Package: BiocWorkflowTools

Version: 1.9.3

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocWorkflowTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BiocWorkflowTools_1.9.3.tar.gz

StartedAt: 2019-04-09 01:22:24 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:23:06 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 42.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocWorkflowTools.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:BiocWorkflowTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BiocWorkflowTools_1.9.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BiocWorkflowTools.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocWorkflowTools/DESCRIPTION' ... OK
* this is package 'BiocWorkflowTools' version '1.9.3'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'BiocWorkflowTools' 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
Namespace in Imports field not imported from: 'devtools'
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  'BiocStyle:::auth_affil_latex' 'BiocStyle:::modifyLines'
  'rmarkdown:::partition_yaml_front_matter'
  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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'createBiocWorkflow':
createBiocWorkflow
  Code: function(path, description = getOption("devtools.desc"),
                 rstudio = TRUE, open = rstudio)
  Docs: function(path, description = getOption("devtools.desc"),
                 rstudio = TRUE, ..., open = rstudio)
  Argument names in docs not in code:
    ...
  Mismatches in argument names:
    Position: 4 Code: open Docs: ...

* 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
** 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/BiocWorkflowTools.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/BiocWorkflowTools_1.9.3.tar.gz && rm -rf BiocWorkflowTools.buildbin-libdir && mkdir BiocWorkflowTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocWorkflowTools.buildbin-libdir BiocWorkflowTools_1.9.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL BiocWorkflowTools_1.9.3.zip && rm BiocWorkflowTools_1.9.3.tar.gz BiocWorkflowTools_1.9.3.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100  460k  100  460k    0     0  3596k      0 --:--:-- --:--:-- --:--:-- 3807k

install for i386

* installing *source* package 'BiocWorkflowTools' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocWorkflowTools'
    finding HTML links ... done
    createBiocWorkflow                      html  
    finding level-2 HTML links ... done

    f1000_article                           html  
    markdownToLatex                         html  
    uploadToOverleaf                        html  
** 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 'BiocWorkflowTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocWorkflowTools' as BiocWorkflowTools_1.9.3.zip
* DONE (BiocWorkflowTools)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'BiocWorkflowTools' successfully unpacked and MD5 sums checked