Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gep2pep_1.26.0.tar.gz |
StartedAt: 2024-11-19 22:32:32 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 22:38:16 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 344.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gep2pep.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gep2pep_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gep2pep.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 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 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-3.20-bioc/meat/gep2pep.Rcheck/00check.log’ for details.
gep2pep.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gep2pep ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 2271 | SKIP 1 | PASS 154 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_rawMode.R:216:1' [ FAIL 0 | WARN 2271 | SKIP 1 | PASS 154 ] > > proc.time() user system elapsed 20.637 1.457 22.307
gep2pep.Rcheck/gep2pep-Ex.timings
name | user | system | elapsed | |
CategorizedCollection | 0.094 | 0.013 | 0.108 | |
CondSEA | 0.551 | 0.091 | 0.651 | |
PathSEA | 0.468 | 0.096 | 0.580 | |
addSingleGeneSets | 0.408 | 0.045 | 0.458 | |
as.CategorizedCollection | 0.253 | 0.064 | 0.322 | |
buildPEPs | 0.396 | 0.074 | 0.477 | |
checkRepository | 0.155 | 0.043 | 0.201 | |
clearCache | 0.496 | 0.091 | 0.595 | |
createMergedRepository | 0.472 | 0.127 | 0.610 | |
createRepository | 0.134 | 0.042 | 0.182 | |
exportSEA | 0.393 | 0.083 | 0.486 | |
gene2pathways | 0.132 | 0.042 | 0.176 | |
getCollections | 0.129 | 0.039 | 0.171 | |
getDetails | 0.389 | 0.080 | 0.478 | |
getResults | 0.479 | 0.075 | 0.561 | |
importFromRawMode | 0.428 | 0.069 | 0.504 | |
importMSigDB.xml | 0.126 | 0.039 | 0.169 | |
loadCollection | 0.128 | 0.041 | 0.172 | |
loadESmatrix | 0.349 | 0.073 | 0.428 | |
loadPVmatrix | 0.344 | 0.074 | 0.423 | |
loadSampleGEP | 0.001 | 0.001 | 0.002 | |
loadSamplePWS | 0.000 | 0.000 | 0.002 | |
makeCollectionIDs | 0.041 | 0.003 | 0.044 | |
openRepository | 0.124 | 0.043 | 0.170 | |
setId2setName | 0.027 | 0.001 | 0.028 | |