Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
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 |
Package 844/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gep2pep 1.26.0 (landing page) Francesco Napolitano
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the gep2pep package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gep2pep.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: gep2pep |
Version: 1.26.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gep2pep_1.26.0.tar.gz |
StartedAt: 2024-12-20 00:24:28 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:30:16 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 348.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gep2pep.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gep2pep_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gep2pep.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 ‘gep2pep/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gep2pep’ version ‘1.26.0’ * 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 ‘gep2pep’ 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) as.CategorizedCollection.Rd:27: Lost braces; missing escapes or markup? 27 | in the collection to {CategorizedCollection}. If | ^ checkRd: (-1) gep2pep-package.Rd:50-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) gep2pep-package.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) gep2pep-package.Rd:55-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) gep2pep-package.Rd:58-61: Lost braces in \itemize; meant \describe ? checkRd: (-1) gep2pep-package.Rd:63-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) gep2pep-package.Rd:67-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) gep2pep-package.Rd:71-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) loadESmatrix.Rd:19: Lost braces 19 | reports the ES for the pathway \code{i}, condition{j}. If | ^ checkRd: (-1) loadPVmatrix.Rd:19: Lost braces 19 | reports the PV for the pathway \code{i}, condition{j}. If | ^ * 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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/gep2pep.Rcheck/00check.log’ for details.
gep2pep.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL gep2pep ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘gep2pep’ ... ** 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 (gep2pep)
gep2pep.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(gep2pep) > > test_check("gep2pep") Chunk 1 of 2, 521 bytes (current file size: 4.3 Kb) Chunk 2 of 2, 666 bytes (current file size: 16.3 Kb) Chunk 1 of 2, 541 bytes (current file size: 4.3 Kb) Chunk 2 of 2, 692 bytes (current file size: 16.3 Kb) Chunk 1 of 2, 550 bytes (current file size: 4.3 Kb) Chunk 2 of 2, 686 bytes (current file size: 16.3 Kb) [ FAIL 0 | WARN 2273 | SKIP 1 | PASS 154 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_rawMode.R:216:1' [ FAIL 0 | WARN 2273 | SKIP 1 | PASS 154 ] > > proc.time() user system elapsed 22.302 0.854 23.243
gep2pep.Rcheck/gep2pep-Ex.timings
name | user | system | elapsed | |
CategorizedCollection | 0.079 | 0.001 | 0.079 | |
CondSEA | 0.690 | 0.038 | 0.801 | |
PathSEA | 0.791 | 0.012 | 0.804 | |
addSingleGeneSets | 0.437 | 0.057 | 0.493 | |
as.CategorizedCollection | 0.244 | 0.023 | 0.268 | |
buildPEPs | 0.412 | 0.020 | 0.432 | |
checkRepository | 0.152 | 0.007 | 0.159 | |
clearCache | 0.539 | 0.045 | 0.583 | |
createMergedRepository | 0.484 | 0.027 | 0.512 | |
createRepository | 0.120 | 0.014 | 0.133 | |
exportSEA | 0.418 | 0.021 | 0.440 | |
gene2pathways | 0.140 | 0.008 | 0.148 | |
getCollections | 0.122 | 0.018 | 0.153 | |
getDetails | 0.420 | 0.036 | 0.456 | |
getResults | 0.410 | 0.018 | 0.428 | |
importFromRawMode | 0.455 | 0.013 | 0.469 | |
importMSigDB.xml | 0.136 | 0.003 | 0.140 | |
loadCollection | 0.133 | 0.013 | 0.146 | |
loadESmatrix | 0.376 | 0.031 | 0.407 | |
loadPVmatrix | 0.372 | 0.009 | 0.382 | |
loadSampleGEP | 0.001 | 0.000 | 0.001 | |
loadSamplePWS | 0.001 | 0.000 | 0.001 | |
makeCollectionIDs | 0.033 | 0.000 | 0.033 | |
openRepository | 0.121 | 0.012 | 0.132 | |
setId2setName | 0.032 | 0.000 | 0.033 | |