Habil Zare
| Snapshot Date: 2025-09-12 13:45 -0400 (Fri, 12 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/Pigengene |
| git_branch: devel |
| git_last_commit: 126d6fd |
| git_last_commit_date: 2025-08-27 09:50:33 -0400 (Wed, 27 Aug 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-13 12:03 -0400 (Sat, 13 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4719 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4538 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4522 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4543 |
| 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 1576/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Pigengene 1.35.0 (landing page) Habil Zare
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Pigengene_1.35.0.tar.gz |
| StartedAt: 2025-09-13 02:40:15 -0400 (Sat, 13 Sep 2025) |
| EndedAt: 2025-09-13 02:53:21 -0400 (Sat, 13 Sep 2025) |
| EllapsedTime: 786.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Pigengene.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Pigengene_1.35.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Pigengene.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 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 77.949 0.834 78.788
Pigengene-package 72.113 1.200 73.279
get.enriched.pw 60.660 3.558 64.253
module.heatmap 35.799 0.434 36.230
make.filter 18.296 0.256 18.553
learn.bn 16.334 0.213 16.540
determine.modules 14.966 0.030 14.996
combine.networks 14.840 0.004 14.839
apply.filter 14.259 0.193 14.453
wgcna.one.step 13.216 0.015 13.232
compute.pigengene 12.385 0.239 12.625
make.decision.tree 11.101 0.114 11.215
compact.tree 9.738 0.057 9.795
gene.mapping 6.689 0.893 13.221
pigengene 6.485 0.106 6.592
plot.pigengene 6.448 0.045 6.493
project.eigen 5.972 0.059 6.032
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/Pigengene.Rcheck/00check.log’
for details.
Pigengene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Pigengene ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 | 72.113 | 1.200 | 73.279 | |
| aml | 0.170 | 0.002 | 0.164 | |
| apply.filter | 14.259 | 0.193 | 14.453 | |
| balance | 0.400 | 0.062 | 0.463 | |
| calculate.beta | 0.804 | 0.014 | 0.818 | |
| check.nas | 0.043 | 0.000 | 0.043 | |
| check.pigengene.input | 0.041 | 0.002 | 0.044 | |
| combine.networks | 14.840 | 0.004 | 14.839 | |
| compact.tree | 9.738 | 0.057 | 9.795 | |
| compute.pigengene | 12.385 | 0.239 | 12.625 | |
| dcor.matrix | 0.164 | 0.012 | 0.178 | |
| determine.modules | 14.966 | 0.030 | 14.996 | |
| draw.bn | 0 | 0 | 0 | |
| eigengenes33 | 0.117 | 0.001 | 0.119 | |
| gene.mapping | 6.689 | 0.893 | 13.221 | |
| get.enriched.pw | 60.660 | 3.558 | 64.253 | |
| get.fitted.leaf | 0.503 | 0.005 | 0.508 | |
| get.genes | 0.561 | 0.015 | 0.577 | |
| get.used.features | 0.488 | 0.008 | 0.496 | |
| learn.bn | 16.334 | 0.213 | 16.540 | |
| make.decision.tree | 11.101 | 0.114 | 11.215 | |
| make.filter | 18.296 | 0.256 | 18.553 | |
| mds | 0.139 | 0.001 | 0.141 | |
| message.if | 0.001 | 0.000 | 0.000 | |
| module.heatmap | 35.799 | 0.434 | 36.230 | |
| one.step.pigengene | 77.949 | 0.834 | 78.788 | |
| pheatmap.type | 0.232 | 0.014 | 0.247 | |
| pigengene | 6.485 | 0.106 | 6.592 | |
| plot.pigengene | 6.448 | 0.045 | 6.493 | |
| preds.at | 0.596 | 0.010 | 0.606 | |
| project.eigen | 5.972 | 0.059 | 6.032 | |
| pvalues.manova | 0.079 | 0.003 | 0.082 | |
| save.if | 0.746 | 0.000 | 0.745 | |
| wgcna.one.step | 13.216 | 0.015 | 13.232 | |