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CHECK report for Pigengene on machv2

This page was generated on 2020-09-11 12:02:25 -0400 (Fri, 11 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Pigengene PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1314/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.14.0
Habil Zare
Snapshot Date: 2020-09-10 14:51:34 -0400 (Thu, 10 Sep 2020)
URL: https://git.bioconductor.org/packages/Pigengene
Branch: RELEASE_3_11
Last Commit: 894dcda
Last Changed Date: 2020-04-27 14:57:53 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Pigengene
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pigengene_1.14.0.tar.gz
StartedAt: 2020-09-11 02:37:22 -0400 (Fri, 11 Sep 2020)
EndedAt: 2020-09-11 02:46:22 -0400 (Fri, 11 Sep 2020)
EllapsedTime: 540.3 seconds
RetCode: 0
Status:  OK 
CheckDir: Pigengene.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pigengene_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Pigengene.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.0’
* 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")

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 ... NOTE
Output for data("pigengene", package = "Pigengene"):
  
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
one.step.pigengene 80.120  2.142  82.882
Pigengene-package  78.075  2.646  81.222
module.heatmap     24.073  0.753  24.919
make.decision.tree 19.417  0.774  20.367
compact.tree       18.898  0.751  19.699
gene.mapping       15.712  0.501  21.322
learn.bn           13.168  0.102  13.300
pigengene           9.250  0.545  10.093
compute.pigengene   8.795  0.419   9.258
combine.networks    9.124  0.039   9.212
plot.pigengene      8.422  0.439   8.907
wgcna.one.step      8.373  0.033   8.425
project.eigen       7.941  0.364   8.327
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/Pigengene.Rcheck/00check.log’
for details.



Installation output

Pigengene.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Pigengene
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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-package78.075 2.64681.222
aml0.2410.0080.256
balance0.6860.0330.719
calculate.beta1.1370.0581.196
check.nas0.0750.0030.078
check.pigengene.input0.0740.0030.078
combine.networks9.1240.0399.212
compact.tree18.898 0.75119.699
compute.pigengene8.7950.4199.258
dcor.matrix0.2200.0130.234
draw.bn000
eigengenes330.1410.0070.214
gene.mapping15.712 0.50121.322
get.fitted.leaf0.9820.0371.026
get.genes0.8480.0210.877
get.used.features0.8570.0220.885
learn.bn13.168 0.10213.300
make.decision.tree19.417 0.77420.367
mds0.1530.0060.160
message.if0.0010.0000.001
module.heatmap24.073 0.75324.919
one.step.pigengene80.120 2.14282.882
pheatmap.type0.3760.0080.391
pigengene 9.250 0.54510.093
plot.pigengene8.4220.4398.907
preds.at1.0090.0191.055
project.eigen7.9410.3648.327
pvalues.manova0.1170.0050.125
save.if0.6110.0500.663
wgcna.one.step8.3730.0338.425