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This page was generated on 2021-10-15 15:05:48 -0400 (Fri, 15 Oct 2021).

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? here 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 1394/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.18.10  (landing page)
Habil Zare
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/Pigengene
git_branch: RELEASE_3_13
git_last_commit: 72e780a
git_last_commit_date: 2021-09-27 19:01:24 -0400 (Mon, 27 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Pigengene
Version: 1.18.10
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Pigengene_1.18.10.tar.gz
StartedAt: 2021-10-14 11:02:12 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:09:22 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 429.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Pigengene.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Pigengene_1.18.10.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/Pigengene.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.18.10’
* 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.
Package in Depends field not imported from: ‘BiocStyle’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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")

combine.networks: no visible binding for global variable ‘netwok’
Undefined global functions or variables:
  netwok
* 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
Pigengene-package  71.095  1.049  72.150
one.step.pigengene 65.542  0.899  66.446
module.heatmap     34.854  0.412  35.268
learn.bn           16.459  0.215  16.675
combine.networks   14.741  0.020  14.762
wgcna.one.step     11.014  0.068  11.083
make.decision.tree 10.317  0.132  10.449
compact.tree       10.055  0.052  10.108
gene.mapping        8.624  0.440  12.667
compute.pigengene   5.736  0.128   5.864
pigengene           5.572  0.152   5.727
project.eigen       5.240  0.136   5.376
plot.pigengene      5.032  0.084   5.117
* 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-3.13-bioc/meat/Pigengene.Rcheck/00check.log’
for details.



Installation output

Pigengene.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Pigengene
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.13-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-package71.095 1.04972.150
aml0.1570.0000.157
balance0.4100.0640.474
calculate.beta1.3260.0001.326
check.nas0.0360.0070.043
check.pigengene.input0.0430.0000.043
combine.networks14.741 0.02014.762
compact.tree10.055 0.05210.108
compute.pigengene5.7360.1285.864
dcor.matrix0.1460.0110.157
draw.bn0.0000.0000.001
eigengenes330.0760.0000.076
gene.mapping 8.624 0.44012.667
get.fitted.leaf0.4920.0120.504
get.genes0.5650.0090.573
get.used.features0.4910.0080.499
learn.bn16.459 0.21516.675
make.decision.tree10.317 0.13210.449
mds0.0890.0000.089
message.if0.0000.0000.001
module.heatmap34.854 0.41235.268
one.step.pigengene65.542 0.89966.446
pheatmap.type0.1730.0030.176
pigengene5.5720.1525.727
plot.pigengene5.0320.0845.117
preds.at0.5420.0080.551
project.eigen5.2400.1365.376
pvalues.manova0.0630.0040.067
save.if0.7030.0080.712
wgcna.one.step11.014 0.06811.083