Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-02-04 11:44 -0500 (Tue, 04 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4716
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4478
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4489
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4442
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 1204/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetaboDynamics 0.99.18  (landing page)
Katja Danielzik
Snapshot Date: 2025-02-03 13:40 -0500 (Mon, 03 Feb 2025)
git_url: https://git.bioconductor.org/packages/MetaboDynamics
git_branch: devel
git_last_commit: 8ec64e1
git_last_commit_date: 2025-02-01 18:21:19 -0500 (Sat, 01 Feb 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES

CHECK results for MetaboDynamics on kjohnson3

To the developers/maintainers of the MetaboDynamics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetaboDynamics.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.

raw results


Summary

Package: MetaboDynamics
Version: 0.99.18
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetaboDynamics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetaboDynamics_0.99.18.tar.gz
StartedAt: 2025-02-03 20:37:05 -0500 (Mon, 03 Feb 2025)
EndedAt: 2025-02-03 20:39:40 -0500 (Mon, 03 Feb 2025)
EllapsedTime: 154.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MetaboDynamics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetaboDynamics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetaboDynamics_0.99.18.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MetaboDynamics.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaboDynamics/DESCRIPTION’ ... OK
* this is package ‘MetaboDynamics’ version ‘0.99.18’
* 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 ‘MetaboDynamics’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... 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 ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ORA_hypergeometric.Rd: SummarizedExperiment
  compare_dynamics.Rd: SummarizedExperiment
  compare_metabolites.Rd: SummarizedExperiment
  estimates_dynamics.Rd: SummarizedExperiment
  fit_dynamics_model.Rd: SummarizedExperiment
  get_ORA_annotations.Rd: SummarizedExperiment
  heatmap_dynamics.Rd: SummarizedExperiment
  heatmap_metabolites.Rd: SummarizedExperiment
  longitudinalMetabolomics.Rd: SummarizedExperiment
  plot_ORA.Rd: SummarizedExperiment
  plot_PPC.Rd: SummarizedExperiment
  plot_diagnostics.Rd: SummarizedExperiment
  plot_estimates.Rd: SummarizedExperiment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 shell scripts ... 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 ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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
compare_dynamics 30.268  0.714  31.702
heatmap_dynamics 29.603  0.611  30.453
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/MetaboDynamics.Rcheck/00check.log’
for details.

Installation output

MetaboDynamics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MetaboDynamics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘MetaboDynamics’ ...
** this is package ‘MetaboDynamics’ version ‘0.99.18’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++17
using SDK: ‘MacOSX11.3.sdk’


