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CHECK report for alpineData on malbec2

This page was generated on 2021-01-21 16:01:01 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE alpineData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 13/386HostnameOS / ArchINSTALLBUILDCHECK
alpineData 1.17.0
Michael Love
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/alpineData
Branch: master
Last Commit: e1c33cf
Last Changed Date: 2020-10-27 10:21:31 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK 

Summary

Package: alpineData
Version: 1.17.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:alpineData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings alpineData_1.17.0.tar.gz
StartedAt: 2021-01-21 11:39:38 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:42:07 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 148.3 seconds
RetCode: 0
Status:  OK 
CheckDir: alpineData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:alpineData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings alpineData_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/alpineData.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alpineData/DESCRIPTION’ ... OK
* this is package ‘alpineData’ version ‘1.17.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘alpineData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicAlignments’
A package should be listed in only one of these fields.
* 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: ‘GenomicAlignments’
  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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
alpineData-package 5.517  0.256   7.129
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/alpineData.Rcheck/00check.log’
for details.



Installation output

alpineData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL alpineData
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘alpineData’ ...
** 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 (alpineData)

Tests output


Example timings

alpineData.Rcheck/alpineData-Ex.timings

nameusersystemelapsed
alpineData-package5.5170.2567.129