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This page was generated on 2024-05-27 11:35:29 -0400 (Mon, 27 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4752
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4517
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 1568/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.30.0  (landing page)
Habil Zare
Snapshot Date: 2024-05-26 14:00:09 -0400 (Sun, 26 May 2024)
git_url: https://git.bioconductor.org/packages/Pigengene
git_branch: RELEASE_3_19
git_last_commit: a1faa8a
git_last_commit_date: 2024-04-30 10:51:21 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  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 13.6.5 Ventura / arm64see weekly results here

CHECK results for Pigengene on nebbiolo1


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: 1.30.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Pigengene_1.30.0.tar.gz
StartedAt: 2024-05-27 01:46:56 -0400 (Mon, 27 May 2024)
EndedAt: 2024-05-27 02:00:16 -0400 (Mon, 27 May 2024)
EllapsedTime: 800.2 seconds
RetCode: 0
Status:   OK  
CheckDir: Pigengene.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Pigengene_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Pigengene.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 85.659  0.684  86.346
Pigengene-package  80.032  1.672  81.624
get.enriched.pw    70.522  3.303  73.828
module.heatmap     36.406  0.308  36.700
apply.filter       16.444  0.552  16.997
make.filter        16.484  0.224  16.709
learn.bn           16.506  0.162  16.667
combine.networks   15.021  0.244  15.248
determine.modules  15.034  0.145  15.179
wgcna.one.step     13.672  0.048  13.721
make.decision.tree 10.788  0.104  10.892
compact.tree       10.782  0.096  10.877
gene.mapping        6.929  0.656  12.846
pigengene           7.092  0.104   7.197
compute.pigengene   6.920  0.236   7.157
plot.pigengene      6.724  0.083   6.807
project.eigen       6.444  0.064   6.507
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/Pigengene.Rcheck/00check.log’
for details.


Installation output

Pigengene.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Pigengene
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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)

Tests output


Example timings

Pigengene.Rcheck/Pigengene-Ex.timings

nameusersystemelapsed
Pigengene-package80.032 1.67281.624
aml0.1690.0040.160
apply.filter16.444 0.55216.997
balance0.4410.0600.500
calculate.beta0.9320.0280.960
check.nas0.0430.0000.043
check.pigengene.input0.0380.0110.048
combine.networks15.021 0.24415.248
compact.tree10.782 0.09610.877
compute.pigengene6.9200.2367.157
dcor.matrix0.1260.0080.135
determine.modules15.034 0.14515.179
draw.bn000
eigengenes330.0810.0080.088
gene.mapping 6.929 0.65612.846
get.enriched.pw70.522 3.30373.828
get.fitted.leaf0.4940.0000.493
get.genes0.5630.0080.570
get.used.features0.4720.0000.472
learn.bn16.506 0.16216.667
make.decision.tree10.788 0.10410.892
make.filter16.484 0.22416.709
mds0.0950.0040.099
message.if0.0010.0000.000
module.heatmap36.406 0.30836.700
one.step.pigengene85.659 0.68486.346
pheatmap.type0.190.000.19
pigengene7.0920.1047.197
plot.pigengene6.7240.0836.807
preds.at0.6050.0040.609
project.eigen6.4440.0646.507
pvalues.manova0.0680.0000.069
save.if0.9340.0000.934
wgcna.one.step13.672 0.04813.721