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CHECK report for GenomicScores on malbec1

This page was generated on 2019-04-16 11:52:44 -0400 (Tue, 16 Apr 2019).

Package 629/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicScores 1.6.0
Robert Castelo
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/GenomicScores
Branch: RELEASE_3_8
Last Commit: 6644e90
Last Changed Date: 2018-10-30 11:42:04 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: GenomicScores
Version: 1.6.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GenomicScores.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GenomicScores_1.6.0.tar.gz
StartedAt: 2019-04-16 00:12:38 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:16:37 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 238.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomicScores.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GenomicScores.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GenomicScores_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/GenomicScores.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicScores/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicScores’ version ‘1.6.0’
* 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:
  inst/gscores-template/inst/extdata/.gitkeep
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 ‘GenomicScores’ 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 ... 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 ... WARNING
Missing link or links in documentation object 'GScores-class.Rd':
  ‘phastCons100way.UCSC.hg19’

Missing link or links in documentation object 'gscores.Rd':
  ‘phastCons100way.UCSC.hg19’ ‘MafDb.1Kgenomes.phase1.hs37d5’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 or elapsed time > 5s
                user system elapsed
gscores       21.744  2.760  25.883
GScores-class  8.016  0.444   8.734
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/GenomicScores.Rcheck/00check.log’
for details.



Installation output

GenomicScores.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL GenomicScores
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘GenomicScores’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘score’ with signature ‘"MafDb"’: no definition for class “MafDb”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicScores)

Tests output


Example timings

GenomicScores.Rcheck/GenomicScores-Ex.timings

nameusersystemelapsed
GScores-class8.0160.4448.734
MafDb-class0.0000.0000.001
gscores21.744 2.76025.883