Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-13 11:32:03 -0400 (Mon, 13 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 571/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
divergence 1.21.0 (landing page) Wikum Dinalankara
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the divergence 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: divergence |
Version: 1.21.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:divergence.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings divergence_1.21.0.tar.gz |
StartedAt: 2024-05-12 11:56:40 -0400 (Sun, 12 May 2024) |
EndedAt: 2024-05-12 11:59:57 -0400 (Sun, 12 May 2024) |
EllapsedTime: 197.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: divergence.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:divergence.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings divergence_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/divergence.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 ‘divergence/DESCRIPTION’ ... OK * this is package ‘divergence’ version ‘1.21.0’ * package encoding: UTF-8 * 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 ‘divergence’ 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... NOTE check_SE: no visible binding for global variable ‘data’ computeSingleFeaturesetBinaryVector: no visible global function definition for ‘dist’ computeSingleFeaturesetSupport: no visible global function definition for ‘dist’ computeSingleFeaturesetSupport: no visible global function definition for ‘quantile’ computeSingleRange: no visible global function definition for ‘quantile’ getRangesBySections: no visible global function definition for ‘detectCores’ rowChiSq: no visible global function definition for ‘chisq.test’ rowChiSq: no visible global function definition for ‘xtabs’ Undefined global functions or variables: chisq.test data detectCores dist quantile xtabs Consider adding importFrom("stats", "chisq.test", "dist", "quantile", "xtabs") importFrom("utils", "data") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) computeMultivariateDigitization.Rd:26: Lost braces; missing escapes or markup? 26 | By default gamma = {0.01, 0.02, ... 0.09, 0.1, 0.2, ..., 0.9}.} | ^ checkRd: (-1) computeUnivariateDigitization.Rd:22: Lost braces; missing escapes or markup? 22 | By default gamma = {0.01, 0.02, ... 0.09, 0.1, 0.2, ..., 0.9}.} | ^ * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed computeChiSquaredTest 21.613 13.286 9.059 computeUnivariateDigitization 15.347 14.792 6.876 findUnivariateGammaWithSupport 13.722 10.527 5.345 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... NOTE Package vignette with \VignetteEngine{} not specifying an engine package: ‘divergence.Rmd’ Engines should be specified as \VignetteEngine{PKG::ENG}. * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/divergence.Rcheck/00check.log’ for details.
divergence.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL divergence ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘divergence’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (divergence)
divergence.Rcheck/divergence-Ex.timings
name | user | system | elapsed | |
computeChiSquaredTest | 21.613 | 13.286 | 9.059 | |
computeMultivariateBinaryMatrix | 1.644 | 0.207 | 1.883 | |
computeMultivariateDigitization | 3.63 | 0.17 | 3.85 | |
computeMultivariateSupport | 0.318 | 0.008 | 0.330 | |
computeQuantileMatrix | 0.048 | 0.001 | 0.049 | |
computeUnivariateDigitization | 15.347 | 14.792 | 6.876 | |
computeUnivariateSupport | 1.316 | 1.158 | 0.621 | |
computeUnivariateTernaryMatrix | 2.348 | 1.742 | 1.848 | |
findMultivariateGammaWithSupport | 0.543 | 0.031 | 0.587 | |
findUnivariateGammaWithSupport | 13.722 | 10.527 | 5.345 | |