Sara Aibar
| Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024) |
| git_url: https://git.bioconductor.org/packages/geNetClassifier |
| git_branch: devel |
| git_last_commit: 610a8f2 |
| git_last_commit_date: 2024-04-30 10:31:27 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:04 -0400 (Mon, 13 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
| 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 789/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| geNetClassifier 1.45.0 (landing page) Sara Aibar
| kjohnson1 | macOS 13.6.6 Ventura / 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: 1.45.0 |
| 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_1.45.0.tar.gz |
| StartedAt: 2024-05-12 14:26:55 -0400 (Sun, 12 May 2024) |
| EndedAt: 2024-05-12 14:28:15 -0400 (Sun, 12 May 2024) |
| EllapsedTime: 80.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: geNetClassifier.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.45.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/geNetClassifier.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geNetClassifier/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geNetClassifier’ version ‘1.45.0’
* 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 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
* 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
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/geNetClassifier.Rcheck/00check.log’
for details.
geNetClassifier.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL geNetClassifier ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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")'.
14:28:01 - 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 -- Sun May 12 14:28:01 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
1.159 0.118 1.270
geNetClassifier.Rcheck/geNetClassifier-Ex.timings
| name | user | system | elapsed | |
| GeNetClassifierReturn-class | 0.752 | 0.062 | 0.840 | |
| GeneralizationError-class | 0.540 | 0.021 | 0.564 | |
| GenesNetwork-class | 2.709 | 0.683 | 3.437 | |
| GenesRanking-class | 0.905 | 0.056 | 0.970 | |
| calculateGenesRanking | 0.663 | 0.035 | 0.712 | |
| externalValidation.probMatrix | 0.773 | 0.049 | 0.842 | |
| externalValidation.stats | 0.551 | 0.029 | 0.616 | |
| gClasses-methods | 0.144 | 0.005 | 0.175 | |
| geNetClassifier | 0.112 | 0.011 | 0.166 | |
| geneSymbols | 0.086 | 0.002 | 0.090 | |
| genesDetails-methods | 0.523 | 0.023 | 0.604 | |
| getEdges-methods | 0.329 | 0.010 | 0.341 | |
| getNodes-methods | 0.325 | 0.012 | 0.343 | |
| getNumEdges-methods | 0.338 | 0.008 | 0.352 | |
| getNumNodes-methods | 0.322 | 0.009 | 0.337 | |
| getRanking-methods | 0.346 | 0.013 | 0.364 | |
| getSubNetwork-methods | 0.352 | 0.013 | 0.367 | |
| getTopRanking-methods | 0.343 | 0.011 | 0.355 | |
| leukemiasClassifier | 0.369 | 0.025 | 0.403 | |
| network2txt | 0.384 | 0.025 | 0.412 | |
| numGenes-methods | 0.172 | 0.008 | 0.183 | |
| numSignificantGenes-methods | 0.163 | 0.009 | 0.177 | |
| overview-methods | 0.198 | 0.013 | 0.219 | |
| plot.GeNetClassifierReturn | 3.102 | 0.400 | 3.625 | |
| plot.GenesRanking | 0.446 | 0.016 | 0.464 | |
| plotAssignments | 0.731 | 0.036 | 0.773 | |
| plotDiscriminantPower | 0.709 | 0.065 | 0.795 | |
| plotExpressionProfiles | 1.018 | 0.083 | 1.129 | |
| plotNetwork | 2.255 | 0.215 | 2.526 | |
| queryGeNetClassifier | 1.146 | 0.048 | 1.198 | |
| querySummary | 0.736 | 0.029 | 0.776 | |