Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:41 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1538/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pigengene 1.29.10 (landing page) Habil Zare
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.29.10 |
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_1.29.10.tar.gz |
StartedAt: 2024-03-02 08:29:57 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 08:51:03 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 1265.8 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_1.29.10.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Pigengene.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Pigengene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pigengene’ version ‘1.29.10’ * 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 130.883 11.730 173.704 Pigengene-package 100.377 3.378 132.865 one.step.pigengene 99.923 3.149 118.321 module.heatmap 72.166 2.807 98.738 make.decision.tree 20.781 0.673 25.624 compact.tree 20.364 0.611 27.644 learn.bn 18.121 0.379 22.412 make.filter 17.128 0.396 20.250 apply.filter 15.842 0.389 21.235 gene.mapping 13.977 1.450 32.738 combine.networks 14.594 0.141 19.034 determine.modules 13.816 0.143 17.564 wgcna.one.step 13.205 0.153 15.470 pigengene 10.486 0.930 13.233 plot.pigengene 10.625 0.481 13.172 compute.pigengene 10.595 0.479 14.462 project.eigen 9.432 0.465 12.412 * 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-3.19-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 | 100.377 | 3.378 | 132.865 | |
aml | 0.264 | 0.012 | 0.370 | |
apply.filter | 15.842 | 0.389 | 21.235 | |
balance | 0.853 | 0.052 | 1.135 | |
calculate.beta | 0.982 | 0.038 | 1.264 | |
check.nas | 0.069 | 0.005 | 0.089 | |
check.pigengene.input | 0.070 | 0.004 | 0.089 | |
combine.networks | 14.594 | 0.141 | 19.034 | |
compact.tree | 20.364 | 0.611 | 27.644 | |
compute.pigengene | 10.595 | 0.479 | 14.462 | |
dcor.matrix | 0.219 | 0.018 | 0.296 | |
determine.modules | 13.816 | 0.143 | 17.564 | |
draw.bn | 0.000 | 0.001 | 0.000 | |
eigengenes33 | 0.165 | 0.012 | 0.229 | |
gene.mapping | 13.977 | 1.450 | 32.738 | |
get.enriched.pw | 130.883 | 11.730 | 173.704 | |
get.fitted.leaf | 0.855 | 0.060 | 1.080 | |
get.genes | 0.815 | 0.060 | 1.029 | |
get.used.features | 0.828 | 0.065 | 1.060 | |
learn.bn | 18.121 | 0.379 | 22.412 | |
make.decision.tree | 20.781 | 0.673 | 25.624 | |
make.filter | 17.128 | 0.396 | 20.250 | |
mds | 0.177 | 0.019 | 0.239 | |
message.if | 0.000 | 0.000 | 0.001 | |
module.heatmap | 72.166 | 2.807 | 98.738 | |
one.step.pigengene | 99.923 | 3.149 | 118.321 | |
pheatmap.type | 0.502 | 0.013 | 0.599 | |
pigengene | 10.486 | 0.930 | 13.233 | |
plot.pigengene | 10.625 | 0.481 | 13.172 | |
preds.at | 1.012 | 0.061 | 1.294 | |
project.eigen | 9.432 | 0.465 | 12.412 | |
pvalues.manova | 0.074 | 0.010 | 0.086 | |
save.if | 0.863 | 0.033 | 1.099 | |
wgcna.one.step | 13.205 | 0.153 | 15.470 | |