Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-09-28 11:35:24 -0400 (Thu, 28 Sep 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 153/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
benchdamic 1.6.4 (landing page) Matteo Calgaro
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
To the developers/maintainers of the benchdamic package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/benchdamic.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: benchdamic |
Version: 1.6.4 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings benchdamic_1.6.4.tar.gz |
StartedAt: 2023-09-27 19:31:17 -0400 (Wed, 27 Sep 2023) |
EndedAt: 2023-09-27 20:02:57 -0400 (Wed, 27 Sep 2023) |
EllapsedTime: 1900.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: benchdamic.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings benchdamic_1.6.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/benchdamic.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘benchdamic/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘benchdamic’ version ‘1.6.4’ * 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 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 ... 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 * 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 ... ‘intro.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
benchdamic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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) The legacy packages maptools, rgdal, and rgeos, underpinning the sp package, which was just loaded, will retire in October 2023. Please refer to R-spatial evolution reports for details, especially https://r-spatial.org/r/2023/05/15/evolution4.html. It may be desirable to make the sf package available; package maintainers should consider adding sf to Suggests:. The sp package is now running under evolution status 2 (status 2 uses the sf package in place of rgdal) > > test_check("benchdamic") |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| [ FAIL 0 | WARN 0 | SKIP 0 | PASS 310 ] > > proc.time() user system elapsed 170.097 6.068 216.028
benchdamic.Rcheck/benchdamic-Ex.timings
name | user | system | elapsed | |
CAT | 0.006 | 0.000 | 0.006 | |
DA_ALDEx2 | 3.796 | 0.148 | 3.945 | |
DA_ANCOM | 4.742 | 0.148 | 4.891 | |
DA_DESeq2 | 2.57 | 0.04 | 2.61 | |
DA_MAST | 1.537 | 0.015 | 1.527 | |
DA_Maaslin2 | 0.242 | 0.016 | 0.260 | |
DA_NOISeq | 1.663 | 0.088 | 1.751 | |
DA_Seurat | 0.579 | 0.012 | 0.591 | |
DA_ZicoSeq | 0.620 | 0.008 | 0.628 | |
DA_basic | 0.031 | 0.000 | 0.031 | |
DA_corncob | 1.323 | 0.060 | 1.388 | |
DA_dearseq | 0.057 | 0.004 | 0.060 | |
DA_edgeR | 0.315 | 0.000 | 0.315 | |
DA_limma | 0.073 | 0.000 | 0.073 | |
DA_linda | 0.027 | 0.004 | 0.032 | |
DA_metagenomeSeq | 0.243 | 0.000 | 0.244 | |
RMSE | 0.001 | 0.000 | 0.001 | |
addKnowledge | 0.160 | 0.008 | 0.168 | |
areaCAT | 3.831 | 0.072 | 3.903 | |
checkNormalization | 0.001 | 0.000 | 0.000 | |
createColors | 0.005 | 0.000 | 0.005 | |
createConcordance | 4.153 | 0.052 | 4.205 | |
createEnrichment | 0.238 | 0.004 | 0.241 | |
createMocks | 0.004 | 0.000 | 0.003 | |
createPositives | 0.790 | 0.004 | 0.794 | |
createSplits | 0.03 | 0.00 | 0.03 | |
createTIEC | 2.453 | 0.036 | 2.489 | |
enrichmentTest | 0.113 | 0.000 | 0.113 | |
extractDA | 0.158 | 0.004 | 0.162 | |
extractStatistics | 0.157 | 0.000 | 0.157 | |
fitDM | 0.030 | 0.000 | 0.031 | |
fitHURDLE | 0.693 | 0.012 | 0.706 | |
fitModels | 2.372 | 0.032 | 2.405 | |
fitNB | 0.043 | 0.000 | 0.043 | |
fitZIG | 0.049 | 0.000 | 0.049 | |
fitZINB | 0.405 | 0.000 | 0.404 | |
getDA | 0.074 | 0.008 | 0.082 | |
getPositives | 0.075 | 0.000 | 0.075 | |
getStatistics | 0.070 | 0.000 | 0.069 | |
get_counts_metadata | 0.207 | 0.000 | 0.206 | |
iterative_ordering | 0.009 | 0.001 | 0.010 | |
meanDifferences | 0.000 | 0.002 | 0.002 | |
norm_CSS | 0.064 | 0.000 | 0.064 | |
norm_DESeq2 | 0.397 | 0.000 | 0.398 | |
norm_TSS | 0.028 | 0.000 | 0.029 | |
norm_edgeR | 0.034 | 0.000 | 0.033 | |
plotConcordance | 4.765 | 0.084 | 4.848 | |
plotContingency | 1.194 | 0.020 | 1.215 | |
plotEnrichment | 1.123 | 0.000 | 1.123 | |
plotFDR | 2.217 | 0.012 | 2.228 | |
plotFPR | 2.194 | 0.044 | 2.237 | |
plotKS | 2.268 | 0.004 | 2.271 | |
plotLogP | 2.136 | 0.076 | 2.212 | |
plotMD | 3.709 | 0.068 | 3.776 | |
plotMutualFindings | 1.092 | 0.008 | 1.100 | |
plotPositives | 0.799 | 0.000 | 0.799 | |
plotQQ | 2.129 | 0.028 | 2.157 | |
plotRMSE | 2.933 | 0.000 | 2.933 | |
prepareObserved | 0.001 | 0.000 | 0.001 | |
runDA | 0.461 | 0.000 | 0.461 | |
runMocks | 0.711 | 0.004 | 0.715 | |
runNormalizations | 0.434 | 0.000 | 0.434 | |
runSplits | 3.368 | 0.032 | 3.400 | |
setNormalizations | 0.001 | 0.000 | 0.001 | |
set_ALDEx2 | 0.006 | 0.000 | 0.006 | |
set_ANCOM | 0.007 | 0.000 | 0.007 | |
set_DESeq2 | 0.007 | 0.000 | 0.007 | |
set_MAST | 0.003 | 0.000 | 0.003 | |
set_Maaslin2 | 0.004 | 0.000 | 0.004 | |
set_NOISeq | 0.003 | 0.000 | 0.003 | |
set_Seurat | 0.001 | 0.004 | 0.005 | |
set_ZicoSeq | 0.003 | 0.003 | 0.006 | |
set_basic | 0.001 | 0.000 | 0.002 | |
set_corncob | 0.004 | 0.000 | 0.003 | |
set_dearseq | 0.002 | 0.000 | 0.002 | |
set_edgeR | 0.002 | 0.008 | 0.011 | |
set_limma | 0.008 | 0.000 | 0.008 | |
set_linda | 0.006 | 0.000 | 0.005 | |
set_metagenomeSeq | 0.005 | 0.000 | 0.005 | |
weights_ZINB | 0.404 | 0.000 | 0.404 | |