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CHECK report for leeBamViews on malbec1

This page was generated on 2021-05-06 14:10:11 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the leeBamViews package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 199/398HostnameOS / ArchINSTALLBUILDCHECK
leeBamViews 1.26.0  (landing page)
VJ Carey
Snapshot Date: 2021-05-06 09:00:13 -0400 (Thu, 06 May 2021)
URL: https://git.bioconductor.org/packages/leeBamViews
Branch: RELEASE_3_12
Last Commit: e8f0e19
Last Changed Date: 2020-10-27 09:51:45 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: leeBamViews
Version: 1.26.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:leeBamViews.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings leeBamViews_1.26.0.tar.gz
StartedAt: 2021-05-06 12:17:15 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 12:20:02 -0400 (Thu, 06 May 2021)
EllapsedTime: 166.5 seconds
RetCode: 0
Status:   OK  
CheckDir: leeBamViews.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:leeBamViews.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings leeBamViews_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/leeBamViews.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘leeBamViews/DESCRIPTION’ ... OK
* this is package ‘leeBamViews’ version ‘1.26.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘leeBamViews’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.1Mb
  sub-directories of 1Mb or more:
    bam  10.1Mb
* checking package directory ... OK
* checking ‘build’ 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 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
tabulateReads 5.836  0.104   5.951
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-data-experiment/meat/leeBamViews.Rcheck/00check.log’
for details.



Installation output

leeBamViews.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL leeBamViews
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘leeBamViews’ ...
** using staged installation
** R
** data
** 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 (leeBamViews)

Tests output


Example timings

leeBamViews.Rcheck/leeBamViews-Ex.timings

nameusersystemelapsed
bs11.0400.0361.510
leeRPKM0.0360.0040.038
leeUnn0.0680.0000.068
tabulateReads5.8360.1045.951
totalReadCounts1.7720.0081.876