| Back to Multiple platform build/check report for BioC 3.22: simplified long | 
 | 
This page was generated on 2025-10-30 12:36 -0400 (Thu, 30 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 | 
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 | 
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 | 
| 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 456/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CoSIA 1.10.0  (landing page) Amanda D. Clark 
 | nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK |  | ||||||||
| 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. | 
| Package: CoSIA | 
| Version: 1.10.0 | 
| 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_1.10.0.tar.gz | 
| StartedAt: 2025-10-30 01:34:31 -0400 (Thu, 30 Oct 2025) | 
| EndedAt: 2025-10-30 02:01:01 -0400 (Thu, 30 Oct 2025) | 
| EllapsedTime: 1590.7 seconds | 
| RetCode: 0 | 
| Status: OK | 
| CheckDir: CoSIA.Rcheck | 
| Warnings: 0 | 
##############################################################################
##############################################################################
###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CoSIA.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoSIA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoSIA’ version ‘1.10.0’
* 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 ‘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      336.309  6.564 345.292
plotCVGEx                    324.816  6.243 333.741
getTissues                   113.880  1.408 115.619
plotDSGEx-CoSIAn-method      110.334  2.540 114.966
plotSpeciesGEx               110.833  1.690 114.693
plotTissueGEx-CoSIAn-method  109.728  1.041 111.455
plotSpeciesGEx-CoSIAn-method 108.287  0.841 109.689
plotTissueGEx                106.498  1.320 108.261
plotDSGEx                    103.207  1.394 104.914
getGEx-CoSIAn-method          22.382  0.284  22.980
getGExMetrics-CoSIAn-method   21.210  0.291  21.890
getGExMetrics                 20.815  0.283  21.408
getGEx                        20.115  0.248  20.764
* 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-3.22-bioc/meat/CoSIA.Rcheck/00check.log’
for details.
CoSIA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CoSIA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘CoSIA’ ... ** this is package ‘CoSIA’ version ‘1.10.0’ ** 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)
CoSIA.Rcheck/CoSIA-Ex.timings
| name | user | system | elapsed | |
| CoSIA-constructor | 0.001 | 0.001 | 0.001 | |
| getConversion-CoSIAn-method | 1.768 | 0.045 | 1.821 | |
| getConversion | 0.860 | 0.019 | 0.881 | |
| getGEx-CoSIAn-method | 22.382 | 0.284 | 22.980 | |
| getGEx | 20.115 | 0.248 | 20.764 | |
| getGExMetrics-CoSIAn-method | 21.210 | 0.291 | 21.890 | |
| getGExMetrics | 20.815 | 0.283 | 21.408 | |
| getTissues | 113.880 | 1.408 | 115.619 | |
| plotCVGEx-CoSIAn-method | 336.309 | 6.564 | 345.292 | |
| plotCVGEx | 324.816 | 6.243 | 333.741 | |
| plotDSGEx-CoSIAn-method | 110.334 | 2.540 | 114.966 | |
| plotDSGEx | 103.207 | 1.394 | 104.914 | |
| plotSpeciesGEx-CoSIAn-method | 108.287 | 0.841 | 109.689 | |
| plotSpeciesGEx | 110.833 | 1.690 | 114.693 | |
| plotTissueGEx-CoSIAn-method | 109.728 | 1.041 | 111.455 | |
| plotTissueGEx | 106.498 | 1.320 | 108.261 | |
| viewCoSIAn-CoSIAn-method | 0.000 | 0.000 | 0.001 | |
| viewCoSIAn | 0.001 | 0.000 | 0.000 | |