Marouen Ben Guebila
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/netZooR |
| git_branch: master |
| git_last_commit: 2baf915 |
| git_last_commit_date: 2021-11-10 09:05:42 -0400 (Wed, 10 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:10 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1299/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netZooR 0.99.85 (landing page) Marouen Ben Guebila
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: netZooR |
| Version: 0.99.85 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:netZooR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings netZooR_0.99.85.tar.gz |
| StartedAt: 2022-03-17 19:44:06 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:50:51 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 404.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: netZooR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:netZooR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings netZooR_0.99.85.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/netZooR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'netZooR/DESCRIPTION' ... OK
* this is package 'netZooR' version '0.99.85'
* 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 5.5Mb
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 27.14 2.42 29.56
monsterPrintMonsterAnalysis 26.67 1.24 27.91
monster 5.25 0.50 5.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/netZooR.Rcheck/00check.log'
for details.
netZooR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL netZooR
###
##############################################################################
##############################################################################
* installing to library 'D:/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
converting help for package 'netZooR'
finding HTML links ... done
alpaca html
alpacaCommunityStructureRotation html
alpacaComputeDWBMmatmScale html
alpacaComputeWBMmat html
alpacaDeltaZAnalysis html
alpacaDeltaZAnalysisLouvain html
alpacaExtractTopGenes html
alpacaGOtabtogenes html
alpacaGenLouvain html
alpacaGoToGenes html
alpacaListToGo html
alpacaMetaNetwork html
alpacaNodeToGene html
alpacaRotationAnalysis html
alpacaRotationAnalysisLouvain html
alpacaSimulateNetwork html
alpacaTestNodeRank html
alpacaTidyConfig html
alpacaTopEnsembltoTopSym html
alpacaWBMlouvain html
condorCluster html
condorCoreEnrich html
condorMatrixModularity html
condorModularityMax html
condorPlotCommunities html
condorPlotHeatmap html
condorQscore html
createCondorObject html
createPandaStyle html
exon.size html
genes html
lioness html
lionessPy html
monster html
monsterBereFull html
monsterCalculateTmPValues html
monsterCheckDataType html
monsterGetTm html
monsterHclHeatmapPlot html
monsterMonsterNI html
monsterPlotMonsterAnalysis html
monsterPrintMonsterAnalysis html
monsterRes html
monsterTransformationMatrix html
monsterTransitionNetworkPlot html
monsterTransitionPCAPlot html
monsterdTFIPlot html
mut.ucec html
otter html
pandaPy html
pandaToAlpaca html
pandaToCondorObject html
runEgret html
sambar html
sambarConvertgmt html
sambarCorgenelength html
sambarDesparsify html
small1976 html
sourcePPI html
visPandaInCytoscape html
yeast html
** 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)
Making 'packages.html' ... done
netZooR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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'
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'
length 15200389 bytes (14.5 MB)
==================================================
downloaded 14.5 MB
>
> test_check("netZooR")
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0"
[1] "Q = 0"
[1] "Q = 0.15702479338843"
[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 0 | WARN 0 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
22.84 2.60 47.71
netZooR.Rcheck/netZooR-Ex.timings
| name | user | system | elapsed | |
| alpaca | 0.61 | 0.03 | 0.64 | |
| alpacaCommunityStructureRotation | 0 | 0 | 0 | |
| alpacaComputeDWBMmatmScale | 0 | 0 | 0 | |
| alpacaComputeWBMmat | 0 | 0 | 0 | |
| alpacaDeltaZAnalysis | 0 | 0 | 0 | |
| alpacaDeltaZAnalysisLouvain | 0 | 0 | 0 | |
| alpacaExtractTopGenes | 0.42 | 0.00 | 0.42 | |
| alpacaGOtabtogenes | 0 | 0 | 0 | |
| alpacaGenLouvain | 0 | 0 | 0 | |
| alpacaGoToGenes | 0 | 0 | 0 | |
| alpacaListToGo | 0 | 0 | 0 | |
| alpacaMetaNetwork | 0 | 0 | 0 | |
| alpacaNodeToGene | 0 | 0 | 0 | |
| alpacaRotationAnalysis | 0 | 0 | 0 | |
| alpacaRotationAnalysisLouvain | 0 | 0 | 0 | |
| alpacaSimulateNetwork | 0 | 0 | 0 | |
| alpacaTestNodeRank | 0 | 0 | 0 | |
| alpacaTidyConfig | 0 | 0 | 0 | |
| alpacaTopEnsembltoTopSym | 0 | 0 | 0 | |
| alpacaWBMlouvain | 0 | 0 | 0 | |
| condorCluster | 0.81 | 0.00 | 0.81 | |
| condorCoreEnrich | 1.34 | 0.04 | 1.37 | |
| condorMatrixModularity | 0.02 | 0.00 | 0.02 | |
| condorModularityMax | 0.01 | 0.00 | 0.01 | |
| condorPlotCommunities | 0.85 | 0.00 | 0.85 | |
| condorPlotHeatmap | 0.18 | 0.02 | 0.21 | |
| condorQscore | 0.80 | 0.00 | 0.79 | |
| createCondorObject | 0 | 0 | 0 | |
| createPandaStyle | 0 | 0 | 0 | |
| lioness | 3.00 | 0.36 | 3.36 | |
| lionessPy | 0 | 0 | 0 | |
| monster | 5.25 | 0.50 | 5.75 | |
| monsterBereFull | 2.72 | 0.36 | 3.08 | |
| monsterCalculateTmPValues | 0.03 | 0.00 | 0.03 | |
| monsterCheckDataType | 0.39 | 0.21 | 0.61 | |
| monsterGetTm | 0 | 0 | 0 | |
| monsterHclHeatmapPlot | 0.80 | 0.08 | 0.87 | |
| monsterMonsterNI | 2.06 | 0.06 | 2.13 | |
| monsterPlotMonsterAnalysis | 27.14 | 2.42 | 29.56 | |
| monsterPrintMonsterAnalysis | 26.67 | 1.24 | 27.91 | |
| monsterTransformationMatrix | 0.52 | 0.01 | 0.53 | |
| monsterTransitionNetworkPlot | 0.17 | 0.02 | 0.18 | |
| monsterTransitionPCAPlot | 0.10 | 0.01 | 0.11 | |
| monsterdTFIPlot | 0.12 | 0.00 | 0.13 | |
| otter | 0 | 0 | 0 | |
| pandaPy | 0 | 0 | 0 | |
| pandaToAlpaca | 0.02 | 0.00 | 0.01 | |
| pandaToCondorObject | 0 | 0 | 0 | |
| runEgret | 0.01 | 0.00 | 0.02 | |
| sambar | 1.52 | 0.10 | 1.75 | |
| sourcePPI | 0 | 0 | 0 | |
| visPandaInCytoscape | 0 | 0 | 0 | |