Multiple platform build/check report for BioC 3.20 - CHECK results for mogsa on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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*

CHECK results for mogsa on nebbiolo2

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.

raw results

Summary

Package: mogsa

Version: 1.40.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mogsa.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mogsa_1.40.0.tar.gz

StartedAt: 2024-12-20 02:56:34 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 03:04:12 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 458.3 seconds

RetCode: 0

Status: OK

CheckDir: mogsa.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mogsa.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mogsa_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/mogsa.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘mogsa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mogsa’ version ‘1.40.0’
* 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 ‘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 loading without being on the library search path ... 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 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/mogsa.Rcheck/00check.log’
for details.

Installation output

mogsa.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL mogsa
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘mogsa’ ...
** 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)

Tests output

Example timings

mogsa.Rcheck/mogsa-Ex.timings

name	user	system	elapsed
GIS	0.581	0.007	0.589
annotate.gs	0.098	0.000	0.100
bootMbpca	0	0	0
bootMoa	0	0	0
box.gs.feature	0.161	0.001	0.163
combine-methods	0.570	0.002	0.570
decompose.gs.group	0.106	0.012	0.119
decompose.gs.ind	0.097	0.001	0.098
distMoa	0.213	0.002	0.215
getmgsa	0.092	0.012	0.106
matpower	0.000	0.000	0.001
mbpca	2.497	0.070	2.568
mgsa-class	0.179	0.007	0.186
moGap	2.238	0.013	2.251
moa-class	0.070	0.004	0.075
moa	0.603	0.019	0.623
moa.sup-class	0.088	0.001	0.089
moaCoef	0.241	0.000	0.242
moaScore	0.241	0.001	0.242
mogsa-package	0.194	0.001	0.195
mogsa	0.271	0.001	0.271
pairwise.rv	0.01	0.00	0.01
plotGS	0.114	0.000	0.114
prepGraphite	0.279	0.003	0.282
prepMsigDB	0.002	0.000	0.002
prepSupMoa	4.350	0.138	4.489
softK	0	0	0
sup.moa	0.220	0.002	0.222
wsvd	0.001	0.000	0.001