Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:42 -0400 (Tue, 09 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 1568/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pigengene 1.30.0 (landing page) Habil Zare
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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: 1.30.0 |
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_1.30.0.tar.gz |
StartedAt: 2024-07-08 09:29:37 -0400 (Mon, 08 Jul 2024) |
EndedAt: 2024-07-08 09:51:57 -0400 (Mon, 08 Jul 2024) |
EllapsedTime: 1340.5 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_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Pigengene.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Pigengene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pigengene’ version ‘1.30.0’ * 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 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 ... 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 ... NOTE checkRd: (-1) draw.bn.Rd:47: Lost braces 47 | rename the nodes name. See code{rename.node}.} | ^ checkRd: (-1) eigengenes33.Rd:21-22: Lost braces 21 | {A 202 by 34 matrix. | ^ checkRd: (-1) eigengenes33.Rd:25: Lost braces; missing escapes or markup? 25 | {A 164 by 34 matrix for MDS cases with columns similar to aml.} | ^ checkRd: (-1) eigengenes33.Rd:28: Lost braces; missing escapes or markup? 28 | {A numeric vector of length 9166 labeling members of each module. Named by Entrez ID.} | ^ checkRd: (-1) pigengene-class.Rd:22-23: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:24-26: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:27-34: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:35-36: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:37-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:40-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:43-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:45-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:48-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:51-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:53-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:55-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:59-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:68-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:72-74: Lost braces in \itemize; meant \describe ? * 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 139.199 11.795 178.054 one.step.pigengene 105.474 2.904 125.757 Pigengene-package 103.255 3.481 134.486 module.heatmap 78.182 2.595 95.844 make.decision.tree 21.909 0.700 27.951 compact.tree 21.232 0.691 26.569 learn.bn 18.600 0.603 22.491 make.filter 17.205 0.466 22.219 apply.filter 16.849 0.367 20.736 gene.mapping 14.267 1.516 76.316 determine.modules 15.137 0.150 18.765 combine.networks 15.087 0.164 18.220 wgcna.one.step 13.733 0.130 16.709 pigengene 10.708 0.873 12.828 plot.pigengene 10.949 0.456 12.798 compute.pigengene 10.441 0.500 13.370 project.eigen 9.783 0.442 11.958 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-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/4.4-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 | 103.255 | 3.481 | 134.486 | |
aml | 0.276 | 0.013 | 0.355 | |
apply.filter | 16.849 | 0.367 | 20.736 | |
balance | 0.847 | 0.020 | 1.054 | |
calculate.beta | 1.068 | 0.065 | 1.384 | |
check.nas | 0.074 | 0.009 | 0.100 | |
check.pigengene.input | 0.077 | 0.008 | 0.103 | |
combine.networks | 15.087 | 0.164 | 18.220 | |
compact.tree | 21.232 | 0.691 | 26.569 | |
compute.pigengene | 10.441 | 0.500 | 13.370 | |
dcor.matrix | 0.230 | 0.021 | 0.313 | |
determine.modules | 15.137 | 0.150 | 18.765 | |
draw.bn | 0.001 | 0.001 | 0.000 | |
eigengenes33 | 0.170 | 0.013 | 0.221 | |
gene.mapping | 14.267 | 1.516 | 76.316 | |
get.enriched.pw | 139.199 | 11.795 | 178.054 | |
get.fitted.leaf | 0.872 | 0.058 | 1.093 | |
get.genes | 0.969 | 0.080 | 1.213 | |
get.used.features | 0.833 | 0.056 | 0.990 | |
learn.bn | 18.600 | 0.603 | 22.491 | |
make.decision.tree | 21.909 | 0.700 | 27.951 | |
make.filter | 17.205 | 0.466 | 22.219 | |
mds | 0.167 | 0.018 | 0.408 | |
message.if | 0.001 | 0.001 | 0.001 | |
module.heatmap | 78.182 | 2.595 | 95.844 | |
one.step.pigengene | 105.474 | 2.904 | 125.757 | |
pheatmap.type | 0.522 | 0.012 | 0.614 | |
pigengene | 10.708 | 0.873 | 12.828 | |
plot.pigengene | 10.949 | 0.456 | 12.798 | |
preds.at | 1.051 | 0.074 | 1.258 | |
project.eigen | 9.783 | 0.442 | 11.958 | |
pvalues.manova | 0.078 | 0.009 | 0.115 | |
save.if | 0.912 | 0.036 | 1.560 | |
wgcna.one.step | 13.733 | 0.130 | 16.709 | |