Package: BiocWorkflowTools

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocWorkflowTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiocWorkflowTools_1.8.0.tar.gz

StartedAt: 2019-04-13 00:48:26 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 00:50:10 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 104.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocWorkflowTools.Rcheck

Warnings: 2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocWorkflowTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiocWorkflowTools_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiocWorkflowTools.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.8.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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
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 ... 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' ... WARNING
Found the following significant warnings:

  Warning: 'create' is deprecated.
  Warning: 'setup' is deprecated.
  Warning: 'create_description' is deprecated.
  Warning: 'use_rstudio' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'create' is deprecated.
  Warning: 'setup' is deprecated.
  Warning: 'create_description' is deprecated.
  Warning: 'use_rstudio' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiocWorkflowTools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/BiocWorkflowTools_1.8.0.tar.gz && rm -rf BiocWorkflowTools.buildbin-libdir && mkdir BiocWorkflowTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocWorkflowTools.buildbin-libdir BiocWorkflowTools_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BiocWorkflowTools_1.8.0.zip && rm BiocWorkflowTools_1.8.0.tar.gz BiocWorkflowTools_1.8.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100  461k  100  461k    0     0  9888k      0 --:--:-- --:--:-- --:--:-- 10.7M

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
In R CMD INSTALL

install for x64

* installing *source* package 'BiocWorkflowTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocWorkflowTools' as BiocWorkflowTools_1.8.0.zip
* DONE (BiocWorkflowTools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BiocWorkflowTools' successfully unpacked and MD5 sums checked
In R CMD INSTALL