Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1197/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metabCombiner 1.16.0 (landing page) Hani Habra
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the metabCombiner package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metabCombiner.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: metabCombiner |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metabCombiner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metabCombiner_1.16.0.tar.gz |
StartedAt: 2024-12-20 05:41:21 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:46:03 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 281.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metabCombiner.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metabCombiner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metabCombiner_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/metabCombiner.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘metabCombiner/DESCRIPTION’ ... OK * this is package ‘metabCombiner’ version ‘1.16.0’ * 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 ‘metabCombiner’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 whether startup messages can be suppressed ... 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) combineData.Rd:22: Lost braces 22 | (quasi)merge of the /code{/link{combinedTable}} and /code{/link{featData}} | ^ checkRd: (-1) combineData.Rd:22: Lost braces 22 | (quasi)merge of the /code{/link{combinedTable}} and /code{/link{featData}} | ^ checkRd: (-1) combineData.Rd:22: Lost braces 22 | (quasi)merge of the /code{/link{combinedTable}} and /code{/link{featData}} | ^ checkRd: (-1) combineData.Rd:22: Lost braces 22 | (quasi)merge of the /code{/link{combinedTable}} and /code{/link{featData}} | ^ * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed evaluateParams 6.848 0.132 7.139 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/metabCombiner.Rcheck/00check.log’ for details.
metabCombiner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metabCombiner ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘metabCombiner’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c binByMZ.c -o binByMZ.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c duplicates.c -o duplicates.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c labelRows.c -o labelRows.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c metabCombiner_init.c -o metabCombiner_init.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c resolveRows.c -o resolveRows.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c selectAnchors.c -o selectAnchors.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c write2file.c -o write2file.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o metabCombiner.so binByMZ.o duplicates.o labelRows.o metabCombiner_init.o resolveRows.o selectAnchors.o write2file.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-metabCombiner/00new/metabCombiner/libs ** R ** data ** demo ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (metabCombiner)
metabCombiner.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > library(testthat) > library(metabCombiner) > > test_check("metabCombiner") [ FAIL 0 | WARN 9 | SKIP 0 | PASS 35 ] [ FAIL 0 | WARN 9 | SKIP 0 | PASS 35 ] > > proc.time() user system elapsed 29.556 1.089 32.589
metabCombiner.Rcheck/metabCombiner-Ex.timings
name | user | system | elapsed | |
adductdata | 0.392 | 0.014 | 0.415 | |
batchCombine | 0.001 | 0.000 | 0.001 | |
calcScores | 3.320 | 0.085 | 3.661 | |
calcScoresParam | 0.001 | 0.001 | 0.001 | |
combineData | 0.347 | 0.008 | 0.359 | |
combinedTable | 0.334 | 0.008 | 0.345 | |
datasets | 0.642 | 0.010 | 0.658 | |
evaluateParams | 6.848 | 0.132 | 7.139 | |
featdata | 0.342 | 0.008 | 0.361 | |
filtered | 0.159 | 0.005 | 0.166 | |
fit_gam | 4.490 | 0.065 | 4.629 | |
fit_loess | 2.586 | 0.029 | 2.639 | |
fitgamParam | 0.001 | 0.001 | 0.001 | |
fitloessParam | 0.001 | 0.001 | 0.002 | |
getAnchors | 0.892 | 0.017 | 0.912 | |
getCoefficients | 2.873 | 0.048 | 2.936 | |
getData | 0.164 | 0.005 | 0.169 | |
getExtra | 0.485 | 0.012 | 0.503 | |
getModel | 1.133 | 0.024 | 1.172 | |
getSamples | 0.699 | 0.015 | 0.716 | |
getStats | 1.691 | 0.068 | 1.772 | |
iddata | 0.325 | 0.007 | 0.335 | |
labelRows | 3.916 | 0.083 | 4.084 | |
labelRowsParam | 0.000 | 0.001 | 0.001 | |
metabCombine | 0.001 | 0.001 | 0.001 | |
metabCombiner | 0.743 | 0.017 | 0.804 | |
metabData | 0.768 | 0.029 | 0.827 | |
mzFit | 0.001 | 0.000 | 0.001 | |
mzfitParam | 0.000 | 0.000 | 0.001 | |
nonmatched | 0.336 | 0.014 | 0.353 | |
opts.duplicate | 0.331 | 0.012 | 0.356 | |
plot_fit | 1.126 | 0.019 | 1.158 | |
rtdata | 0.332 | 0.006 | 0.341 | |
selectAnchors | 1.313 | 0.020 | 1.348 | |
selectAnchorsParam | 0.000 | 0.001 | 0.001 | |
updateTables | 3.928 | 0.048 | 4.011 | |
write2file | 3.898 | 0.066 | 4.024 | |