Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-03-28 11:32:16 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
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 153/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
benchdamic 1.8.2 (landing page) Matteo Calgaro
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the benchdamic 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: benchdamic |
Version: 1.8.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings benchdamic_1.8.2.tar.gz |
StartedAt: 2024-03-27 06:24:35 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 06:39:36 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 900.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: benchdamic.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings benchdamic_1.8.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/benchdamic.Rcheck’ * using R version 4.3.3 (2024-02-29) * 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 Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘benchdamic/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘benchdamic’ version ‘1.8.2’ * 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 ‘benchdamic’ 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 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 DA_ALDEx2 6.393 0.845 7.387 areaCAT 5.508 0.150 5.854 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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
benchdamic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘benchdamic’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (benchdamic)
benchdamic.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 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. > library(testthat) > library(benchdamic) > > test_check("benchdamic") |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| [ FAIL 0 | WARN 0 | SKIP 1 | PASS 310 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_DA_paired.R:3:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 310 ] > > proc.time() user system elapsed 180.705 3.964 237.190
benchdamic.Rcheck/benchdamic-Ex.timings
name | user | system | elapsed | |
CAT | 0.007 | 0.001 | 0.009 | |
DA_ALDEx2 | 6.393 | 0.845 | 7.387 | |
DA_ANCOM | 3.858 | 0.132 | 4.147 | |
DA_DESeq2 | 3.077 | 0.032 | 3.181 | |
DA_MAST | 1.479 | 0.036 | 1.538 | |
DA_Maaslin2 | 0.289 | 0.039 | 0.365 | |
DA_NOISeq | 2.053 | 0.039 | 2.121 | |
DA_Seurat | 3.590 | 0.056 | 3.684 | |
DA_ZicoSeq | 0.669 | 0.020 | 0.715 | |
DA_basic | 0.038 | 0.003 | 0.045 | |
DA_dearseq | 0.080 | 0.006 | 0.096 | |
DA_edgeR | 0.313 | 0.016 | 0.340 | |
DA_limma | 0.095 | 0.006 | 0.107 | |
DA_linda | 0.036 | 0.004 | 0.043 | |
DA_metagenomeSeq | 0.281 | 0.016 | 0.312 | |
DA_mixMC | 0.461 | 0.037 | 0.548 | |
RMSE | 0.000 | 0.000 | 0.001 | |
addKnowledge | 0.202 | 0.009 | 0.222 | |
areaCAT | 5.508 | 0.150 | 5.854 | |
checkNormalization | 0 | 0 | 0 | |
createColors | 0.007 | 0.001 | 0.008 | |
createConcordance | 4.545 | 0.157 | 4.751 | |
createEnrichment | 0.249 | 0.008 | 0.262 | |
createMocks | 0.002 | 0.001 | 0.004 | |
createPositives | 0.801 | 0.022 | 0.831 | |
createSplits | 0.031 | 0.003 | 0.035 | |
createTIEC | 2.613 | 0.063 | 2.721 | |
enrichmentTest | 0.115 | 0.006 | 0.122 | |
extractDA | 0.168 | 0.006 | 0.179 | |
extractStatistics | 0.170 | 0.007 | 0.177 | |
fitDM | 0.030 | 0.002 | 0.033 | |
fitHURDLE | 0.769 | 0.009 | 0.786 | |
fitModels | 2.480 | 0.050 | 2.554 | |
fitNB | 0.041 | 0.000 | 0.041 | |
fitZIG | 0.055 | 0.001 | 0.056 | |
fitZINB | 0.414 | 0.005 | 0.435 | |
getDA | 0.083 | 0.008 | 0.092 | |
getPositives | 0.079 | 0.005 | 0.085 | |
getStatistics | 0.067 | 0.006 | 0.073 | |
get_counts_metadata | 0.192 | 0.003 | 0.196 | |
iterative_ordering | 0.012 | 0.002 | 0.014 | |
meanDifferences | 0.002 | 0.000 | 0.002 | |
norm_CSS | 0.066 | 0.001 | 0.067 | |
norm_DESeq2 | 0.535 | 0.004 | 0.554 | |
norm_TSS | 0.030 | 0.001 | 0.031 | |
norm_edgeR | 0.035 | 0.001 | 0.035 | |
plotConcordance | 4.648 | 0.066 | 4.758 | |
plotContingency | 1.088 | 0.020 | 1.117 | |
plotEnrichment | 1.004 | 0.012 | 1.025 | |
plotFDR | 2.148 | 0.033 | 2.197 | |
plotFPR | 2.232 | 0.031 | 2.277 | |
plotKS | 2.065 | 0.033 | 2.159 | |
plotLogP | 1.534 | 0.034 | 1.826 | |
plotMD | 3.389 | 0.031 | 3.521 | |
plotMutualFindings | 1.066 | 0.014 | 1.101 | |
plotPositives | 0.677 | 0.008 | 0.696 | |
plotQQ | 2.128 | 0.029 | 2.216 | |
plotRMSE | 2.854 | 0.027 | 2.956 | |
prepareObserved | 0.001 | 0.000 | 0.002 | |
runDA | 0.566 | 0.005 | 0.578 | |
runMocks | 0.662 | 0.013 | 0.676 | |
runNormalizations | 0.451 | 0.003 | 0.457 | |
runSplits | 3.163 | 0.065 | 3.359 | |
setNormalizations | 0 | 0 | 0 | |
set_ALDEx2 | 0.007 | 0.000 | 0.007 | |
set_ANCOM | 0.009 | 0.001 | 0.012 | |
set_DESeq2 | 0.007 | 0.000 | 0.008 | |
set_MAST | 0.003 | 0.000 | 0.005 | |
set_Maaslin2 | 0.005 | 0.001 | 0.009 | |
set_NOISeq | 0.005 | 0.001 | 0.008 | |
set_Seurat | 0.006 | 0.001 | 0.007 | |
set_ZicoSeq | 0.007 | 0.000 | 0.007 | |
set_basic | 0.002 | 0.000 | 0.002 | |
set_dearseq | 0.002 | 0.000 | 0.002 | |
set_edgeR | 0.012 | 0.000 | 0.012 | |
set_limma | 0.009 | 0.000 | 0.009 | |
set_linda | 0.006 | 0.001 | 0.006 | |
set_metagenomeSeq | 0.005 | 0.000 | 0.005 | |
set_mixMC | 0.002 | 0.000 | 0.003 | |
weights_ZINB | 0.407 | 0.003 | 0.469 | |