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This page was generated on 2022-10-19 13:20:40 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for Pigengene on nebbiolo1


To the developers/maintainers of the Pigengene package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1458/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.22.0  (landing page)
Habil Zare
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/Pigengene
git_branch: RELEASE_3_15
git_last_commit: 9b1948a
git_last_commit_date: 2022-04-26 11:32:36 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: Pigengene
Version: 1.22.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Pigengene_1.22.0.tar.gz
StartedAt: 2022-10-18 21:08:25 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:18:59 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 633.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Pigengene.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Pigengene_1.22.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/Pigengene.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pigengene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pigengene’ version ‘1.22.0’
* 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 R 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 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 ... OK
* 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 78.035  0.644  78.683
Pigengene-package  74.070  1.229  75.304
get.enriched.pw    63.232  3.716  67.194
module.heatmap     35.030  0.488  35.518
learn.bn           18.144  0.146  18.291
make.filter        16.862  0.160  17.022
combine.networks   15.376  0.070  15.446
apply.filter       15.247  0.176  15.423
determine.modules  14.877  0.004  14.880
wgcna.one.step     14.411  0.016  14.442
make.decision.tree 10.901  0.124  11.026
compact.tree        9.711  0.040   9.751
gene.mapping        7.740  0.508  34.114
plot.pigengene      6.205  0.024   6.230
compute.pigengene   5.915  0.176   6.091
pigengene           5.613  0.124   5.739
project.eigen       5.360  0.060   5.420
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/Pigengene.Rcheck/00check.log’
for details.



Installation output

Pigengene.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL Pigengene
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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-package74.070 1.22975.304
aml0.1460.0040.149
apply.filter15.247 0.17615.423
balance0.3900.0320.422
calculate.beta0.8700.0040.874
check.nas0.0410.0000.042
check.pigengene.input0.0420.0000.042
combine.networks15.376 0.07015.446
compact.tree9.7110.0409.751
compute.pigengene5.9150.1766.091
dcor.matrix0.1620.0120.174
determine.modules14.877 0.00414.880
draw.bn000
eigengenes330.0810.0000.081
gene.mapping 7.740 0.50834.114
get.enriched.pw63.232 3.71667.194
get.fitted.leaf0.4920.0040.497
get.genes0.4790.0040.483
get.used.features0.4610.0000.461
learn.bn18.144 0.14618.291
make.decision.tree10.901 0.12411.026
make.filter16.862 0.16017.022
mds0.0970.0000.096
message.if0.0010.0000.000
module.heatmap35.030 0.48835.518
one.step.pigengene78.035 0.64478.683
pheatmap.type0.1760.0040.181
pigengene5.6130.1245.739
plot.pigengene6.2050.0246.230
preds.at0.5840.0080.592
project.eigen5.360.065.42
pvalues.manova0.0670.0000.067
save.if0.8480.0000.848
wgcna.one.step14.411 0.01614.442