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This page was generated on 2024-07-24 11:38 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 1528/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.31.2  (landing page)
Habil Zare
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024)
git_url: https://git.bioconductor.org/packages/Pigengene
git_branch: devel
git_last_commit: e04cac6
git_last_commit_date: 2024-06-23 12:56:04 -0400 (Sun, 23 Jun 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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 13.6.5 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: 1.31.2
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Pigengene_1.31.2.tar.gz
StartedAt: 2024-07-24 02:37:30 -0400 (Wed, 24 Jul 2024)
EndedAt: 2024-07-24 02:50:29 -0400 (Wed, 24 Jul 2024)
EllapsedTime: 778.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Pigengene.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Pigengene_1.31.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Pigengene.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.31.2’
* 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 ... 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
Pigengene-package  76.661  1.040  77.621
one.step.pigengene 74.379  0.573  74.952
get.enriched.pw    67.444  2.275  69.733
module.heatmap     34.985  0.272  35.243
combine.networks   16.119  0.060  16.159
learn.bn           16.120  0.014  16.121
apply.filter       15.549  0.184  15.733
make.filter        15.631  0.060  15.691
determine.modules  13.662  0.105  13.766
wgcna.one.step     12.791  0.028  12.820
compute.pigengene  12.409  0.188  12.596
make.decision.tree 10.200  0.012  10.212
compact.tree       10.178  0.031  10.209
pigengene           6.915  0.160   7.076
plot.pigengene      6.521  0.040   6.562
gene.mapping        6.182  0.281  12.053
project.eigen       6.174  0.088   6.262
* 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-3.20-bioc/meat/Pigengene.Rcheck/00check.log’
for details.


Installation output

Pigengene.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Pigengene
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.20-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-package76.661 1.04077.621
aml0.1790.0040.168
apply.filter15.549 0.18415.733
balance0.4390.0600.498
calculate.beta0.8470.0080.856
check.nas0.0420.0000.043
check.pigengene.input0.0400.0030.043
combine.networks16.119 0.06016.159
compact.tree10.178 0.03110.209
compute.pigengene12.409 0.18812.596
dcor.matrix0.1700.0040.174
determine.modules13.662 0.10513.766
draw.bn000
eigengenes330.1210.0000.121
gene.mapping 6.182 0.28112.053
get.enriched.pw67.444 2.27569.733
get.fitted.leaf0.4910.0040.495
get.genes0.4670.0000.466
get.used.features0.5250.0080.534
learn.bn16.120 0.01416.121
make.decision.tree10.200 0.01210.212
make.filter15.631 0.06015.691
mds0.1260.0040.130
message.if0.0010.0000.000
module.heatmap34.985 0.27235.243
one.step.pigengene74.379 0.57374.952
pheatmap.type0.1880.0040.193
pigengene6.9150.1607.076
plot.pigengene6.5210.0406.562
preds.at0.5700.0080.578
project.eigen6.1740.0886.262
pvalues.manova0.0800.0000.079
save.if0.9110.0000.911
wgcna.one.step12.791 0.02812.820