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This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 441/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoSIA 1.6.0  (landing page)
Amanda D. Clark
Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024)
git_url: https://git.bioconductor.org/packages/CoSIA
git_branch: RELEASE_3_20
git_last_commit: dfc812d
git_last_commit_date: 2024-10-29 11:34:25 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for CoSIA on kjohnson3

To the developers/maintainers of the CoSIA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoSIA.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: CoSIA
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoSIA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoSIA_1.6.0.tar.gz
StartedAt: 2024-11-08 23:41:48 -0500 (Fri, 08 Nov 2024)
EndedAt: 2024-11-08 23:55:42 -0500 (Fri, 08 Nov 2024)
EllapsedTime: 834.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CoSIA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoSIA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoSIA_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CoSIA.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoSIA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoSIA’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ‘CoSIA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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 ... 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
plotCVGEx-CoSIAn-method      157.582  4.729 163.105
plotCVGEx                    131.384  3.988 136.047
getTissues                    40.175  0.661  41.038
plotSpeciesGEx-CoSIAn-method  35.776  0.680  36.821
plotTissueGEx-CoSIAn-method   32.871  0.480  33.637
plotTissueGEx                 32.433  0.515  33.151
plotSpeciesGEx                32.201  0.391  32.797
plotDSGEx                     31.872  0.604  32.670
plotDSGEx-CoSIAn-method       31.216  0.524  31.975
getGEx-CoSIAn-method           8.029  0.277   8.739
getGExMetrics-CoSIAn-method    6.990  0.135   7.307
getGEx                         6.438  0.136   6.801
getGExMetrics                  6.327  0.113   6.622
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CoSIA.Rcheck/00check.log’
for details.


Installation output

CoSIA.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘CoSIA’ ...
** 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 (CoSIA)

Tests output


Example timings

CoSIA.Rcheck/CoSIA-Ex.timings

nameusersystemelapsed
CoSIA-constructor0.0010.0000.001
getConversion-CoSIAn-method1.4500.0381.499
getConversion0.7200.0220.741
getGEx-CoSIAn-method8.0290.2778.739
getGEx6.4380.1366.801
getGExMetrics-CoSIAn-method6.9900.1357.307
getGExMetrics6.3270.1136.622
getTissues40.175 0.66141.038
plotCVGEx-CoSIAn-method157.582 4.729163.105
plotCVGEx131.384 3.988136.047
plotDSGEx-CoSIAn-method31.216 0.52431.975
plotDSGEx31.872 0.60432.670
plotSpeciesGEx-CoSIAn-method35.776 0.68036.821
plotSpeciesGEx32.201 0.39132.797
plotTissueGEx-CoSIAn-method32.871 0.48033.637
plotTissueGEx32.433 0.51533.151
viewCoSIAn-CoSIAn-method0.0010.0000.000
viewCoSIAn0.0010.0000.000