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This page was generated on 2021-07-24 12:06:41 -0400 (Sat, 24 Jul 2021).

CHECK results for Pigengene on merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pigengene_1.19.10.tar.gz
StartedAt: 2021-07-24 05:10:04 -0400 (Sat, 24 Jul 2021)
EndedAt: 2021-07-24 05:20:00 -0400 (Sat, 24 Jul 2021)
EllapsedTime: 596.0 seconds
RetCode: 0
Status:   OK  
CheckDir: Pigengene.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pigengene_1.19.10.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/Pigengene.Rcheck’
* using R version 4.1.0 RC (2021-05-16 r80304)
* 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 ‘1.19.10’
* 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 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
Pigengene-package  81.503  2.228  83.839
one.step.pigengene 80.715  1.470  82.306
module.heatmap     56.317  0.931  57.377
learn.bn           18.198  0.124  18.352
compact.tree       17.139  0.515  17.668
make.decision.tree 16.928  0.489  17.438
gene.mapping       15.790  0.546  18.136
combine.networks   11.950  0.055  12.014
wgcna.one.step     10.688  0.035  10.764
plot.pigengene      8.277  0.294   8.582
pigengene           8.103  0.408   8.528
compute.pigengene   7.997  0.355   8.368
project.eigen       7.730  0.285   8.024
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/Pigengene.Rcheck/00check.log’
for details.



Installation output

Pigengene.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Pigengene
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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-package81.503 2.22883.839
aml0.2500.0050.254
balance0.7330.0220.756
calculate.beta1.3750.0451.426
check.nas0.0700.0040.074
check.pigengene.input0.0660.0030.069
combine.networks11.950 0.05512.014
compact.tree17.139 0.51517.668
compute.pigengene7.9970.3558.368
dcor.matrix0.2040.0090.216
draw.bn000
eigengenes330.1370.0280.166
gene.mapping15.790 0.54618.136
get.fitted.leaf0.8750.0180.895
get.genes0.7770.0170.796
get.used.features0.7540.0150.783
learn.bn18.198 0.12418.352
make.decision.tree16.928 0.48917.438
mds0.1280.0050.134
message.if0.0000.0010.001
module.heatmap56.317 0.93157.377
one.step.pigengene80.715 1.47082.306
pheatmap.type0.3270.0030.332
pigengene8.1030.4088.528
plot.pigengene8.2770.2948.582
preds.at0.8860.0220.910
project.eigen7.7300.2858.024
pvalues.manova0.1030.0020.106
save.if0.6720.0290.703
wgcna.one.step10.688 0.03510.764