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CHECK report for pcxnData on malbec2

This page was generated on 2021-01-14 15:59:04 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE pcxnData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 261/385HostnameOS / ArchINSTALLBUILDCHECK
pcxnData 2.13.0
Sokratis Kariotis
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/pcxnData
Branch: master
Last Commit: bc0ba62
Last Changed Date: 2020-10-27 10:24:20 -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: pcxnData
Version: 2.13.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:pcxnData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings pcxnData_2.13.0.tar.gz
StartedAt: 2021-01-14 12:33:49 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 12:34:19 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 30.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: pcxnData.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:pcxnData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings pcxnData_2.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/pcxnData.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 ‘pcxnData/DESCRIPTION’ ... OK
* this is package ‘pcxnData’ version ‘2.13.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  .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 ‘pcxnData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 40.4Mb
  sub-directories of 1Mb or more:
    data  40.3Mb
* 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 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 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 contents of ‘data’ directory ... WARNING
File ‘data/datalist’ contains malformed line(s):
  ‘cp_gs_v5.1:cp_gs_v5.1’ ‘gobp_gs_v5.1:gobp_gs_v5.1’
  ‘h_gs_v5.1:h_gs_v5.1’ ‘pathprint.Hs.gs:pathprint.Hs.gs’
  ‘pathCor_CPv5.1_dframe:pathCor_CPv5.1_dframe’
  ‘pathCor_GOBPv5.1_dframe:pathCor_GOBPv5.1_dframe’
  ‘pathCor_Hv5.1_dframe:pathCor_Hv5.1_dframe’
  ‘pathCor_pathprint_v1.2.3_dframe:pathCor_pathprint_v1.2.3_dframe’
  ‘pathCor_CPv5.1_unadjusted_dframe:pathCor_CPv5.1_unadjusted_dframe’
  ‘pathCor_GOBPv5.1_unadjusted_dframe:pathCor_GOBPv5.1_unadjusted_dframe’
  ‘pathCor_Hv5.1_unadjusted_dframe:pathCor_Hv5.1_unadjusted_dframe’
  ‘pathCor_pathprint_v1.2.3_unadjusted_dframe:pathCor_pathprint_v1.2.3_unadjusted_dframe’
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/pcxnData.Rcheck/00check.log’
for details.



Installation output

pcxnData.Rcheck/00install.out

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

Tests output


Example timings

pcxnData.Rcheck/pcxnData-Ex.timings

nameusersystemelapsed
pcxnData3.8740.0763.951