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CHECK report for BiocWorkflowTools on tokay1

This page was generated on 2020-08-06 12:03:29 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BiocWorkflowTools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 165/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocWorkflowTools 1.15.0
Mike Smith
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/BiocWorkflowTools
Branch: master
Last Commit: 69240d4
Last Changed Date: 2020-04-27 15:01:39 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocWorkflowTools
Version: 1.15.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocWorkflowTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiocWorkflowTools_1.15.0.tar.gz
StartedAt: 2020-08-06 03:24:29 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 03:25:05 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 35.8 seconds
RetCode: 0
Status:  OK  
CheckDir: BiocWorkflowTools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocWorkflowTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiocWorkflowTools_1.15.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiocWorkflowTools.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.15.0'
* 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: 'knitr'
  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 ... 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
** 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiocWorkflowTools.Rcheck/00check.log'
for details.



Installation output

BiocWorkflowTools.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BiocWorkflowTools_1.15.0.tar.gz && rm -rf BiocWorkflowTools.buildbin-libdir && mkdir BiocWorkflowTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocWorkflowTools.buildbin-libdir BiocWorkflowTools_1.15.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BiocWorkflowTools_1.15.0.zip && rm BiocWorkflowTools_1.15.0.tar.gz BiocWorkflowTools_1.15.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  456k  100  456k    0     0  9847k      0 --:--:-- --:--:-- --:--:-- 10.3M

install for i386

* installing *source* package 'BiocWorkflowTools' ...
** using staged installation
** 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  
    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_1.15.0.zip
* DONE (BiocWorkflowTools)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BiocWorkflowTools' successfully unpacked and MD5 sums checked

Tests output


Example timings

BiocWorkflowTools.Rcheck/examples_i386/BiocWorkflowTools-Ex.timings

nameusersystemelapsed
createBiocWorkflow0.940.101.14
f1000_article000
uploadToOverleaf000

BiocWorkflowTools.Rcheck/examples_x64/BiocWorkflowTools-Ex.timings

nameusersystemelapsed
createBiocWorkflow0.970.111.14
f1000_article000
uploadToOverleaf000