Back to Build/check report for BioC 3.19 experimental data |
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This page was generated on 2024-07-25 14:51 -0400 (Thu, 25 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4748 |
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 27/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
BioPlex 1.10.0 (landing page) Ludwig Geistlinger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the BioPlex package: - 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: BioPlex |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BioPlex.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BioPlex_1.10.0.tar.gz |
StartedAt: 2024-07-25 11:10:21 -0400 (Thu, 25 Jul 2024) |
EndedAt: 2024-07-25 11:16:28 -0400 (Thu, 25 Jul 2024) |
EllapsedTime: 366.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BioPlex.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BioPlex.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BioPlex_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/BioPlex.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘BioPlex/DESCRIPTION’ ... OK * this is package ‘BioPlex’ version ‘1.10.0’ * 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 ‘BioPlex’ 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 ... NOTE getCorum: no visible binding for global variable ‘Organism’ Undefined global functions or variables: Organism * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed ccleProteome2SummarizedExperiment 35.212 1.412 37.015 annotatePFAM 14.332 1.202 16.461 bioplex2graph 7.448 0.360 7.855 mapSummarizedExperimentOntoGraph 6.445 0.088 6.668 hasSubunit 5.913 0.160 6.379 corum2graphlist 5.555 0.248 6.103 * 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-3.19-data-experiment/meat/BioPlex.Rcheck/00check.log’ for details.
BioPlex.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BioPlex ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘BioPlex’ ... ** 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 (BioPlex)
BioPlex.Rcheck/BioPlex-Ex.timings
name | user | system | elapsed | |
annotatePFAM | 14.332 | 1.202 | 16.461 | |
bioplex2graph | 7.448 | 0.360 | 7.855 | |
ccleProteome2SummarizedExperiment | 35.212 | 1.412 | 37.015 | |
corum2graphlist | 5.555 | 0.248 | 6.103 | |
corum2list | 1.488 | 0.096 | 1.751 | |
getBioPlex | 1.380 | 0.056 | 1.530 | |
getBioplexProteome | 0.213 | 0.016 | 0.259 | |
getCorum | 1.671 | 0.149 | 2.093 | |
getGSE122425 | 0.368 | 0.007 | 0.377 | |
getHEK293GenomeTrack | 0.258 | 0.004 | 0.433 | |
hasSubunit | 5.913 | 0.160 | 6.379 | |
mapSummarizedExperimentOntoGraph | 6.445 | 0.088 | 6.668 | |