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This page was generated on 2021-06-17 02:38:27 -0400 (Thu, 17 Jun 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 1.18.0  (landing page)
Habil Zare
Snapshot Date: 2021-06-15 06:50:12 -0400 (Tue, 15 Jun 2021)
URL: https://git.bioconductor.org/packages/Pigengene
Branch: RELEASE_3_13
Last Commit: 848d21a
Last Changed Date: 2021-05-19 12:20:45 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Pigengene
Version: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2021-06-15 13:02:00 -0400 (Tue, 15 Jun 2021)
EndedAt: 2021-06-15 13:09:23 -0400 (Tue, 15 Jun 2021)
EllapsedTime: 443.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Pigengene.Rcheck
Warnings: 1

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_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/Pigengene.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.18.0’
* 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 ... WARNING
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘Pigengene’
* 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 73.681  0.563  74.246
Pigengene-package  72.151  1.791  73.952
module.heatmap     35.420  0.371  35.792
learn.bn           18.651  0.190  18.842
combine.networks   13.428  0.028  13.457
wgcna.one.step     12.208  0.024  12.233
make.decision.tree 10.722  0.122  10.843
compact.tree       10.254  0.008  10.262
gene.mapping        8.588  0.408  11.410
compute.pigengene   6.167  0.120   6.287
plot.pigengene      6.139  0.080   6.218
pigengene           5.521  0.156   5.677
project.eigen       5.462  0.024   5.486
* 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: 1 WARNING, 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
###
##############################################################################
##############################################################################


* 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-package72.151 1.79173.952
aml0.1410.0080.149
balance0.4730.1440.617
calculate.beta1.5380.0121.550
check.nas0.0420.0000.042
check.pigengene.input0.0400.0040.044
combine.networks13.428 0.02813.457
compact.tree10.254 0.00810.262
compute.pigengene6.1670.1206.287
dcor.matrix0.1860.0080.193
draw.bn000
eigengenes330.0820.0000.081
gene.mapping 8.588 0.40811.410
get.fitted.leaf0.4950.0160.510
get.genes0.5290.0240.554
get.used.features0.4680.0200.488
learn.bn18.651 0.19018.842
make.decision.tree10.722 0.12210.843
mds0.0960.0000.097
message.if0.0000.0000.001
module.heatmap35.420 0.37135.792
one.step.pigengene73.681 0.56374.246
pheatmap.type0.1850.0040.190
pigengene5.5210.1565.677
plot.pigengene6.1390.0806.218
preds.at0.5870.0200.608
project.eigen5.4620.0245.486
pvalues.manova0.0690.0000.068
save.if0.8360.0000.837
wgcna.one.step12.208 0.02412.233