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This page was generated on 2025-08-08 12:06 -0400 (Fri, 08 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1566/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.35.0  (landing page)
Habil Zare
Snapshot Date: 2025-08-07 13:45 -0400 (Thu, 07 Aug 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)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for Pigengene on nebbiolo2

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.

raw results


Summary

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: 2025-08-08 01:25:04 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 01:37:21 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 736.7 seconds
RetCode: 0
Status:   OK  
CheckDir: Pigengene.Rcheck
Warnings: 0

Command output

##############################################################################
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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 (2025-06-13)
* 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 24.04.2 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 74.429  0.618  75.053
Pigengene-package  69.163  1.069  70.205
get.enriched.pw    59.443  3.237  62.703
module.heatmap     35.300  0.470  35.769
make.filter        17.370  0.269  17.643
learn.bn           15.661  0.204  15.859
determine.modules  14.021  0.019  14.041
apply.filter       12.848  0.196  13.044
combine.networks   12.352  0.077  12.425
compute.pigengene  11.928  0.213  12.142
wgcna.one.step     11.595  0.047  11.642
make.decision.tree  9.918  0.143  10.062
compact.tree        9.617  0.038   9.657
gene.mapping        6.421  0.360   8.243
pigengene           6.276  0.130   6.407
plot.pigengene      6.188  0.030   6.218
project.eigen       5.807  0.055   5.862
* 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.


Installation output

Pigengene.Rcheck/00install.out

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###
### 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)

Tests output


Example timings

Pigengene.Rcheck/Pigengene-Ex.timings

nameusersystemelapsed
Pigengene-package69.163 1.06970.205
aml0.1690.0050.168
apply.filter12.848 0.19613.044
balance0.3950.0770.473
calculate.beta0.7570.0140.772
check.nas0.0400.0020.042
check.pigengene.input0.0410.0010.042
combine.networks12.352 0.07712.425
compact.tree9.6170.0389.657
compute.pigengene11.928 0.21312.142
dcor.matrix0.1630.0060.169
determine.modules14.021 0.01914.041
draw.bn000
eigengenes330.1140.0010.115
gene.mapping6.4210.3608.243
get.enriched.pw59.443 3.23762.703
get.fitted.leaf0.5110.0150.526
get.genes0.4780.0060.484
get.used.features0.4870.0040.492
learn.bn15.661 0.20415.859
make.decision.tree 9.918 0.14310.062
make.filter17.370 0.26917.643
mds0.1390.0050.145
message.if000
module.heatmap35.300 0.47035.769
one.step.pigengene74.429 0.61875.053
pheatmap.type0.1820.0080.191
pigengene6.2760.1306.407
plot.pigengene6.1880.0306.218
preds.at0.5810.0030.584
project.eigen5.8070.0555.862
pvalues.manova0.0790.0000.079
save.if0.6990.0710.771
wgcna.one.step11.595 0.04711.642