Torben Kimhofer
| Snapshot Date: 2026-04-24 13:40 -0400 (Fri, 24 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/metabom8 |
| git_branch: devel |
| git_last_commit: ba8bfc3 |
| git_last_commit_date: 2026-04-21 12:01:31 -0400 (Tue, 21 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-25 11:36 -0400 (Sat, 25 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4978 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4722 |
| 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 1273/2415 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metabom8 0.99.10 (landing page) Torben Kimhofer
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for metabom8 in R Universe. | ||||||||||||||
|
To the developers/maintainers of the metabom8 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metabom8.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: metabom8 |
| Version: 0.99.10 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metabom8.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metabom8_0.99.10.tar.gz |
| StartedAt: 2026-04-24 20:42:17 -0400 (Fri, 24 Apr 2026) |
| EndedAt: 2026-04-24 20:43:45 -0400 (Fri, 24 Apr 2026) |
| EllapsedTime: 88.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metabom8.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:metabom8.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings metabom8_0.99.10.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/metabom8.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-25 00:42:17 UTC
* using option ‘--no-vignettes’
* checking for file ‘metabom8/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metabom8’ version ‘0.99.10’
* 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 ‘metabom8’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking C++ specification ... INFO
specified C++17
* checking installed package size ... INFO
installed size is 8.3Mb
sub-directories of 1Mb or more:
data 5.5Mb
extdata 1.8Mb
* 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 ... NOTE
.check_preprocess: no visible binding for global variable ‘X_mean’
.check_preprocess: no visible binding for global variable ‘X_sd’
Undefined global functions or variables:
X_mean X_sd
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
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
align_spectra 17.154 0.179 17.549
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/metabom8.Rcheck/00check.log’
for details.
metabom8.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL metabom8
###
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##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘metabom8’ ...
** this is package ‘metabom8’ version ‘0.99.10’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++17
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppOplsHelpers.cpp -o RcppOplsHelpers.o
In file included from RcppOplsHelpers.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from RcppOplsHelpers.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from RcppOplsHelpers.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from RcppOplsHelpers.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phasing.cpp -o phasing.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sd_scaleXY.cpp -o sd_scaleXY.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o metabom8.so RcppExports.o RcppOplsHelpers.o phasing.o sd_scaleXY.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-metabom8/00new/metabom8/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘loadings’ from package ‘stats’ in package ‘metabom8’
** 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 (metabom8)
metabom8.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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(metabom8)
>
> test_check("metabom8")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 361 ]
>
> proc.time()
user system elapsed
28.421 0.478 29.234
metabom8.Rcheck/metabom8-Ex.timings
| name | user | system | elapsed | |
| add_note | 0.190 | 0.007 | 0.200 | |
| align_segment | 0.330 | 0.036 | 0.367 | |
| align_spectra | 17.154 | 0.179 | 17.549 | |
| balanced_boot | 0.003 | 0.000 | 0.004 | |
| balanced_mc | 0.002 | 0.001 | 0.002 | |
| binning | 0.002 | 0.000 | 0.003 | |
| calibrate | 0.085 | 0.005 | 0.094 | |
| cliffs_d | 0.005 | 0.001 | 0.007 | |
| correct_baseline | 0.575 | 0.016 | 0.629 | |
| correct_lw | 0.068 | 0.001 | 0.070 | |
| covid | 0.151 | 0.005 | 0.161 | |
| covid_raw | 0.063 | 0.001 | 0.064 | |
| cv_anova | 0.519 | 0.017 | 0.557 | |
| dmodx | 0.470 | 0.010 | 0.489 | |
| dot-fidApodisationFct | 0.004 | 0.000 | 0.005 | |
| ellipse2d | 0.003 | 0.000 | 0.003 | |
| excise | 0.003 | 0.000 | 0.004 | |
| fitted | 0.289 | 0.002 | 0.295 | |
| get_idx | 0.067 | 0.002 | 0.079 | |
| get_provenance | 0.254 | 0.004 | 0.259 | |
| hiit_raw | 0.097 | 0.001 | 0.098 | |
| hotellingsT2 | 0.001 | 0.001 | 0.002 | |
| kfold | 0.001 | 0.000 | 0.001 | |
| list_preprocessing | 0 | 0 | 0 | |
| loadings-m8_model-method | 0.244 | 0.007 | 0.256 | |
| lw | 0.002 | 0.001 | 0.003 | |
| m8_model-class | 0.283 | 0.003 | 0.289 | |
| mc | 0.000 | 0.000 | 0.001 | |
| minmax | 0.001 | 0.000 | 0.001 | |
| noise_sd | 0.120 | 0.003 | 0.124 | |
| norm_eretic | 0.074 | 0.016 | 0.094 | |
| opls | 0.635 | 0.013 | 0.661 | |
| pareto_scaling | 0.001 | 0.001 | 0.002 | |
| pca | 0.213 | 0.003 | 0.217 | |
| plotStocsy | 0.869 | 0.008 | 0.881 | |
| plot_spec | 1.354 | 0.029 | 1.405 | |
| pls | 0.267 | 0.004 | 0.275 | |
| ppick | 0.177 | 0.003 | 0.190 | |
| ppick2 | 0.617 | 0.018 | 0.645 | |
| pqn | 0.053 | 0.007 | 0.060 | |
| prep_X | 0.001 | 0.000 | 0.001 | |
| print_preprocessing | 0.000 | 0.001 | 0.001 | |
| print_provenance | 0.162 | 0.002 | 0.166 | |
| read1d | 0.045 | 0.003 | 0.053 | |
| read1d_raw | 0.433 | 0.006 | 0.447 | |
| scRange | 0.007 | 0.000 | 0.008 | |
| scores | 0.208 | 0.002 | 0.212 | |
| stocsy | 1.007 | 0.392 | 1.414 | |
| storm | 0.009 | 0.000 | 0.009 | |
| stratified_kfold | 0.001 | 0.000 | 0.002 | |
| unscaled | 0.002 | 0.000 | 0.001 | |
| uv_scaling | 0.001 | 0.000 | 0.001 | |
| vip | 0.207 | 0.002 | 0.210 | |
| weights | 0.221 | 0.004 | 0.233 | |
| xres | 0.211 | 0.002 | 0.213 | |