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This page was generated on 2024-10-17 14:51 -0400 (Thu, 17 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 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 306/430HostnameOS / ArchINSTALLBUILDCHECK
pumadata 2.40.0  (landing page)
Xuejun liu
Snapshot Date: 2024-10-17 07:30 -0400 (Thu, 17 Oct 2024)
git_url: https://git.bioconductor.org/packages/pumadata
git_branch: RELEASE_3_19
git_last_commit: 58c7c2d
git_last_commit_date: 2024-04-30 10:27:58 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for pumadata on nebbiolo1

To the developers/maintainers of the pumadata 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: pumadata
Version: 2.40.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:pumadata.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings pumadata_2.40.0.tar.gz
StartedAt: 2024-10-17 11:55:01 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 11:58:23 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 201.5 seconds
RetCode: 0
Status:   OK  
CheckDir: pumadata.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:pumadata.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings pumadata_2.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/pumadata.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘pumadata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pumadata’ version ‘2.40.0’
* 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 ‘pumadata’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 102.7Mb
  sub-directories of 1Mb or more:
    data  102.6Mb
* 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 code 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) affybatch.estrogen.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) eset_estrogen_comb.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) eset_estrogen_mmgmos.Rd:15: Escaped LaTeX specials: \_
checkRd: (-1) eset_estrogen_pmmmgmos.Rd:15: Escaped LaTeX specials: \_
checkRd: (-1) eset_estrogen_rma.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) oligo.estrogen.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) pumapca_estrogen.Rd:15: Escaped LaTeX specials: \_
* 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/pumadata.Rcheck/00check.log’
for details.


Installation output

pumadata.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL pumadata
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘pumadata’ ...
** using staged installation
** R
** data
** 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 (pumadata)

Tests output


Example timings

pumadata.Rcheck/pumadata-Ex.timings

nameusersystemelapsed
eset_estrogen_comb0.0950.0010.094
eset_estrogen_mmgmos0.0960.0000.096
eset_estrogen_pmmmgmos0.1670.0000.166
eset_estrogen_rma0.0190.0030.023
pumapca_estrogen0.0090.0010.009