Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-10-19 13:23:15 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MethylSeekR on merida1


To the developers/maintainers of the MethylSeekR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MethylSeekR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1157/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethylSeekR 1.36.0  (landing page)
Lukas Burger
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/MethylSeekR
git_branch: RELEASE_3_15
git_last_commit: 6024af5
git_last_commit_date: 2022-04-26 11:13:26 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MethylSeekR
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MethylSeekR_1.36.0.tar.gz
StartedAt: 2022-10-19 04:35:36 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 04:45:53 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 616.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MethylSeekR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MethylSeekR_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/MethylSeekR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethylSeekR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethylSeekR’ version ‘1.36.0’
* 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 ‘MethylSeekR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘parallel’
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: ‘geneplotter’
  All declared Imports should be used.
Package in Depends field not imported from: ‘rtracklayer’
  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
PMDviterbiSegmentation : <anonymous>: no visible global function
  definition for ‘values’
PMDviterbiSegmentation : <anonymous>: no visible global function
  definition for ‘predict’
PMDviterbiSegmentation : <anonymous>: no visible global function
  definition for ‘Rle’
PMDviterbiSegmentation : <anonymous>: no visible global function
  definition for ‘runValue’
calculateAlphaDistr : <anonymous>: no visible global function
  definition for ‘Rle’
calculateFDRs: no visible global function definition for ‘values’
calculateFDRs: no visible global function definition for ‘queryHits’
calculateFDRs: no visible global function definition for ‘values<-’
calculateFDRs : <anonymous>: no visible global function definition for
  ‘Rle’
calculateFDRs : <anonymous>: no visible global function definition for
  ‘values’
calculateFDRs : <anonymous>: no visible global function definition for
  ‘runValue’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
  function definition for ‘Rle’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
  function definition for ‘nrun’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
  function definition for ‘runValue’
plotAlphaDistributionOneChr: no visible global function definition for
  ‘values’
plotFinalSegmentation: no visible global function definition for
  ‘values’
plotFinalSegmentation: no visible global function definition for ‘Rle’
plotPMDSegmentation: no visible global function definition for ‘values’
readMethylome: no visible global function definition for ‘values’
removeSNPs: no visible global function definition for ‘queryHits’
savePMDSegments: no visible global function definition for ‘values’
saveUMRLMRSegments: no visible global function definition for ‘values’
segmentUMRsLMRs: no visible global function definition for ‘values’
segmentUMRsLMRs : <anonymous>: no visible global function definition
  for ‘Rle’
segmentUMRsLMRs : <anonymous>: no visible global function definition
  for ‘values’
segmentUMRsLMRs : <anonymous>: no visible global function definition
  for ‘runValue’
segmentUMRsLMRs: no visible global function definition for ‘queryHits’
segmentUMRsLMRs: no visible global function definition for
  ‘subjectHits’
segmentUMRsLMRs: no visible global function definition for ‘Rle’
segmentUMRsLMRs: no visible global function definition for ‘values<-’
segmentUMRsLMRs: no visible global function definition for ‘DataFrame’
segmentUMRsLMRs: no visible global function definition for
  ‘colorRampPalette’
trainPMDHMM: no visible global function definition for ‘values’
Undefined global functions or variables:
  DataFrame Rle colorRampPalette nrun predict queryHits runValue
  subjectHits values values<-
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "predict")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
MethylSeekR-package         79.278  3.043  86.305
segmentPMDs                 52.172  2.107  54.588
savePMDSegments             51.878  2.012  54.020
plotPMDSegmentation         50.793  1.941  52.811
calculateFDRs               10.329  0.376  13.924
plotAlphaDistributionOneChr  9.402  0.372   9.786
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/MethylSeekR.Rcheck/00check.log’
for details.



Installation output

MethylSeekR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MethylSeekR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘MethylSeekR’ ...
** using staged installation
** R
** 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 (MethylSeekR)

Tests output


Example timings

MethylSeekR.Rcheck/MethylSeekR-Ex.timings

nameusersystemelapsed
MethylSeekR-package79.278 3.04386.305
calculateFDRs10.329 0.37613.924
plotAlphaDistributionOneChr9.4020.3729.786
plotFinalSegmentation3.5520.1823.739
plotPMDSegmentation50.793 1.94152.811
readMethylome0.5340.0130.547
readSNPTable0.1600.0080.168
removeSNPs0.6950.0170.711
savePMDSegments51.878 2.01254.020
saveUMRLMRSegments1.9800.0852.072
segmentPMDs52.172 2.10754.588
segmentUMRsLMRs1.8240.0711.904