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This page was generated on 2021-11-26 15:04:57 -0500 (Fri, 26 Nov 2021).

CHECK results for motifbreakR on nebbiolo2

To the developers/maintainers of the motifbreakR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifbreakR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1200/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifbreakR 2.8.0  (landing page)
Simon Gert Coetzee
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/motifbreakR
git_branch: RELEASE_3_14
git_last_commit: 58931f1
git_last_commit_date: 2021-10-26 12:22:28 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: motifbreakR
Version: 2.8.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings motifbreakR_2.8.0.tar.gz
StartedAt: 2021-11-25 10:16:44 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 10:23:15 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 391.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: motifbreakR.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings motifbreakR_2.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/motifbreakR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.8.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘S4Vectors::as.data.frame’ by ‘motifStack::as.data.frame’ when loading ‘motifbreakR’
See ‘/home/biocbuild/bbs-3.14-bioc/meat/motifbreakR.Rcheck/00install.out’ for details.
* 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 LazyData ... 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 36.060  1.376  37.438
motifbreakR    11.926  0.192  12.119
* 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: 3 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/motifbreakR.Rcheck/00check.log’
for details.



Installation output

motifbreakR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL motifbreakR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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.
Warning: replacing previous import ‘S4Vectors::as.data.frame’ by ‘motifStack::as.data.frame’ when loading ‘motifbreakR’
** 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.
Warning: replacing previous import ‘S4Vectors::as.data.frame’ by ‘motifStack::as.data.frame’ when loading ‘motifbreakR’
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import ‘S4Vectors::as.data.frame’ by ‘motifStack::as.data.frame’ when loading ‘motifbreakR’
** testing if installed package keeps a record of temporary installation path
* DONE (motifbreakR)

Tests output


Example timings

motifbreakR.Rcheck/motifbreakR-Ex.timings

nameusersystemelapsed
calculatePvalue0.4190.0130.432
encodemotif0.0320.0040.036
example.results0.0630.0200.083
factorbook0.0080.0030.013
hocomoco0.0160.0010.016
homer0.0140.0000.014
motifbreakR11.926 0.19212.119
motifbreakR_motif0.0410.0040.046
plotMB0.0410.0070.050
snps.from.file1.0380.0131.053
snps.from.rsid36.060 1.37637.438