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This page was generated on 2023-04-07 10:55:37 -0400 (Fri, 07 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4497
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4322
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 missMethyl on nebbiolo2


To the developers/maintainers of the missMethyl package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/missMethyl.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1238/2200HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
missMethyl 1.33.1  (landing page)
Belinda Phipson
Snapshot Date: 2023-04-06 14:00:13 -0400 (Thu, 06 Apr 2023)
git_url: https://git.bioconductor.org/packages/missMethyl
git_branch: devel
git_last_commit: be54308
git_last_commit_date: 2023-03-21 23:34:43 -0400 (Tue, 21 Mar 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  

Summary

Package: missMethyl
Version: 1.33.1
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings missMethyl_1.33.1.tar.gz
StartedAt: 2023-04-07 07:33:34 -0400 (Fri, 07 Apr 2023)
EndedAt: 2023-04-07 08:11:12 -0400 (Fri, 07 Apr 2023)
EllapsedTime: 2257.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: missMethyl.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings missMethyl_1.33.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘missMethyl/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘missMethyl’ version ‘1.33.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘missMethyl’ 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 loading without being on the library search path ... 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 ... NOTE
goregion: no visible global function definition for ‘seqlevelsStyle<-’
Undefined global functions or variables:
  seqlevelsStyle<-
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
RUVadj             37.487  1.960  39.448
SWAN               27.220  0.720  27.941
RUVfit             26.448  0.764  27.213
getAdj             23.393  0.386  23.781
topRUV             23.492  0.264  23.758
topGSA             19.124  0.256  19.381
densityByProbeType 11.623  0.132  11.756
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘missMethyl.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘missMethyl.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/betasByType-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/mdsplot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/top4-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/mdsplotadj-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/mdsplotadj1-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/top4DV-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/top4DVhapmap-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/vign_test/missMethyl/vignettes/missMethyl_files/figure-html/gometh4-1.png" but not available.
Killed

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/missMethyl.Rcheck/00check.log’
for details.


Installation output

missMethyl.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL missMethyl
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘missMethyl’ ...
** 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 (missMethyl)

Tests output


Example timings

missMethyl.Rcheck/missMethyl-Ex.timings

nameusersystemelapsed
RUVadj37.487 1.96039.448
RUVfit26.448 0.76427.213
SWAN27.220 0.72027.941
contrasts.varFit0.0410.0000.042
densityByProbeType11.623 0.13211.756
getAdj23.393 0.38623.781
getINCs0.2060.0000.206
getLeveneResiduals0.0080.0000.008
getMappedEntrezIDs000
gometh000
goregion0.0010.0000.000
gsameth000
gsaregion0.0000.0000.001
gsaseq000
topGSA19.124 0.25619.381
topRUV23.492 0.26423.758
topVar0.010.000.01
varFit0.0090.0000.009