BioC 3.6: CHECK report for BiocCheck on tokay1

Package: BiocCheck

Version: 1.13.1

Command: rm -rf BiocCheck.buildbin-libdir BiocCheck.Rcheck && mkdir BiocCheck.buildbin-libdir BiocCheck.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocCheck.buildbin-libdir BiocCheck_1.13.1.tar.gz >BiocCheck.Rcheck\00install.out 2>&1 && cp BiocCheck.Rcheck\00install.out BiocCheck-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BiocCheck.buildbin-libdir --install="check:BiocCheck-install.out" --force-multiarch --no-vignettes --timings BiocCheck_1.13.1.tar.gz

StartedAt: 2017-08-15 21:58:24 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:00:50 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 145.7 seconds

RetCode: 0

Status:  OK

CheckDir: BiocCheck.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf BiocCheck.buildbin-libdir BiocCheck.Rcheck && mkdir BiocCheck.buildbin-libdir BiocCheck.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocCheck.buildbin-libdir BiocCheck_1.13.1.tar.gz >BiocCheck.Rcheck\00install.out 2>&1 && cp BiocCheck.Rcheck\00install.out BiocCheck-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BiocCheck.buildbin-libdir --install="check:BiocCheck-install.out" --force-multiarch --no-vignettes --timings BiocCheck_1.13.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BiocCheck.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 'BiocCheck/DESCRIPTION' ... OK
* this is package 'BiocCheck' version '1.13.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'codetoolsBioC'
* 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 'BiocCheck' 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
* 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
Unexported objects imported by ':::' calls:
  'knitr:::detect_pattern' 'tools:::RdTags'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
checkValidDevelopmentURL: no visible global function definition for
  'url.exists'
Undefined global functions or variables:
  url.exists
* 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
BiocCheck 4.57   0.11    5.82
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BiocCheck.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'BiocCheck' ...
** 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 'BiocCheck' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocCheck' as BiocCheck_1.13.1.zip
* DONE (BiocCheck)

name	user	system	elapsed
BiocCheck	4.57	0.11	5.82

name	user	system	elapsed
BiocCheck	3.39	0.11	4.50