Back to Build/check report for BioC 3.20 experimental data
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This page was generated on 2024-10-31 19:08 -0400 (Thu, 31 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
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

Package 43/431HostnameOS / ArchINSTALLBUILDCHECK
bsseqData 0.44.0  (landing page)
Kasper Daniel Hansen
Snapshot Date: 2024-10-31 07:30 -0400 (Thu, 31 Oct 2024)
git_url: https://git.bioconductor.org/packages/bsseqData
git_branch: RELEASE_3_20
git_last_commit: 4c65f5e
git_last_commit_date: 2024-10-29 09:29:48 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published


CHECK results for bsseqData on nebbiolo2

To the developers/maintainers of the bsseqData package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: bsseqData
Version: 0.44.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:bsseqData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings bsseqData_0.44.0.tar.gz
StartedAt: 2024-10-31 13:23:15 -0400 (Thu, 31 Oct 2024)
EndedAt: 2024-10-31 13:29:15 -0400 (Thu, 31 Oct 2024)
EllapsedTime: 359.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: bsseqData.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:bsseqData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings bsseqData_0.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/bsseqData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘bsseqData/DESCRIPTION’ ... OK
* this is package ‘bsseqData’ version ‘0.44.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘bsseqData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 144.3Mb
  sub-directories of 1Mb or more:
    data   83.3Mb
    umtab  60.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... 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 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 LazyData ... WARNING
  LazyData DB of 83.3 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/bsseqData.Rcheck/00check.log’
for details.


Installation output

bsseqData.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL bsseqData
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘bsseqData’ ...
** using staged installation
** data
*** moving datasets to lazyload DB
** inst
** help
*** installing help indices
** building package indices
** 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 (bsseqData)

Tests output


Example timings

bsseqData.Rcheck/bsseqData-Ex.timings

nameusersystemelapsed
BS.cancer.ex0.8810.0720.954
BS.cancer.ex.fit2.3700.2322.601
BS.cancer.ex.tstat0.1550.0540.210
keepLoci.ex0.0010.0020.002