| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 792/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| geNetClassifier 1.40.0 (landing page) Sara Aibar
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the geNetClassifier package: - 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: 1.40.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geNetClassifier_1.40.0.tar.gz |
| StartedAt: 2023-10-17 21:10:14 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 21:12:18 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 124.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: geNetClassifier.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geNetClassifier_1.40.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/geNetClassifier.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geNetClassifier/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geNetClassifier’ version ‘1.40.0’
* 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 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 2.895 1.518 7.179
plot.GeNetClassifierReturn 3.000 0.321 8.297
* 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
geNetClassifier.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL geNetClassifier ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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, 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, 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")'.
21:11:58 - 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 Oct 17 21:11:58 2023
***********************************************
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
1.124 0.127 1.868
geNetClassifier.Rcheck/geNetClassifier-Ex.timings
| name | user | system | elapsed | |
| GeNetClassifierReturn-class | 0.659 | 0.062 | 1.046 | |
| GeneralizationError-class | 0.406 | 0.021 | 0.539 | |
| GenesNetwork-class | 2.895 | 1.518 | 7.179 | |
| GenesRanking-class | 0.702 | 0.038 | 1.097 | |
| calculateGenesRanking | 0.504 | 0.021 | 0.762 | |
| externalValidation.probMatrix | 0.634 | 0.030 | 0.966 | |
| externalValidation.stats | 0.632 | 0.022 | 0.959 | |
| gClasses-methods | 0.261 | 0.007 | 0.394 | |
| geNetClassifier | 0.247 | 0.010 | 0.368 | |
| geneSymbols | 0.082 | 0.003 | 0.125 | |
| genesDetails-methods | 0.352 | 0.011 | 0.537 | |
| getEdges-methods | 0.275 | 0.007 | 0.391 | |
| getNodes-methods | 0.276 | 0.008 | 0.433 | |
| getNumEdges-methods | 0.275 | 0.007 | 0.411 | |
| getNumNodes-methods | 0.274 | 0.007 | 0.404 | |
| getRanking-methods | 0.299 | 0.010 | 0.453 | |
| getSubNetwork-methods | 0.322 | 0.011 | 0.504 | |
| getTopRanking-methods | 0.278 | 0.009 | 0.436 | |
| leukemiasClassifier | 0.308 | 0.013 | 0.475 | |
| network2txt | 0.359 | 0.031 | 0.596 | |
| numGenes-methods | 0.271 | 0.009 | 0.433 | |
| numSignificantGenes-methods | 0.275 | 0.009 | 0.436 | |
| overview-methods | 0.322 | 0.017 | 0.517 | |
| plot.GeNetClassifierReturn | 3.000 | 0.321 | 8.297 | |
| plot.GenesRanking | 0.369 | 0.013 | 0.578 | |
| plotAssignments | 0.683 | 0.026 | 1.044 | |
| plotDiscriminantPower | 0.598 | 0.054 | 0.981 | |
| plotExpressionProfiles | 0.847 | 0.064 | 1.362 | |
| plotNetwork | 2.065 | 0.124 | 3.446 | |
| queryGeNetClassifier | 0.779 | 0.030 | 1.197 | |
| querySummary | 0.580 | 0.022 | 0.955 | |