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This page was generated on 2021-07-24 12:05:35 -0400 (Sat, 24 Jul 2021).

CHECK results for Pigengene on nebbiolo2

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 1371/2008HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.19.10  (landing page)
Habil Zare
Snapshot Date: 2021-07-23 14:50:08 -0400 (Fri, 23 Jul 2021)
URL: https://git.bioconductor.org/packages/Pigengene
Branch: master
Last Commit: 5448a04
Last Changed Date: 2021-07-22 15:18:12 -0400 (Thu, 22 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  NO, package depends on 'Rgraphviz' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Pigengene
Version: 1.19.10
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Pigengene_1.19.10.tar.gz
StartedAt: 2021-07-23 20:43:18 -0400 (Fri, 23 Jul 2021)
EndedAt: 2021-07-23 20:50:47 -0400 (Fri, 23 Jul 2021)
EllapsedTime: 448.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Pigengene.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Pigengene_1.19.10.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/Pigengene.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* 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 ‘1.19.10’
* 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
one.step.pigengene 74.088  1.188  75.278
Pigengene-package  73.417  1.407  74.839
module.heatmap     37.151  0.380  37.534
learn.bn           18.926  0.233  19.160
combine.networks   15.761  0.002  15.764
wgcna.one.step     11.501  0.068  11.570
make.decision.tree 10.552  0.124  10.676
compact.tree       10.460  0.012  10.473
gene.mapping        8.670  0.304  12.119
pigengene           6.107  0.128   6.235
compute.pigengene   6.133  0.100   6.233
plot.pigengene      5.835  0.052   5.888
project.eigen       5.593  0.076   5.669
* 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-3.14-bioc/meat/Pigengene.Rcheck/00check.log’
for details.



Installation output

Pigengene.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Pigengene
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-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-package73.417 1.40774.839
aml0.1950.0000.195
balance0.4720.0240.497
calculate.beta1.8240.0201.844
check.nas0.0440.0000.044
check.pigengene.input0.0440.0000.044
combine.networks15.761 0.00215.764
compact.tree10.460 0.01210.473
compute.pigengene6.1330.1006.233
dcor.matrix0.1660.0080.174
draw.bn000
eigengenes330.0860.0000.086
gene.mapping 8.670 0.30412.119
get.fitted.leaf0.4950.0240.518
get.genes0.5610.0080.569
get.used.features0.4730.0120.486
learn.bn18.926 0.23319.160
make.decision.tree10.552 0.12410.676
mds0.0900.0040.093
message.if000
module.heatmap37.151 0.38037.534
one.step.pigengene74.088 1.18875.278
pheatmap.type0.1870.0000.187
pigengene6.1070.1286.235
plot.pigengene5.8350.0525.888
preds.at0.5230.0120.535
project.eigen5.5930.0765.669
pvalues.manova0.0660.0000.066
save.if0.6930.0160.710
wgcna.one.step11.501 0.06811.570