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This page was generated on 2022-01-28 11:06:08 -0500 (Fri, 28 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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 geNetClassifier on nebbiolo1


To the developers/maintainers of the geNetClassifier package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/geNetClassifier.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.

raw results

Package 735/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geNetClassifier 1.35.0  (landing page)
Sara Aibar
Snapshot Date: 2022-01-27 13:55:17 -0500 (Thu, 27 Jan 2022)
git_url: https://git.bioconductor.org/packages/geNetClassifier
git_branch: master
git_last_commit: fd508f1
git_last_commit_date: 2021-10-26 12:07:41 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: geNetClassifier
Version: 1.35.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings geNetClassifier_1.35.0.tar.gz
StartedAt: 2022-01-27 19:20:28 -0500 (Thu, 27 Jan 2022)
EndedAt: 2022-01-27 19:21:27 -0500 (Thu, 27 Jan 2022)
EllapsedTime: 58.8 seconds
RetCode: 0
Status:   OK  
CheckDir: geNetClassifier.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings geNetClassifier_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/geNetClassifier.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geNetClassifier/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geNetClassifier’ version ‘1.35.0’
* 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 ‘geNetClassifier’ 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 ... OK
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK


Installation output

geNetClassifier.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘geNetClassifier’ ...
** 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 (geNetClassifier)

Tests output

geNetClassifier.Rcheck/tests/runTests.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
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.

> BiocGenerics:::testPackage("geNetClassifier")

Attaching package: 'BiocGenerics'

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")'.

19:21:22 - Filtering data and calculating the genes ranking...
Warning in plotExpressionProfiles(eset = myEset, genes = rownames(myEset),  :
  The argument 'sampleLabels' had to be converted into a factor.
Warning in plotExpressionProfiles(eset = myEset, genes = rownames(myEset),  :
  The data labels vector is not named, it will be assumed the labels are in order: the first label applies to the first sample... 


RUNIT TEST PROTOCOL -- Thu Jan 27 19:21:23 2022 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
geNetClassifier RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In geNetClassifier(matrix(sample(50000, 5 * 2), 5, 2), c(rep("one",  :
  The argument 'classification sampleLabels' had to be converted into a factor.
2: In geNetClassifier(matrix(sample(50000, 5 * 3), 5, 3), c(rep("one",  :
  The argument 'classification sampleLabels' had to be converted into a factor.
3: In geNetClassifier(matrix(sample(50000, 5 * 3), 5, 3), c(rep("one",  :
  The data labels vector is not named, it is assumed the labels are in order: the first label applies to the first sample... 
4: In geNetClassifier(matrix(sample(50000, 5 * 3), 5, 3), c(rep("one",  :
  It is recommended to have the *same* number of samples in each class in order to obtain balanced external validation stats.
> 
> proc.time()
   user  system elapsed 
  0.901   0.090   0.976 

Example timings

geNetClassifier.Rcheck/geNetClassifier-Ex.timings

nameusersystemelapsed
GeNetClassifierReturn-class0.5390.0680.610
GeneralizationError-class0.3750.0290.404
GenesNetwork-class1.7790.1391.925
GenesRanking-class0.5070.0350.541
calculateGenesRanking0.5750.0240.598
externalValidation.probMatrix0.5390.0490.585
externalValidation.stats0.5550.0190.574
gClasses-methods0.2290.0080.237
geNetClassifier0.1470.0120.160
geneSymbols0.0880.0000.087
genesDetails-methods0.4780.0250.501
getEdges-methods0.2520.0040.255
getNodes-methods0.2670.0070.276
getNumEdges-methods0.3540.0090.362
getNumNodes-methods0.3510.0040.355
getRanking-methods0.2620.0150.278
getSubNetwork-methods0.2800.0080.288
getTopRanking-methods0.3680.0110.380
leukemiasClassifier0.2740.0170.290
network2txt0.4190.0120.431
numGenes-methods0.2510.0040.255
numSignificantGenes-methods0.3010.0100.313
overview-methods0.3460.0210.366
plot.GeNetClassifierReturn3.0280.1533.188
plot.GenesRanking0.3950.0160.411
plotAssignments0.4810.0360.516
plotDiscriminantPower0.6330.0320.660
plotExpressionProfiles0.9220.0570.974
plotNetwork1.6540.0521.702
queryGeNetClassifier0.6990.0490.744
querySummary0.4200.0320.451