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 12:07 -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 115/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
attract 1.58.0 (landing page) Samuel Zimmerman
| 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 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: 1.58.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:attract.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings attract_1.58.0.tar.gz |
StartedAt: 2024-12-20 11:37:59 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 11:43:16 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 317.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: attract.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:attract.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings attract_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/attract.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘attract/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘attract’ version ‘1.58.0’ * 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 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 ... 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 ... NOTE checkRd: (-1) attract-package.Rd:34: Lost braces 34 | M\"{u}ller F et al. 2008. Regulatory networks define phenotypic classes of human stem cell lines. Nature. 455(7211): 401. | ^ checkRd: (-1) exprs.dat.Rd:29: Lost braces 29 | M\"{u}ller F, et al., Regulatory networks define phenotypic classes of human stem cell lines. Nature, 2008. 455(7211): p. 401-405. | ^ checkRd: (-1) findOnepwaySynexprs.Rd:15: Lost braces 15 | a single character string denoting the KEGG or reactome ID of the pathway module to be analyzed or a character code{vector} of gene names of a pathway. | ^ checkRd: (-1) findSynexprs.Rd:16: Lost braces 16 | It may also be a character code{vector} of gene names of a pathway if defining a custom pathway. | ^ checkRd: (-1) loring.eset.Rd:23: Lost braces 23 | M\"{u}ller, F, et al., Regulatory networks define phenotypic classes of human stem cell lines. Nature, 2008. 455(7211): p. 401-405. | ^ checkRd: (-1) samp.info.Rd:28: Lost braces 28 | M\"{u}ller F, et al., Regulatory networks define phenotypic classes of human stem cell lines. Nature, 2008. 455(7211): p. 401-405. | ^ checkRd: (-1) subset.loring.eset.Rd:25: Lost braces 25 | M\"{u}ller, F, et al., Regulatory networks define phenotypic classes of human stem cell lines. Nature, 2008. 455(7211): p. 401-405. | ^ * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed calcFuncSynexprs 79.899 8.031 90.302 findAttractors 32.164 1.750 35.460 findCorrPartners 4.663 0.214 5.522 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/attract.Rcheck/00check.log’ for details.
attract.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL attract ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 | 0 | 0 | |
SynExpressionSet-class | 0.001 | 0.000 | 0.001 | |
attract-package | 0.000 | 0.000 | 0.001 | |
buildCorMatrix | 0.000 | 0.001 | 0.001 | |
buildKeggIncidenceMatrix | 0.000 | 0.000 | 0.001 | |
calcFuncSynexprs | 79.899 | 8.031 | 90.302 | |
calcInform | 0.000 | 0.001 | 0.000 | |
calcModfstat | 0.000 | 0.001 | 0.000 | |
calcRss | 0 | 0 | 0 | |
exprs.dat | 0.194 | 0.008 | 0.202 | |
filterDataSet | 0.299 | 0.039 | 0.339 | |
findAttractors | 32.164 | 1.750 | 35.460 | |
findCorrPartners | 4.663 | 0.214 | 5.522 | |
findOnepwaySynexprs | 0.001 | 0.001 | 0.001 | |
findSynexprs | 3.525 | 0.048 | 3.946 | |
flagPwayExists | 0.000 | 0.000 | 0.001 | |
getCustomGenes | 0.000 | 0.000 | 0.001 | |
getPwayGenes | 0 | 0 | 0 | |
loring.eset | 0.233 | 0.015 | 0.252 | |
plotsynexprs | 2.973 | 0.063 | 3.426 | |
removeFlatGenes | 0.199 | 0.014 | 0.214 | |
samp.info | 0.001 | 0.002 | 0.003 | |
subset.loring.eset | 0.109 | 0.004 | 0.115 | |