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CHECK report for EatonEtAlChIPseq on malbec2

This page was generated on 2021-01-11 15:59:21 -0500 (Mon, 11 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE EatonEtAlChIPseq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 108/385HostnameOS / ArchINSTALLBUILDCHECK
EatonEtAlChIPseq 0.29.0
Patrick Aboyoun
Snapshot Date: 2021-01-11 09:00:09 -0500 (Mon, 11 Jan 2021)
URL: https://git.bioconductor.org/packages/EatonEtAlChIPseq
Branch: master
Last Commit: 7adbe25
Last Changed Date: 2020-10-27 09:51:54 -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: EatonEtAlChIPseq
Version: 0.29.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:EatonEtAlChIPseq.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings EatonEtAlChIPseq_0.29.0.tar.gz
StartedAt: 2021-01-11 11:59:04 -0500 (Mon, 11 Jan 2021)
EndedAt: 2021-01-11 12:01:07 -0500 (Mon, 11 Jan 2021)
EllapsedTime: 123.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: EatonEtAlChIPseq.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:EatonEtAlChIPseq.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings EatonEtAlChIPseq_0.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/EatonEtAlChIPseq.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 ‘EatonEtAlChIPseq/DESCRIPTION’ ... OK
* this is package ‘EatonEtAlChIPseq’ version ‘0.29.0’
* 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 ‘EatonEtAlChIPseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.6Mb
  sub-directories of 1Mb or more:
    extdata  20.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* 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
Output for data("orcAlignsRep1", package = "EatonEtAlChIPseq"):
  Search path was changed
Output for data("orcAlignsRep2", package = "EatonEtAlChIPseq"):
  Search path was changed
Output for data("orcPeaksRep1", package = "EatonEtAlChIPseq"):
  Search path was changed
Output for data("orcPeaksRep2", package = "EatonEtAlChIPseq"):
  Search path was changed
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
orcAligns 7.502  0.108   7.609
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/EatonEtAlChIPseq.Rcheck/00check.log’
for details.



Installation output

EatonEtAlChIPseq.Rcheck/00install.out

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

Tests output


Example timings

EatonEtAlChIPseq.Rcheck/EatonEtAlChIPseq-Ex.timings

nameusersystemelapsed
orcAligns7.5020.1087.609
orcPeaks0.2470.0000.247