Package: BiocWorkflowTools

Version: 1.9.3

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocWorkflowTools.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocWorkflowTools_1.9.3.tar.gz

StartedAt: 2019-04-08 23:03:33 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:03:58 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 25.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocWorkflowTools.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocWorkflowTools.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocWorkflowTools_1.9.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocWorkflowTools.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocWorkflowTools.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BiocWorkflowTools
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘BiocWorkflowTools’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (BiocWorkflowTools)

name	user	system	elapsed
createBiocWorkflow	0.302	0.008	0.581
f1000_article	0	0	0
markdownToLatex	0.000	0.000	0.001
uploadToOverleaf	0.000	0.000	0.001