Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:35:11 -0400 (Mon, 16 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 110/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
attract 1.52.0 (landing page) Samuel Zimmerman
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the attract package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/attract.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: attract |
Version: 1.52.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:attract.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings attract_1.52.0.tar.gz |
StartedAt: 2023-10-15 19:17:50 -0400 (Sun, 15 Oct 2023) |
EndedAt: 2023-10-15 19:26:29 -0400 (Sun, 15 Oct 2023) |
EllapsedTime: 518.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: attract.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:attract.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings attract_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/attract.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘attract/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘attract’ version ‘1.52.0’ * 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 ‘attract’ 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 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 plotsynexprs: warning in axis(1, at = tickMarks, lab = tickLabels): partial argument match of 'lab' to 'labels' removeFlatGenes: warning in topTable(fit2, coef = (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)): partial argument match of 'n' to 'number' removeFlatGenes: warning in topTable(fit2, coef = (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)): partial argument match of 'adjust' to 'adjust.method' * 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed calcFuncSynexprs 70.499 3.979 75.989 findAttractors 40.006 2.188 43.694 findCorrPartners 4.875 0.120 5.423 plotsynexprs 4.214 0.360 5.163 findSynexprs 4.101 0.036 5.078 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘attract.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/attract.Rcheck/00check.log’ for details.
attract.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL attract ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘attract’ ... ** 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 (attract)
attract.Rcheck/attract-Ex.timings
name | user | system | elapsed | |
AttractorModuleSet-class | 0.000 | 0.000 | 0.001 | |
SynExpressionSet-class | 0.001 | 0.000 | 0.001 | |
attract-package | 0 | 0 | 0 | |
buildCorMatrix | 0 | 0 | 0 | |
buildKeggIncidenceMatrix | 0.001 | 0.000 | 0.000 | |
calcFuncSynexprs | 70.499 | 3.979 | 75.989 | |
calcInform | 0 | 0 | 0 | |
calcModfstat | 0.001 | 0.000 | 0.000 | |
calcRss | 0.001 | 0.000 | 0.000 | |
exprs.dat | 0.129 | 0.004 | 0.133 | |
filterDataSet | 0.195 | 0.008 | 0.202 | |
findAttractors | 40.006 | 2.188 | 43.694 | |
findCorrPartners | 4.875 | 0.120 | 5.423 | |
findOnepwaySynexprs | 0 | 0 | 0 | |
findSynexprs | 4.101 | 0.036 | 5.078 | |
flagPwayExists | 0 | 0 | 0 | |
getCustomGenes | 0.001 | 0.000 | 0.000 | |
getPwayGenes | 0.000 | 0.000 | 0.001 | |
loring.eset | 0.123 | 0.016 | 0.139 | |
plotsynexprs | 4.214 | 0.360 | 5.163 | |
removeFlatGenes | 0.117 | 0.008 | 0.125 | |
samp.info | 0.001 | 0.000 | 0.001 | |
subset.loring.eset | 0.070 | 0.008 | 0.078 | |