Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:40:55 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
kjohnson3 | macOS 13.6.5 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: Pigengene |
Version: 1.30.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Pigengene_1.30.0.tar.gz |
StartedAt: 2024-05-04 10:36:05 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 10:55:12 -0000 (Sat, 04 May 2024) |
EllapsedTime: 1147.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Pigengene.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Pigengene_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Pigengene.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed one.step.pigengene 252.214 0.568 253.190 Pigengene-package 242.286 0.447 243.065 get.enriched.pw 92.948 3.038 96.159 module.heatmap 48.702 0.267 49.058 make.filter 25.760 0.132 25.933 apply.filter 23.212 0.075 23.325 pigengene 20.027 0.151 20.218 learn.bn 19.717 0.114 19.865 plot.pigengene 18.928 0.052 19.017 project.eigen 18.459 0.116 18.611 compute.pigengene 18.493 0.080 18.597 make.decision.tree 16.312 0.064 16.413 compact.tree 15.796 0.036 15.867 combine.networks 15.744 0.051 15.818 determine.modules 15.339 0.008 15.374 wgcna.one.step 14.816 0.028 14.877 gene.mapping 8.131 0.598 20.135 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/Pigengene.Rcheck/00check.log’ for details.
Pigengene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL Pigengene ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 | 242.286 | 0.447 | 243.065 | |
aml | 0.171 | 0.004 | 0.173 | |
apply.filter | 23.212 | 0.075 | 23.325 | |
balance | 0.22 | 0.04 | 0.26 | |
calculate.beta | 0.874 | 0.008 | 0.884 | |
check.nas | 0.043 | 0.004 | 0.047 | |
check.pigengene.input | 0.043 | 0.000 | 0.044 | |
combine.networks | 15.744 | 0.051 | 15.818 | |
compact.tree | 15.796 | 0.036 | 15.867 | |
compute.pigengene | 18.493 | 0.080 | 18.597 | |
dcor.matrix | 0.154 | 0.004 | 0.159 | |
determine.modules | 15.339 | 0.008 | 15.374 | |
draw.bn | 0 | 0 | 0 | |
eigengenes33 | 0.1 | 0.0 | 0.1 | |
gene.mapping | 8.131 | 0.598 | 20.135 | |
get.enriched.pw | 92.948 | 3.038 | 96.159 | |
get.fitted.leaf | 0.574 | 0.000 | 0.577 | |
get.genes | 0.661 | 0.004 | 0.667 | |
get.used.features | 0.535 | 0.008 | 0.545 | |
learn.bn | 19.717 | 0.114 | 19.865 | |
make.decision.tree | 16.312 | 0.064 | 16.413 | |
make.filter | 25.760 | 0.132 | 25.933 | |
mds | 0.107 | 0.000 | 0.108 | |
message.if | 0.001 | 0.000 | 0.001 | |
module.heatmap | 48.702 | 0.267 | 49.058 | |
one.step.pigengene | 252.214 | 0.568 | 253.190 | |
pheatmap.type | 0.254 | 0.004 | 0.260 | |
pigengene | 20.027 | 0.151 | 20.218 | |
plot.pigengene | 18.928 | 0.052 | 19.017 | |
preds.at | 0.677 | 0.012 | 0.691 | |
project.eigen | 18.459 | 0.116 | 18.611 | |
pvalues.manova | 0.077 | 0.000 | 0.078 | |
save.if | 0.866 | 0.000 | 0.867 | |
wgcna.one.step | 14.816 | 0.028 | 14.877 | |