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This page was generated on 2022-07-01 12:05:37 -0400 (Fri, 01 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 nebbiolo1


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 1325/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netZooR 1.0.0  (landing page)
Marouen Ben Guebila
Snapshot Date: 2022-06-30 13:55:04 -0400 (Thu, 30 Jun 2022)
git_url: https://git.bioconductor.org/packages/netZooR
git_branch: RELEASE_3_15
git_last_commit: 9f0e4a2
git_last_commit_date: 2022-04-26 12:20:14 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: netZooR
Version: 1.0.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings netZooR_1.0.0.tar.gz
StartedAt: 2022-06-30 21:01:26 -0400 (Thu, 30 Jun 2022)
EndedAt: 2022-06-30 21:08:56 -0400 (Thu, 30 Jun 2022)
EllapsedTime: 450.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: netZooR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings netZooR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/netZooR.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.0.0’
* 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 ... 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 ... 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
monsterPlotMonsterAnalysis  31.576  0.548  32.125
monsterPrintMonsterAnalysis 30.530  0.347  30.878
monster                      6.924  0.134   7.057
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/netZooR.Rcheck/00check.log’
for details.


Installation output

netZooR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL netZooR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 (2022-04-22) -- "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 = 0.148760330578512"
[1] "Q = 0.148760330578512"
[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
alpaca1.0250.0131.037
alpacaCommunityStructureRotation000
alpacaComputeDWBMmatmScale000
alpacaComputeWBMmat000
alpacaDeltaZAnalysis0.0000.0000.001
alpacaDeltaZAnalysisLouvain000
alpacaExtractTopGenes0.4810.0480.529
alpacaGOtabtogenes000
alpacaGenLouvain0.0010.0000.000
alpacaGoToGenes0.0000.0000.001
alpacaListToGo000
alpacaMetaNetwork000
alpacaNodeToGene000
alpacaRotationAnalysis0.0010.0000.000
alpacaRotationAnalysisLouvain000
alpacaSimulateNetwork0.0000.0000.001
alpacaTestNodeRank000
alpacaTidyConfig000
alpacaTopEnsembltoTopSym0.0000.0010.000
alpacaWBMlouvain000
condorCluster1.1910.0201.210
condorCoreEnrich1.8720.0681.939
condorMatrixModularity0.0080.0000.008
condorModularityMax0.0170.0040.021
condorPlotCommunities1.1330.0321.165
condorPlotHeatmap0.2160.0120.228
condorQscore1.2160.0561.271
createCondorObject0.0020.0000.003
createPandaStyle0.0000.0000.001
lioness4.1470.1684.317
lionessPy0.0000.0020.002
monster6.9240.1347.057
monsterBereFull2.9890.0403.029
monsterCalculateTmPValues0.0150.0000.015
monsterCheckDataType0.1980.7160.914
monsterGetTm0.0030.0000.004
monsterHclHeatmapPlot0.6790.0230.703
monsterMonsterNI1.7560.0321.787
monsterPlotMonsterAnalysis31.576 0.54832.125
monsterPrintMonsterAnalysis30.530 0.34730.878
monsterTransformationMatrix0.5880.0200.608
monsterTransitionNetworkPlot0.230.000.23
monsterTransitionPCAPlot0.1190.0000.119
monsterdTFIPlot0.1660.0040.169
otter0.0020.0000.002
pandaPy0.0000.0020.003
pandaToAlpaca0.0020.0000.003
pandaToCondorObject0.0020.0010.002
runEgret0.0110.0000.012
sambar1.5300.0321.562
sourcePPI0.0070.0000.009
visPandaInCytoscape000