Chen Meng
| Snapshot Date: 2025-12-04 13:45 -0500 (Thu, 04 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/mogsa |
| git_branch: RELEASE_3_22 |
| git_last_commit: f89a88e |
| git_last_commit_date: 2025-10-29 10:25:17 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-08 12:01 -0500 (Mon, 08 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4668 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 1347/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mogsa 1.44.0 (landing page) Chen Meng
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the mogsa package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mogsa.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: mogsa |
| Version: 1.44.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mogsa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mogsa_1.44.0.tar.gz |
| StartedAt: 2025-12-05 08:05:16 -0500 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 08:11:35 -0500 (Fri, 05 Dec 2025) |
| EllapsedTime: 379.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mogsa.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mogsa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mogsa_1.44.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/mogsa.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mogsa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mogsa’ version ‘1.44.0’
* 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 ‘mogsa’ can be installed ... OK
* checking installed package size ... OK
* 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 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) GIS.Rd:57: Lost braces; missing escapes or markup?
57 | log2(var(GS_{-i})/var(GS))
| ^
checkRd: (-1) GIS.Rd:59: Lost braces; missing escapes or markup?
59 | where GS is the gene set score, and the GS_{-i} is a recalculate of
| ^
checkRd: (-1) GIS.Rd:65: Lost braces; missing escapes or markup?
65 | log2(F(GS_{-i})/F(GS))
| ^
checkRd: (-1) NCI60_4array_supdata.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:15-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4array_supdata.Rd:19: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4array_supdata.Rd:23: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4array_supdata.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:27-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:21: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:33: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:33-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mgsa-class.Rd:22-24: Lost braces
22 | \item{combine}{\code{signature(x = "mgsa", y = "mgsa")}}{
| ^
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
prepSupMoa 6.433 0.162 8.084
mbpca 4.968 0.195 6.872
moGap 3.660 0.112 5.260
* 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/mogsa.Rcheck/00check.log’
for details.
mogsa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mogsa ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘mogsa’ ... ** this is package ‘mogsa’ version ‘1.44.0’ ** using staged installation ** R ** data ** 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 (mogsa)
mogsa.Rcheck/mogsa-Ex.timings
| name | user | system | elapsed | |
| GIS | 0.926 | 0.035 | 1.184 | |
| annotate.gs | 0.225 | 0.025 | 0.298 | |
| bootMbpca | 0 | 0 | 0 | |
| bootMoa | 0 | 0 | 0 | |
| box.gs.feature | 0.430 | 0.021 | 0.545 | |
| combine-methods | 0.424 | 0.024 | 0.571 | |
| decompose.gs.group | 0.259 | 0.017 | 0.342 | |
| decompose.gs.ind | 0.237 | 0.018 | 0.318 | |
| distMoa | 0.417 | 0.015 | 0.564 | |
| getmgsa | 0.714 | 0.017 | 1.012 | |
| matpower | 0.001 | 0.001 | 0.002 | |
| mbpca | 4.968 | 0.195 | 6.872 | |
| mgsa-class | 0.392 | 0.021 | 0.539 | |
| moGap | 3.660 | 0.112 | 5.260 | |
| moa-class | 0.162 | 0.008 | 0.234 | |
| moa | 1.018 | 0.050 | 1.456 | |
| moa.sup-class | 0.203 | 0.010 | 0.275 | |
| moaCoef | 0.476 | 0.016 | 0.686 | |
| moaScore | 0.475 | 0.014 | 0.673 | |
| mogsa-package | 0.426 | 0.023 | 0.596 | |
| mogsa | 0.628 | 0.029 | 0.866 | |
| pairwise.rv | 0.016 | 0.003 | 0.028 | |
| plotGS | 0.733 | 0.023 | 0.961 | |
| prepGraphite | 0.662 | 0.025 | 0.867 | |
| prepMsigDB | 0.004 | 0.002 | 0.005 | |
| prepSupMoa | 6.433 | 0.162 | 8.084 | |
| softK | 0.000 | 0.001 | 0.001 | |
| sup.moa | 0.712 | 0.029 | 1.063 | |
| wsvd | 0.002 | 0.001 | 0.002 | |