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This page was generated on 2022-06-24 11:06:52 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 palomino4


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 1312/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netZooR 1.1.0  (landing page)
Marouen Ben Guebila
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 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    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: netZooR
Version: 1.1.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:netZooR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings netZooR_1.1.0.tar.gz
StartedAt: 2022-06-24 03:57:02 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:05:13 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 491.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: netZooR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:netZooR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings netZooR_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/netZooR.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (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 whether package 'netZooR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  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
monsterPlotMonsterAnalysis  37.66   2.11   39.81
monsterPrintMonsterAnalysis 38.10   1.02   39.10
monster                      7.55   0.80    8.35
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/netZooR.Rcheck/00check.log'
for details.


Installation output

netZooR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/netZooR_1.1.0.tar.gz && rm -rf netZooR.buildbin-libdir && mkdir netZooR.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=netZooR.buildbin-libdir netZooR_1.1.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL netZooR_1.1.0.zip && rm netZooR_1.1.0.tar.gz netZooR_1.1.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 28 20.5M   28 5942k    0     0  11.6M      0  0:00:01 --:--:--  0:00:01 11.7M
100 20.5M  100 20.5M    0     0  15.8M      0  0:00:01  0:00:01 --:--:-- 15.8M
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'netZooR' as netZooR_1.1.0.zip
* DONE (netZooR)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'netZooR' successfully unpacked and MD5 sums checked

Tests output

netZooR.Rcheck/tests/testthat.Rout.fail


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 = 0.198347107438017"
[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
alpaca0.840.020.86
alpacaCommunityStructureRotation000
alpacaComputeDWBMmatmScale000
alpacaComputeWBMmat000
alpacaDeltaZAnalysis000
alpacaDeltaZAnalysisLouvain000
alpacaExtractTopGenes0.750.000.75
alpacaGOtabtogenes0.010.000.02
alpacaGenLouvain000
alpacaGoToGenes000
alpacaListToGo000
alpacaMetaNetwork000
alpacaNodeToGene000
alpacaRotationAnalysis000
alpacaRotationAnalysisLouvain000
alpacaSimulateNetwork000
alpacaTestNodeRank000
alpacaTidyConfig000
alpacaTopEnsembltoTopSym000
alpacaWBMlouvain000
condorCluster1.210.001.20
condorCoreEnrich1.950.062.01
condorMatrixModularity000
condorModularityMax0.030.000.04
condorPlotCommunities1.190.001.18
condorPlotHeatmap0.220.040.25
condorQscore1.150.001.16
createCondorObject000
createPandaStyle000
lioness3.100.103.33
lionessPy0.010.000.01
monster7.550.808.35
monsterBereFull3.300.553.84
monsterCalculateTmPValues0.010.000.02
monsterCheckDataType0.350.250.59
monsterGetTm0.010.000.02
monsterHclHeatmapPlot0.690.060.75
monsterMonsterNI2.140.032.17
monsterPlotMonsterAnalysis37.66 2.1139.81
monsterPrintMonsterAnalysis38.10 1.0239.10
monsterTransformationMatrix0.680.010.71
monsterTransitionNetworkPlot0.250.000.25
monsterTransitionPCAPlot0.130.000.12
monsterdTFIPlot0.190.000.19
otter000
pandaPy000
pandaToAlpaca0.010.000.02
pandaToCondorObject000
runEgret0.030.000.03
sambar1.990.102.08
sourcePPI0.010.000.01
visPandaInCytoscape000