Habil Zare
| Snapshot Date: 2025-04-16 13:40 -0400 (Wed, 16 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/Pigengene |
| git_branch: RELEASE_3_21 |
| git_last_commit: 04213d7 |
| git_last_commit_date: 2025-04-15 11:02:19 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-17 11:47 -0400 (Thu, 17 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4667 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 1583/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Pigengene 1.34.0 (landing page) Habil Zare
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | 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 | | ||||||||
| kunpeng2 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Pigengene |
| Version: 1.34.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Pigengene_1.34.0.tar.gz |
| StartedAt: 2025-04-17 10:03:13 -0000 (Thu, 17 Apr 2025) |
| EndedAt: 2025-04-17 10:27:23 -0000 (Thu, 17 Apr 2025) |
| EllapsedTime: 1450.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Pigengene.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Pigengene_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Pigengene.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (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 ‘1.34.0’
* 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: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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
one.step.pigengene 390.578 1.017 392.186
Pigengene-package 384.742 0.790 386.295
get.enriched.pw 84.398 3.475 88.208
module.heatmap 48.133 0.291 48.512
compute.pigengene 44.416 0.140 44.635
make.filter 25.787 0.108 25.943
apply.filter 23.723 0.064 23.851
plot.pigengene 23.543 0.112 23.694
pigengene 23.488 0.119 23.647
project.eigen 23.259 0.080 23.386
learn.bn 19.793 0.223 20.059
combine.networks 15.757 0.008 15.817
determine.modules 15.487 0.067 15.579
compact.tree 15.419 0.059 15.528
make.decision.tree 15.345 0.064 15.446
wgcna.one.step 14.857 0.012 14.901
gene.mapping 8.402 0.456 12.530
* 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
‘/home/biocbuild/bbs-3.21-bioc/meat/Pigengene.Rcheck/00check.log’
for details.
Pigengene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Pigengene ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘Pigengene’ ... ** this is package ‘Pigengene’ version ‘1.34.0’ ** 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 | 384.742 | 0.790 | 386.295 | |
| aml | 0.164 | 0.000 | 0.166 | |
| apply.filter | 23.723 | 0.064 | 23.851 | |
| balance | 0.392 | 0.016 | 0.409 | |
| calculate.beta | 0.889 | 0.004 | 0.895 | |
| check.nas | 0.041 | 0.000 | 0.041 | |
| check.pigengene.input | 0.04 | 0.00 | 0.04 | |
| combine.networks | 15.757 | 0.008 | 15.817 | |
| compact.tree | 15.419 | 0.059 | 15.528 | |
| compute.pigengene | 44.416 | 0.140 | 44.635 | |
| dcor.matrix | 0.194 | 0.016 | 0.212 | |
| determine.modules | 15.487 | 0.067 | 15.579 | |
| draw.bn | 0 | 0 | 0 | |
| eigengenes33 | 0.147 | 0.000 | 0.148 | |
| gene.mapping | 8.402 | 0.456 | 12.530 | |
| get.enriched.pw | 84.398 | 3.475 | 88.208 | |
| get.fitted.leaf | 0.552 | 0.008 | 0.562 | |
| get.genes | 0.533 | 0.004 | 0.539 | |
| get.used.features | 0.533 | 0.004 | 0.539 | |
| learn.bn | 19.793 | 0.223 | 20.059 | |
| make.decision.tree | 15.345 | 0.064 | 15.446 | |
| make.filter | 25.787 | 0.108 | 25.943 | |
| mds | 0.167 | 0.000 | 0.169 | |
| message.if | 0 | 0 | 0 | |
| module.heatmap | 48.133 | 0.291 | 48.512 | |
| one.step.pigengene | 390.578 | 1.017 | 392.186 | |
| pheatmap.type | 0.253 | 0.000 | 0.253 | |
| pigengene | 23.488 | 0.119 | 23.647 | |
| plot.pigengene | 23.543 | 0.112 | 23.694 | |
| preds.at | 0.672 | 0.020 | 0.695 | |
| project.eigen | 23.259 | 0.080 | 23.386 | |
| pvalues.manova | 0.086 | 0.004 | 0.091 | |
| save.if | 0.894 | 0.000 | 0.895 | |
| wgcna.one.step | 14.857 | 0.012 | 14.901 | |