Habil Zare
| Snapshot Date: 2025-06-12 13:25 -0400 (Thu, 12 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/Pigengene |
| git_branch: devel |
| git_last_commit: ab1017c |
| git_last_commit_date: 2025-04-15 11:02:19 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-13 12:09 -0400 (Fri, 13 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4797 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4538 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4571 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4515 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4483 |
| 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 1564/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Pigengene 1.35.0 (landing page) Habil Zare
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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: 1.35.0 |
| 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_1.35.0.tar.gz |
| StartedAt: 2025-06-12 22:41:58 -0400 (Thu, 12 Jun 2025) |
| EndedAt: 2025-06-12 22:52:51 -0400 (Thu, 12 Jun 2025) |
| EllapsedTime: 653.5 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_1.35.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Pigengene.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pigengene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pigengene’ version ‘1.35.0’
* 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:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:27-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:30-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:45-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:60-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:64-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:73-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pigengene-class.Rd:77-79: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'draw.bn.Rd':
‘[bnlearn:bn.class]{bn-class}’
Non-topic package-anchored link(s) in Rd file 'gene.mapping.Rd':
‘[org.Hs.eg.db:org.Hs.egBASE]{org.Hs.eg.db}’
‘[org.Mm.eg.db:org.Mm.egBASE]{org.Mm.eg.db}’
Non-topic package-anchored link(s) in Rd file 'learn.bn.Rd':
‘[bnlearn:preprocessing]{discretize}’ ‘[bnlearn:bn.class]{bn-class}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 70.808 5.818 77.388
one.step.pigengene 74.312 2.283 77.077
Pigengene-package 70.838 2.635 73.915
module.heatmap 33.307 1.640 35.211
learn.bn 15.624 0.218 15.948
make.filter 14.741 0.285 15.108
apply.filter 13.635 0.293 14.168
combine.networks 12.975 0.108 13.160
determine.modules 12.754 0.111 12.951
wgcna.one.step 12.735 0.073 12.858
compact.tree 11.451 0.626 12.152
compute.pigengene 11.383 0.624 12.083
make.decision.tree 11.272 0.473 11.820
gene.mapping 7.740 0.866 20.172
pigengene 6.417 0.545 7.018
plot.pigengene 6.165 0.350 6.555
project.eigen 6.047 0.333 6.417
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/library’ * installing *source* package ‘Pigengene’ ... ** this is package ‘Pigengene’ version ‘1.35.0’ ** 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 | 70.838 | 2.635 | 73.915 | |
| aml | 0.140 | 0.007 | 0.148 | |
| apply.filter | 13.635 | 0.293 | 14.168 | |
| balance | 0.352 | 0.039 | 0.393 | |
| calculate.beta | 0.754 | 0.029 | 0.789 | |
| check.nas | 0.036 | 0.003 | 0.038 | |
| check.pigengene.input | 0.043 | 0.003 | 0.047 | |
| combine.networks | 12.975 | 0.108 | 13.160 | |
| compact.tree | 11.451 | 0.626 | 12.152 | |
| compute.pigengene | 11.383 | 0.624 | 12.083 | |
| dcor.matrix | 0.143 | 0.016 | 0.161 | |
| determine.modules | 12.754 | 0.111 | 12.951 | |
| draw.bn | 0.000 | 0.001 | 0.000 | |
| eigengenes33 | 0.103 | 0.007 | 0.110 | |
| gene.mapping | 7.740 | 0.866 | 20.172 | |
| get.enriched.pw | 70.808 | 5.818 | 77.388 | |
| get.fitted.leaf | 0.397 | 0.021 | 0.442 | |
| get.genes | 0.385 | 0.022 | 0.411 | |
| get.used.features | 1.234 | 0.110 | 1.354 | |
| learn.bn | 15.624 | 0.218 | 15.948 | |
| make.decision.tree | 11.272 | 0.473 | 11.820 | |
| make.filter | 14.741 | 0.285 | 15.108 | |
| mds | 0.123 | 0.007 | 0.132 | |
| message.if | 0 | 0 | 0 | |
| module.heatmap | 33.307 | 1.640 | 35.211 | |
| one.step.pigengene | 74.312 | 2.283 | 77.077 | |
| pheatmap.type | 0.183 | 0.007 | 0.193 | |
| pigengene | 6.417 | 0.545 | 7.018 | |
| plot.pigengene | 6.165 | 0.350 | 6.555 | |
| preds.at | 0.524 | 0.031 | 0.559 | |
| project.eigen | 6.047 | 0.333 | 6.417 | |
| pvalues.manova | 0.036 | 0.005 | 0.042 | |
| save.if | 0.773 | 0.029 | 0.805 | |
| wgcna.one.step | 12.735 | 0.073 | 12.858 | |