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This page was generated on 2022-06-27 11:05:27 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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? 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 1443/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pigengene 1.23.0  (landing page)
Habil Zare
Snapshot Date: 2022-06-26 14:00:03 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/Pigengene
git_branch: master
git_last_commit: e336303
git_last_commit_date: 2022-04-26 11:32:36 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Pigengene
Version: 1.23.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings Pigengene_1.23.0.tar.gz
StartedAt: 2022-06-26 21:07:23 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 21:17:35 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 611.7 seconds
RetCode: 0
Status:   OK  
CheckDir: Pigengene.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings Pigengene_1.23.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/Pigengene.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* 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 ‘1.23.0’
* 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
Error in completeSubclasses(classDef2, class1, obj, where) : 
  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
'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")

one.step.pigengene: no visible binding for global variable
  ‘org.Hs.eg.db’
Undefined global functions or variables:
  org.Hs.eg.db
* 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  79.551  1.376  80.927
one.step.pigengene 73.781  0.552  74.333
get.enriched.pw    63.749  3.364  67.117
module.heatmap     34.086  0.336  34.423
determine.modules  19.265  0.143  19.406
learn.bn           18.687  0.163  18.851
apply.filter       17.745  0.224  17.969
combine.networks   16.455  0.065  16.520
make.filter        15.334  0.120  15.454
wgcna.one.step     14.060  0.008  14.068
make.decision.tree  9.995  0.064  10.060
compact.tree        9.788  0.048   9.836
plot.pigengene      6.010  0.028   6.038
compute.pigengene   5.839  0.104   5.943
project.eigen       5.644  0.016   5.660
gene.mapping        5.422  0.236  12.590
pigengene           5.520  0.076   5.596
* 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-3.16-bioc/meat/Pigengene.Rcheck/00check.log’
for details.



Installation output

Pigengene.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL Pigengene
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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-package79.551 1.37680.927
aml0.1580.0040.161
apply.filter17.745 0.22417.969
balance0.4460.0480.493
calculate.beta0.9780.0120.990
check.nas0.0420.0000.043
check.pigengene.input0.0430.0000.042
combine.networks16.455 0.06516.520
compact.tree9.7880.0489.836
compute.pigengene5.8390.1045.943
dcor.matrix0.1600.0000.161
determine.modules19.265 0.14319.406
draw.bn000
eigengenes330.1220.0000.123
gene.mapping 5.422 0.23612.590
get.enriched.pw63.749 3.36467.117
get.fitted.leaf0.5660.0120.577
get.genes0.4960.0040.500
get.used.features0.4630.0040.467
learn.bn18.687 0.16318.851
make.decision.tree 9.995 0.06410.060
make.filter15.334 0.12015.454
mds0.0870.0040.091
message.if000
module.heatmap34.086 0.33634.423
one.step.pigengene73.781 0.55274.333
pheatmap.type0.2000.0240.225
pigengene5.5200.0765.596
plot.pigengene6.0100.0286.038
preds.at0.5640.0080.572
project.eigen5.6440.0165.660
pvalues.manova0.0630.0000.064
save.if0.7790.0000.779
wgcna.one.step14.060 0.00814.068