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This page was generated on 2021-11-24 15:05:29 -0500 (Wed, 24 Nov 2021).

CHECK results for geNetClassifier on tokay2

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.
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raw results

Package 737/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geNetClassifier 1.34.0  (landing page)
Sara Aibar
Snapshot Date: 2021-11-23 04:15:06 -0500 (Tue, 23 Nov 2021)
git_url: https://git.bioconductor.org/packages/geNetClassifier
git_branch: RELEASE_3_14
git_last_commit: 2aec9d0
git_last_commit_date: 2021-10-26 12:07:41 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: geNetClassifier
Version: 1.34.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geNetClassifier.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings geNetClassifier_1.34.0.tar.gz
StartedAt: 2021-11-23 22:22:39 -0500 (Tue, 23 Nov 2021)
EndedAt: 2021-11-23 22:24:36 -0500 (Tue, 23 Nov 2021)
EllapsedTime: 117.1 seconds
RetCode: 0
Status:   OK  
CheckDir: geNetClassifier.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geNetClassifier.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings geNetClassifier_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/geNetClassifier.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geNetClassifier/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geNetClassifier' version '1.34.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/geNetClassifier_1.34.0.tar.gz && rm -rf geNetClassifier.buildbin-libdir && mkdir geNetClassifier.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geNetClassifier.buildbin-libdir geNetClassifier_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL geNetClassifier_1.34.0.zip && rm geNetClassifier_1.34.0.tar.gz geNetClassifier_1.34.0.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
100 2704k  100 2704k    0     0  5365k      0 --:--:-- --:--:-- --:--:-- 5377k

install for i386

* installing *source* package 'geNetClassifier' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geNetClassifier'
    finding HTML links ... done
    GeNetClassifierReturn-class             html  
    GeneralizationError-class               html  
    GenesNetwork-class                      html  
    GenesRanking-class                      html  
    calculateGenesRanking                   html  
    externalValidation.probMatrix           html  
    externalValidation.stats                html  
    gClasses-methods                        html  
    geNetClassifier-package                 html  
    geNetClassifier                         html  
    finding level-2 HTML links ... done

    geneSymbols                             html  
    genesDetails-methods                    html  
    getEdges-methods                        html  
    getNodes-methods                        html  
    getNumEdges-methods                     html  
    getNumNodes-methods                     html  
    getRanking-methods                      html  
    getSubNetwork-methods                   html  
    getTopRanking-methods                   html  
    leukemiasClassifier                     html  
    network2txt                             html  
    numGenes-methods                        html  
    numSignificantGenes-methods             html  
    overview-methods                        html  
    plot.GeNetClassifierReturn              html  
    plot.GenesRanking                       html  
    plotAssignments                         html  
    plotDiscriminantPower                   html  
    plotExpressionProfiles                  html  
    plotNetwork                             html  
    queryGeNetClassifier                    html  
    querySummary                            html  
    setProperties-methods                   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

install for x64

* installing *source* package 'geNetClassifier' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geNetClassifier' as geNetClassifier_1.34.0.zip
* DONE (geNetClassifier)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'geNetClassifier' successfully unpacked and MD5 sums checked

Tests output

geNetClassifier.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")'.

22:24:27 - 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 -- Tue Nov 23 22:24:27 2021 
*********************************************** 
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 
   1.23    0.10    1.32 

geNetClassifier.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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.

> 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")'.

22:24:28 - 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 -- Tue Nov 23 22:24:29 2021 
*********************************************** 
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 
   1.34    0.06    1.39 

Example timings

geNetClassifier.Rcheck/examples_i386/geNetClassifier-Ex.timings

nameusersystemelapsed
GeNetClassifierReturn-class1.140.041.39
GeneralizationError-class0.630.030.66
GenesNetwork-class2.860.983.94
GenesRanking-class0.910.030.94
calculateGenesRanking0.620.020.64
externalValidation.probMatrix0.720.010.74
externalValidation.stats0.500.020.51
gClasses-methods0.260.000.26
geNetClassifier0.150.000.14
geneSymbols0.040.020.07
genesDetails-methods0.310.010.32
getEdges-methods0.240.050.28
getNodes-methods0.260.010.29
getNumEdges-methods0.300.000.29
getNumNodes-methods0.280.020.30
getRanking-methods0.30.00.3
getSubNetwork-methods0.250.050.29
getTopRanking-methods0.30.00.3
leukemiasClassifier0.290.000.30
network2txt0.690.040.73
numGenes-methods0.420.030.45
numSignificantGenes-methods0.350.000.35
overview-methods0.360.020.37
plot.GeNetClassifierReturn2.930.173.13
plot.GenesRanking0.610.020.63
plotAssignments0.640.030.67
plotDiscriminantPower0.730.050.78
plotExpressionProfiles0.970.010.99
plotNetwork2.530.032.68
queryGeNetClassifier0.710.050.75
querySummary0.920.000.93

geNetClassifier.Rcheck/examples_x64/geNetClassifier-Ex.timings

nameusersystemelapsed
GeNetClassifierReturn-class0.720.030.75
GeneralizationError-class0.310.020.33
GenesNetwork-class2.311.043.39
GenesRanking-class0.780.050.82
calculateGenesRanking0.880.050.93
externalValidation.probMatrix0.590.040.64
externalValidation.stats0.700.100.79
gClasses-methods0.320.000.32
geNetClassifier0.120.030.15
geneSymbols0.080.000.08
genesDetails-methods0.340.000.34
getEdges-methods0.250.000.25
getNodes-methods0.270.000.27
getNumEdges-methods0.230.020.25
getNumNodes-methods0.210.010.22
getRanking-methods0.230.000.23
getSubNetwork-methods0.250.000.25
getTopRanking-methods0.220.020.24
leukemiasClassifier0.230.010.25
network2txt0.770.030.79
numGenes-methods0.280.000.29
numSignificantGenes-methods0.270.000.26
overview-methods0.290.000.30
plot.GeNetClassifierReturn3.710.133.83
plot.GenesRanking0.310.000.31
plotAssignments0.470.030.50
plotDiscriminantPower0.640.030.67
plotExpressionProfiles1.170.061.24
plotNetwork2.630.022.64
queryGeNetClassifier0.920.010.93
querySummary0.470.050.52