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CHECK report for muscData on riesling1

This page was generated on 2021-01-14 15:59:10 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE muscData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 243/385HostnameOS / ArchINSTALLBUILDCHECK
muscData 1.5.0
Helena L. Crowell
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/muscData
Branch: master
Last Commit: 7badd0c
Last Changed Date: 2020-10-27 10:30:24 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ]

Summary

Package: muscData
Version: 1.5.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:muscData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings muscData_1.5.0.tar.gz
StartedAt: 2021-01-14 11:30:57 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:33:16 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 139.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: muscData.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:muscData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings muscData_1.5.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/muscData.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'muscData/DESCRIPTION' ... OK
* this is package 'muscData' version '1.5.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
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 'muscData' 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
Package in Depends field not imported from: 'SingleCellExperiment'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ... WARNING
Undocumented code objects:
  'Crowell19_4vs4'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
Kang18_8vs8 5.39   0.91    6.78
* 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, 2 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/muscData.Rcheck/00check.log'
for details.



Installation output

muscData.Rcheck/00install.out

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch muscData
###
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* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
* installing *source* package 'muscData' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'muscData'
    finding HTML links ... done
    Kang18_8vs8                             html  
REDIRECT:topic	 Kang18 -> Kang18_8vs8.html [ SUCCESS ]
REDIRECT:topic	 Kang18_8vs8 -> Kang18_8vs8.html [ SUCCESS ]
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2021-01-14
** testing if installed package can be loaded from final location
snapshotDate(): 2021-01-14
** testing if installed package keeps a record of temporary installation path
* DONE (muscData)
Making 'packages.html' ... done

Tests output


Example timings

muscData.Rcheck/muscData-Ex.timings

nameusersystemelapsed
Kang18_8vs85.390.916.78