Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:38:04 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 1551/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pigengene 1.28.0 (landing page) Habil Zare
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the Pigengene package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Pigengene.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: Pigengene |
Version: 1.28.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pigengene_1.28.0.tar.gz |
StartedAt: 2024-03-28 06:54:22 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 07:14:07 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 1185.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Pigengene.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pigengene_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/Pigengene.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Pigengene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pigengene’ version ‘1.28.0’ * 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 ‘Pigengene’ 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 ... NOTE 'library' or 'require' calls in package code: ‘AnnotationDbi’ ‘biomaRt’ ‘energy’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘Pigengene/R/bn.calculation.R’: assignInNamespace("supported.clusters", fixArgs, "bnlearn") one.step.pigengene: no visible binding for global variable ‘org.Hs.eg.db’ Undefined global functions or variables: org.Hs.eg.db * 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 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 get.enriched.pw 130.884 10.865 155.048 one.step.pigengene 103.915 2.487 115.487 Pigengene-package 101.934 3.420 125.333 module.heatmap 75.128 2.470 84.297 make.decision.tree 20.491 0.577 22.813 compact.tree 20.057 0.645 24.993 learn.bn 18.783 0.607 20.500 make.filter 17.951 0.342 19.814 apply.filter 16.826 0.361 20.607 combine.networks 15.047 0.124 18.365 determine.modules 14.754 0.113 17.644 wgcna.one.step 13.436 0.090 14.537 gene.mapping 12.187 1.294 44.028 pigengene 10.496 0.860 12.303 plot.pigengene 10.644 0.430 12.136 compute.pigengene 10.096 0.496 12.740 project.eigen 9.439 0.419 10.639 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc/meat/Pigengene.Rcheck/00check.log’ for details.
Pigengene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Pigengene ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘Pigengene’ ... ** 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 (Pigengene)
Pigengene.Rcheck/Pigengene-Ex.timings
name | user | system | elapsed | |
Pigengene-package | 101.934 | 3.420 | 125.333 | |
aml | 0.269 | 0.014 | 0.358 | |
apply.filter | 16.826 | 0.361 | 20.607 | |
balance | 0.853 | 0.050 | 1.094 | |
calculate.beta | 0.992 | 0.042 | 1.233 | |
check.nas | 0.073 | 0.005 | 0.095 | |
check.pigengene.input | 0.072 | 0.004 | 0.092 | |
combine.networks | 15.047 | 0.124 | 18.365 | |
compact.tree | 20.057 | 0.645 | 24.993 | |
compute.pigengene | 10.096 | 0.496 | 12.740 | |
dcor.matrix | 0.222 | 0.022 | 0.288 | |
determine.modules | 14.754 | 0.113 | 17.644 | |
draw.bn | 0 | 0 | 0 | |
eigengenes33 | 0.158 | 0.012 | 0.202 | |
gene.mapping | 12.187 | 1.294 | 44.028 | |
get.enriched.pw | 130.884 | 10.865 | 155.048 | |
get.fitted.leaf | 0.854 | 0.065 | 0.979 | |
get.genes | 0.811 | 0.057 | 0.917 | |
get.used.features | 0.805 | 0.051 | 0.898 | |
learn.bn | 18.783 | 0.607 | 20.500 | |
make.decision.tree | 20.491 | 0.577 | 22.813 | |
make.filter | 17.951 | 0.342 | 19.814 | |
mds | 0.178 | 0.015 | 0.208 | |
message.if | 0.001 | 0.001 | 0.000 | |
module.heatmap | 75.128 | 2.470 | 84.297 | |
one.step.pigengene | 103.915 | 2.487 | 115.487 | |
pheatmap.type | 0.491 | 0.010 | 0.545 | |
pigengene | 10.496 | 0.860 | 12.303 | |
plot.pigengene | 10.644 | 0.430 | 12.136 | |
preds.at | 1.020 | 0.058 | 1.285 | |
project.eigen | 9.439 | 0.419 | 10.639 | |
pvalues.manova | 0.075 | 0.009 | 0.091 | |
save.if | 0.887 | 0.033 | 0.979 | |
wgcna.one.step | 13.436 | 0.090 | 14.537 | |