Back to Multiple platform build/check report for BioC 3.16
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2022-06-29 11:04:33 -0400 (Wed, 29 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4159
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 netZooR on nebbiolo2


To the developers/maintainers of the netZooR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netZooR.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 1316/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netZooR 1.1.0  (landing page)
Marouen Ben Guebila
Snapshot Date: 2022-06-28 14:00:02 -0400 (Tue, 28 Jun 2022)
git_url: https://git.bioconductor.org/packages/netZooR
git_branch: master
git_last_commit: 9461a1d
git_last_commit_date: 2022-04-26 12:20:14 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    ERROR    OK  

Summary

Package: netZooR
Version: 1.1.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings netZooR_1.1.0.tar.gz
StartedAt: 2022-06-28 20:57:21 -0400 (Tue, 28 Jun 2022)
EndedAt: 2022-06-28 21:04:43 -0400 (Tue, 28 Jun 2022)
EllapsedTime: 441.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: netZooR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings netZooR_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/netZooR.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 ‘netZooR/DESCRIPTION’ ... OK
* this is package ‘netZooR’ version ‘1.1.0’
* package encoding: UTF-8
* 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 ‘netZooR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   2.9Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
runEgret: no visible binding for global variable ‘NA12878’
Undefined global functions or variables:
  NA12878
* 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
monsterPrintMonsterAnalysis 31.133  0.308  31.441
monsterPlotMonsterAnalysis  29.890  0.520  30.409
monster                      5.862  0.096   5.957
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] "Q = 0.231404958677686"
  [1] "Q = 0.231404958677686"
  [1] "modularity of projected graph 0.525346928655047"
  [1] "Q = 0.52666696475026"
  [1] "Q = 0.52666696475026"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-condor.R:24:3): Test CONDOR functions ─────────────────────────
  condor.object$modularity not equal to as.numeric(c("0.231404958677686", "0.231404958677686")).
  Lengths differ: 3 is not 2
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/netZooR.Rcheck/00check.log’
for details.


Installation output

netZooR.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘netZooR’ ...
** 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 (netZooR)

Tests output

netZooR.Rcheck/tests/testthat.Rout.fail


R version 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(netZooR)
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: reticulate
Loading required package: pandaR
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:igraph':

    normalize, path, union

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: yarn
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)


> 
> #download test data
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/ppi.txt','testthat/ppi.txt')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/ppi.txt'
Content type 'text/plain' length 11495523 bytes (11.0 MB)
==================================================
downloaded 11.0 MB

> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/testDataset.RData','testthat/testDataset.RData')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/testDataset.RData'
Content type 'binary/octet-stream' length 15200389 bytes (14.5 MB)
==================================================
downloaded 14.5 MB

> 
> test_check("netZooR")
[1] "modularity of projected graph 0.144628099173554"
[1] "Q = 0.198347107438017"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0"
[1] "Q = 0"
[1] "Q = 0.132231404958678"
[1] "Q = 0.198347107438017"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "Q = 0.198347107438017"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "Q = 0.140495867768595"
[1] "Q = 0.140495867768595"
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0.525346928655047"
[1] "Q = 0.52666696475026"
[1] "Q = 0.52666696475026"
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-condor.R:24:3): Test CONDOR functions ─────────────────────────
condor.object$modularity not equal to as.numeric(c("0.231404958677686", "0.231404958677686")).
Lengths differ: 3 is not 2

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
Error: Test failures
Execution halted

Example timings

netZooR.Rcheck/netZooR-Ex.timings

nameusersystemelapsed
alpaca0.9990.0161.015
alpacaCommunityStructureRotation000
alpacaComputeDWBMmatmScale000
alpacaComputeWBMmat0.0010.0000.000
alpacaDeltaZAnalysis000
alpacaDeltaZAnalysisLouvain0.0000.0000.001
alpacaExtractTopGenes0.4520.0440.496
alpacaGOtabtogenes000
alpacaGenLouvain000
alpacaGoToGenes000
alpacaListToGo0.0000.0000.001
alpacaMetaNetwork000
alpacaNodeToGene0.0000.0000.001
alpacaRotationAnalysis000
alpacaRotationAnalysisLouvain000
alpacaSimulateNetwork000
alpacaTestNodeRank000
alpacaTidyConfig000
alpacaTopEnsembltoTopSym0.0010.0000.000
alpacaWBMlouvain000
condorCluster1.2170.0401.257
condorCoreEnrich1.720.021.74
condorMatrixModularity0.0070.0000.006
condorModularityMax0.020.000.02
condorPlotCommunities1.1520.0601.212
condorPlotHeatmap0.2150.0160.231
condorQscore1.1930.0081.201
createCondorObject0.0020.0000.002
createPandaStyle000
lioness4.0470.2564.305
lionessPy0.0010.0000.002
monster5.8620.0965.957
monsterBereFull3.0010.0363.037
monsterCalculateTmPValues0.0100.0040.013
monsterCheckDataType0.1780.1120.291
monsterGetTm0.0030.0000.003
monsterHclHeatmapPlot0.6490.0240.673
monsterMonsterNI1.7440.0321.776
monsterPlotMonsterAnalysis29.890 0.52030.409
monsterPrintMonsterAnalysis31.133 0.30831.441
monsterTransformationMatrix0.5790.0080.587
monsterTransitionNetworkPlot0.2320.0000.232
monsterTransitionPCAPlot0.1190.0000.119
monsterdTFIPlot0.1640.0040.169
otter0.0030.0000.003
pandaPy0.0020.0000.002
pandaToAlpaca0.0020.0000.002
pandaToCondorObject0.0020.0000.001
runEgret0.0110.0000.011
sambar1.7270.0161.743
sourcePPI0.0060.0000.007
visPandaInCytoscape000