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CHECK report for motifbreakR on malbec2

This page was generated on 2020-10-17 11:55:12 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE motifbreakR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1124/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifbreakR 2.2.0
Simon Gert Coetzee
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/motifbreakR
Branch: RELEASE_3_11
Last Commit: f864d3a
Last Changed Date: 2020-04-27 14:51:05 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: motifbreakR
Version: 2.2.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings motifbreakR_2.2.0.tar.gz
StartedAt: 2020-10-17 03:23:14 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:32:42 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 567.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: motifbreakR.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings motifbreakR_2.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/motifbreakR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifbreakR/DESCRIPTION’ ... OK
* this is package ‘motifbreakR’ version ‘2.2.0’
* 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 ‘motifbreakR’ 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 ... NOTE
Namespaces in Imports field not imported from:
  'compiler' 'grImport'
  All declared Imports should be used.
Package in Depends field not imported from: 'MotifDb'
  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 ... NOTE
formatVcfOut: no visible binding for global variable 'search.genome'
plotMotifLogoStack.2: no visible global function definition for 'par'
preparePWM: no visible binding for global variable 'threshold'
snps.from.file: no visible binding for global variable 'DNA_ALPHABET'
wScore: no visible global function definition for 'scoreMotif'
Undefined global functions or variables:
  DNA_ALPHABET par scoreMotif search.genome threshold
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'rs1006140' 'variants.from.file'
Undocumented data sets:
  'rs1006140'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'motifbreakR'
  ‘legacy.score’

Undocumented arguments in documentation object 'scoreAllWindows'
  ‘snp.seq’ ‘snp.seq.rc’ ‘pwm’ ‘from’ ‘to’ ‘pwm.range’ ‘calcp’

Undocumented arguments in documentation object 'snps.from.file'
  ‘indels’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
snps.from.rsid 46.471  1.348  49.346
motifbreakR    12.408  0.112  12.532
* 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 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/motifbreakR.Rcheck/00check.log’
for details.



Installation output

motifbreakR.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL motifbreakR
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘motifbreakR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package keeps a record of temporary installation path
* DONE (motifbreakR)

Tests output


Example timings

motifbreakR.Rcheck/motifbreakR-Ex.timings

nameusersystemelapsed
calculatePvalue0.3320.0040.336
encodemotif0.0320.0000.032
example.results0.0830.0000.083
factorbook0.0080.0000.008
hocomoco0.0110.0000.011
homer0.0090.0000.009
motifbreakR12.408 0.11212.532
motifbreakR_motif0.0320.0000.032
plotMB0.0540.0000.054
snps.from.file1.2180.0041.401
snps.from.rsid46.471 1.34849.346