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This page was generated on 2023-03-30 12:33:48 -0400 (Thu, 30 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4547
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 msgbsR on nebbiolo1


To the developers/maintainers of the msgbsR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/msgbsR.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 1286/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msgbsR 1.23.0  (landing page)
Benjamin Mayne
Snapshot Date: 2023-03-29 14:00:20 -0400 (Wed, 29 Mar 2023)
git_url: https://git.bioconductor.org/packages/msgbsR
git_branch: devel
git_last_commit: 642ad30
git_last_commit_date: 2022-11-01 11:15:43 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: msgbsR
Version: 1.23.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:msgbsR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings msgbsR_1.23.0.tar.gz
StartedAt: 2023-03-29 21:46:50 -0400 (Wed, 29 Mar 2023)
EndedAt: 2023-03-29 21:54:31 -0400 (Wed, 29 Mar 2023)
EllapsedTime: 460.8 seconds
RetCode: 0
Status:   OK  
CheckDir: msgbsR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:msgbsR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings msgbsR_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/msgbsR.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘msgbsR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msgbsR’ version ‘1.23.0’
* 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 ‘msgbsR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 15.4Mb
  sub-directories of 1Mb or more:
    extdata  15.0Mb
* 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 ... NOTE
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
* 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 ... 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 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
rawCounts 5.925  0.128   6.063
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘msgbsR_Vignette.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/msgbsR.Rcheck/00check.log’
for details.



Installation output

msgbsR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL msgbsR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘msgbsR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘BiocGenerics’ for request: ‘clusterApply’ when loading ‘easyRNASeq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘BiocGenerics’ for request: ‘clusterApply’ when loading ‘easyRNASeq’
** testing if installed package can be loaded from final location
No methods found in package ‘BiocGenerics’ for request: ‘clusterApply’ when loading ‘easyRNASeq’
** testing if installed package keeps a record of temporary installation path
* DONE (msgbsR)

Tests output


Example timings

msgbsR.Rcheck/msgbsR-Ex.timings

nameusersystemelapsed
checkCuts2.3040.2492.589
diffMeth1.0060.0081.013
plotCircos1.2490.0441.294
plotCounts0.3250.0360.362
rawCounts5.9250.1286.063