Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-14 11:40 -0400 (Fri, 14 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4781 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4537 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4567 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4519 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4451 |
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 1313/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mogsa 1.41.0 (landing page) Chen Meng
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | 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: 1.41.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:mogsa.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings mogsa_1.41.0.tar.gz |
StartedAt: 2025-03-13 23:58:54 -0400 (Thu, 13 Mar 2025) |
EndedAt: 2025-03-14 00:02:15 -0400 (Fri, 14 Mar 2025) |
EllapsedTime: 201.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: mogsa.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:mogsa.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings mogsa_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mogsa.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘mogsa/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mogsa’ version ‘1.41.0’ * 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 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 ... ERROR Running examples in ‘mogsa-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: prepGraphite > ### Title: Prepare pathway gene sets from graphite package > ### Aliases: prepGraphite > ### Keywords: pahtways graphite > > ### ** Examples > > library(graphite) > keggdb <- prepGraphite(db = pathways("hsapiens", "kegg")[1:3], id = "entrez") Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Timeout was reached [graphiteweb.bio.unipd.it]: SSL connection timeout Error in fetchRemote(name, path) : cannot download pathway data: are you offline? Calls: prepGraphite -> pathways -> loadData -> fetchRemote Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘moCluster-knitr.Rnw’ using knitr --- finished re-building ‘moCluster-knitr.Rnw’ --- re-building ‘mogsa-knitr.Rnw’ using knitr Warning: 'mode(width)' differs between new and previous ==> NOT changing 'width' Warning: 'mode(width)' differs between new and previous ==> NOT changing 'width' Quitting from lines 278-282 [prepGraphite] (mogsa-knitr.Rnw) Error: processing vignette 'mogsa-knitr.Rnw' failed with diagnostics: cannot download pathway data: are you offline? --- failed re-building ‘mogsa-knitr.Rnw’ SUMMARY: processing the following file failed: ‘mogsa-knitr.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/mogsa.Rcheck/00check.log’ for details.
mogsa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL mogsa ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘mogsa’ ... ** this is package ‘mogsa’ version ‘1.41.0’ ** 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 | 1.050 | 0.095 | 1.145 | |
annotate.gs | 0.099 | 0.017 | 0.116 | |
bootMbpca | 0 | 0 | 0 | |
bootMoa | 0 | 0 | 0 | |
box.gs.feature | 0.162 | 0.003 | 0.165 | |
combine-methods | 0.186 | 0.003 | 0.189 | |
decompose.gs.group | 0.111 | 0.003 | 0.114 | |
decompose.gs.ind | 0.101 | 0.001 | 0.102 | |
distMoa | 0.222 | 0.005 | 0.227 | |
getmgsa | 0.098 | 0.000 | 0.099 | |
matpower | 0.001 | 0.000 | 0.000 | |
mbpca | 2.181 | 0.024 | 2.206 | |
mgsa-class | 0.700 | 0.013 | 0.714 | |
moGap | 1.531 | 0.048 | 1.579 | |
moa-class | 0.071 | 0.007 | 0.078 | |
moa | 0.614 | 0.030 | 0.643 | |
moa.sup-class | 0.092 | 0.001 | 0.093 | |
moaCoef | 0.243 | 0.001 | 0.243 | |
moaScore | 0.239 | 0.000 | 0.239 | |
mogsa-package | 0.205 | 0.001 | 0.206 | |
mogsa | 0.270 | 0.001 | 0.272 | |
pairwise.rv | 0.010 | 0.001 | 0.010 | |
plotGS | 0.113 | 0.001 | 0.113 | |