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This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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

Package 818/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geNetClassifier 1.44.0  (landing page)
Sara Aibar
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/geNetClassifier
git_branch: RELEASE_3_19
git_last_commit: 1e6e885
git_last_commit_date: 2024-04-30 10:31:27 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for geNetClassifier on palomino3

To the developers/maintainers of the geNetClassifier package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: geNetClassifier
Version: 1.44.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:geNetClassifier.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings geNetClassifier_1.44.0.tar.gz
StartedAt: 2024-06-17 04:13:08 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 04:16:24 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 196.4 seconds
RetCode: 0
Status:   OK  
CheckDir: geNetClassifier.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:geNetClassifier.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings geNetClassifier_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/geNetClassifier.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'geNetClassifier/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geNetClassifier' version '1.44.0'
* 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 code 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 ... NOTE
checkRd: (-1) calculateGenesRanking.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculateGenesRanking.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculateGenesRanking.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculateGenesRanking.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) externalValidation.stats.Rd:25-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) externalValidation.stats.Rd:28-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) externalValidation.stats.Rd:32: Lost braces
    32 | \item{confMatrix }{Confussion matrix.}
       |      ^
checkRd: (-1) externalValidation.stats.Rd:32: Lost braces
    32 | \item{confMatrix }{Confussion matrix.}
       |                   ^
checkRd: (-1) plot.GenesRanking.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.GenesRanking.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotDiscriminantPower.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotDiscriminantPower.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) queryGeNetClassifier.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) queryGeNetClassifier.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) queryGeNetClassifier.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) queryGeNetClassifier.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) queryGeNetClassifier.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) querySummary.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) querySummary.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) querySummary.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
GenesNetwork-class 3.53   3.61   39.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/geNetClassifier.Rcheck/00check.log'
for details.


Installation output

geNetClassifier.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL geNetClassifier
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, aperm, 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, 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")'.

04:16:06 - 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 -- Mon Jun 17 04:16:06 2024 
*********************************************** 
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 
   1.07    2.01    2.98 

Example timings

geNetClassifier.Rcheck/geNetClassifier-Ex.timings

nameusersystemelapsed
GeNetClassifierReturn-class0.570.303.85
GeneralizationError-class0.310.060.37
GenesNetwork-class 3.53 3.6139.33
GenesRanking-class0.700.080.78
calculateGenesRanking0.420.150.59
externalValidation.probMatrix0.630.050.67
externalValidation.stats0.540.090.64
gClasses-methods0.210.000.21
geNetClassifier0.110.030.14
geneSymbols0.060.000.06
genesDetails-methods0.390.050.44
getEdges-methods0.230.020.25
getNodes-methods0.190.010.20
getNumEdges-methods0.170.020.19
getNumNodes-methods0.210.000.20
getRanking-methods0.200.010.22
getSubNetwork-methods0.190.010.20
getTopRanking-methods0.220.020.23
leukemiasClassifier0.260.020.29
network2txt0.640.000.64
numGenes-methods0.170.030.20
numSignificantGenes-methods0.190.010.20
overview-methods0.210.030.23
plot.GeNetClassifierReturn2.420.222.71
plot.GenesRanking0.310.050.35
plotAssignments0.420.090.52
plotDiscriminantPower0.470.100.56
plotExpressionProfiles0.730.120.86
plotNetwork1.960.102.05
queryGeNetClassifier0.720.090.83
querySummary0.500.050.54