.22	10.75

name	user	system	elapsed
pvcaBatchAssess	11.50	0.06	11.56