Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 802/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
geNetClassifier 1.47.0 (landing page) Sara Aibar
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: geNetClassifier |
Version: 1.47.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings geNetClassifier_1.47.0.tar.gz |
StartedAt: 2024-12-23 22:18:22 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 22:19:19 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 57.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: geNetClassifier.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings geNetClassifier_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/geNetClassifier.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘geNetClassifier/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘geNetClassifier’ version ‘1.47.0’ * 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 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 loading without being on the library search path ... 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: geNetClassifier.Rd: svm Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/geNetClassifier.Rcheck/00check.log’ for details.
geNetClassifier.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL geNetClassifier ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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)
geNetClassifier.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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")'. 22:19:07 - 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 Dec 23 22:19:07 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 0.854 0.091 0.933
geNetClassifier.Rcheck/geNetClassifier-Ex.timings
name | user | system | elapsed | |
GeNetClassifierReturn-class | 0.533 | 0.070 | 0.605 | |
GeneralizationError-class | 0.339 | 0.028 | 0.367 | |
GenesNetwork-class | 0.376 | 0.019 | 0.395 | |
GenesRanking-class | 0.468 | 0.030 | 0.498 | |
calculateGenesRanking | 0.384 | 0.021 | 0.406 | |
externalValidation.probMatrix | 0.514 | 0.016 | 0.530 | |
externalValidation.stats | 0.583 | 0.014 | 0.597 | |
gClasses-methods | 0.233 | 0.008 | 0.241 | |
geNetClassifier | 0.116 | 0.004 | 0.121 | |
geneSymbols | 0.097 | 0.000 | 0.097 | |
genesDetails-methods | 0.304 | 0.009 | 0.312 | |
getEdges-methods | 0.255 | 0.008 | 0.264 | |
getNodes-methods | 0.253 | 0.002 | 0.256 | |
getNumEdges-methods | 0.252 | 0.005 | 0.258 | |
getNumNodes-methods | 0.254 | 0.005 | 0.258 | |
getRanking-methods | 0.273 | 0.003 | 0.276 | |
getSubNetwork-methods | 0.254 | 0.004 | 0.257 | |
getTopRanking-methods | 0.256 | 0.007 | 0.263 | |
leukemiasClassifier | 0.272 | 0.012 | 0.284 | |
network2txt | 0.281 | 0.009 | 0.289 | |
numGenes-methods | 0.249 | 0.005 | 0.254 | |
numSignificantGenes-methods | 0.246 | 0.004 | 0.250 | |
overview-methods | 0.258 | 0.009 | 0.267 | |
plot.GeNetClassifierReturn | 0.481 | 0.025 | 0.515 | |
plot.GenesRanking | 0.265 | 0.007 | 0.271 | |
plotAssignments | 0.508 | 0.012 | 0.520 | |
plotDiscriminantPower | 0.518 | 0.021 | 0.538 | |
plotExpressionProfiles | 0.758 | 0.021 | 0.780 | |
plotNetwork | 0.308 | 0.003 | 0.311 | |
queryGeNetClassifier | 0.603 | 0.010 | 0.613 | |
querySummary | 0.476 | 0.010 | 0.486 | |