Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:06 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the gep2pep package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 794/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gep2pep 1.19.0 (landing page) Francesco Napolitano
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: gep2pep |
Version: 1.19.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings gep2pep_1.19.0.tar.gz |
StartedAt: 2023-02-07 02:54:20 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 02:57:30 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 189.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gep2pep.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings gep2pep_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/gep2pep.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘gep2pep/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gep2pep’ version ‘1.19.0’ * package encoding: UTF-8 * 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 ‘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 R 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 ... OK * 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
gep2pep.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL gep2pep ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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, 519 bytes (current file size: 4.3 Kb) Chunk 2 of 2, 664 bytes (current file size: 16.3 Kb) Chunk 1 of 2, 540 bytes (current file size: 4.3 Kb) Chunk 2 of 2, 691 bytes (current file size: 16.3 Kb) Chunk 1 of 2, 549 bytes (current file size: 4.3 Kb) Chunk 2 of 2, 684 bytes (current file size: 16.3 Kb) [ FAIL 0 | WARN 2273 | SKIP 1 | PASS 154 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (1) [ FAIL 0 | WARN 2273 | SKIP 1 | PASS 154 ] > > proc.time() user system elapsed 38.540 0.639 39.278
gep2pep.Rcheck/gep2pep-Ex.timings
name | user | system | elapsed | |
CategorizedCollection | 0.133 | 0.004 | 0.137 | |
CondSEA | 1.506 | 0.091 | 1.697 | |
PathSEA | 1.373 | 0.040 | 1.414 | |
addSingleGeneSets | 0.646 | 0.064 | 0.713 | |
as.CategorizedCollection | 0.358 | 0.032 | 0.390 | |
buildPEPs | 1.334 | 0.020 | 1.354 | |
checkRepository | 0.233 | 0.012 | 0.245 | |
clearCache | 1.499 | 0.020 | 1.521 | |
createMergedRepository | 1.424 | 0.040 | 1.465 | |
createRepository | 0.198 | 0.004 | 0.202 | |
exportSEA | 1.284 | 0.028 | 1.311 | |
gene2pathways | 0.196 | 0.028 | 0.223 | |
getCollections | 0.196 | 0.004 | 0.201 | |
getDetails | 1.312 | 0.020 | 1.332 | |
getResults | 1.279 | 0.048 | 1.327 | |
importFromRawMode | 1.341 | 0.052 | 1.393 | |
importMSigDB.xml | 0.193 | 0.004 | 0.198 | |
loadCollection | 0.201 | 0.004 | 0.206 | |
loadESmatrix | 1.237 | 0.020 | 1.259 | |
loadPVmatrix | 1.244 | 0.020 | 1.264 | |
loadSampleGEP | 0.001 | 0.000 | 0.001 | |
loadSamplePWS | 0.001 | 0.000 | 0.001 | |
makeCollectionIDs | 0.052 | 0.000 | 0.052 | |
openRepository | 0.190 | 0.012 | 0.204 | |
setId2setName | 0.049 | 0.000 | 0.049 | |