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/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]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/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]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
5 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c stanExports_m_ANOVA_partial_pooling.cc -o stanExports_m_ANOVA_partial_pooling.o
In file included from stanExports_m_ANOVA_partial_pooling.cc:5:
In file included from ./stanExports_m_ANOVA_partial_pooling.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from stanExports_m_ANOVA_partial_pooling.cc:5:
In file included from ./stanExports_m_ANOVA_partial_pooling.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/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]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/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]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from stanExports_m_ANOVA_partial_pooling.cc:5:
In file included from ./stanExports_m_ANOVA_partial_pooling.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_m_ANOVA_partial_pooling.cc:5:
In file included from ./stanExports_m_ANOVA_partial_pooling.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_m_ANOVA_partial_pooling.cc:5:
In file included from ./stanExports_m_ANOVA_partial_pooling.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from stanExports_m_ANOVA_partial_pooling.cc:5:
In file included from ./stanExports_m_ANOVA_partial_pooling.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
In file included from stanExports_m_ANOVA_partial_pooling.cc:5:
In file included from ./stanExports_m_ANOVA_partial_pooling.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
In file included from stanExports_m_ANOVA_partial_pooling.cc:5:
In file included from ./stanExports_m_ANOVA_partial_pooling.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
    int ret = stan::services::error_codes::CONFIG;
        ^
In file included from stanExports_m_ANOVA_partial_pooling.cc:5:
./stanExports_m_ANOVA_partial_pooling.h:124:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
./stanExports_m_ANOVA_partial_pooling.h:519:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
11 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c stanExports_m_cluster_distances_padded.cc -o stanExports_m_cluster_distances_padded.o
In file included from stanExports_m_cluster_distances_padded.cc:5:
In file included from ./stanExports_m_cluster_distances_padded.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from stanExports_m_cluster_distances_padded.cc:5:
In file included from ./stanExports_m_cluster_distances_padded.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/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]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/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]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from stanExports_m_cluster_distances_padded.cc:5:
In file included from ./stanExports_m_cluster_distances_padded.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_m_cluster_distances_padded.cc:5:
In file included from ./stanExports_m_cluster_distances_padded.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_m_cluster_distances_padded.cc:5:
In file included from ./stanExports_m_cluster_distances_padded.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from stanExports_m_cluster_distances_padded.cc:5:
In file included from ./stanExports_m_cluster_distances_padded.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
In file included from stanExports_m_cluster_distances_padded.cc:5:
In file included from ./stanExports_m_cluster_distances_padded.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
In file included from stanExports_m_cluster_distances_padded.cc:5:
In file included from ./stanExports_m_cluster_distances_padded.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
    int ret = stan::services::error_codes::CONFIG;
        ^
In file included from stanExports_m_cluster_distances_padded.cc:5:
./stanExports_m_cluster_distances_padded.h:274:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
./stanExports_m_cluster_distances_padded.h:309:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
11 warnings generated.
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 MetaboDynamics.so RcppExports.o stanExports_m_ANOVA_partial_pooling.o stanExports_m_cluster_distances_padded.o -L/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -L/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: ignoring duplicate libraries: '-ltbb', '-ltbbmalloc'
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-MetaboDynamics/00new/MetaboDynamics/libs
** R
** data
** 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 (MetaboDynamics)

Tests output

MetaboDynamics.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(MetaboDynamics)
> 
> test_check("MetaboDynamics")

SAMPLING FOR MODEL 'm_cluster_distances_padded' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 1.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:    1 / 2000 [  0%]  (Warmup)
Chain 1: Iteration:  200 / 2000 [ 10%]  (Warmup)
Chain 1: Iteration:  400 / 2000 [ 20%]  (Warmup)
Chain 1: Iteration:  501 / 2000 [ 25%]  (Sampling)
Chain 1: Iteration:  700 / 2000 [ 35%]  (Sampling)
Chain 1: Iteration:  900 / 2000 [ 45%]  (Sampling)
Chain 1: Iteration: 1100 / 2000 [ 55%]  (Sampling)
Chain 1: Iteration: 1300 / 2000 [ 65%]  (Sampling)
Chain 1: Iteration: 1500 / 2000 [ 75%]  (Sampling)
Chain 1: Iteration: 1700 / 2000 [ 85%]  (Sampling)
Chain 1: Iteration: 1900 / 2000 [ 95%]  (Sampling)
Chain 1: Iteration: 2000 / 2000 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.014 seconds (Warm-up)
Chain 1:                0.039 seconds (Sampling)
Chain 1:                0.053 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'm_cluster_distances_padded' NOW (CHAIN 2).
Chain 2: 
Chain 2: Gradient evaluation took 4e-06 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2: 
Chain 2: 
Chain 2: Iteration:    1 / 2000 [  0%]  (Warmup)
Chain 2: Iteration:  200 / 2000 [ 10%]  (Warmup)
Chain 2: Iteration:  400 / 2000 [ 20%]  (Warmup)
Chain 2: Iteration:  501 / 2000 [ 25%]  (Sampling)
Chain 2: Iteration:  700 / 2000 [ 35%]  (Sampling)
Chain 2: Iteration:  900 / 2000 [ 45%]  (Sampling)
Chain 2: Iteration: 1100 / 2000 [ 55%]  (Sampling)
Chain 2: Iteration: 1300 / 2000 [ 65%]  (Sampling)
Chain 2: Iteration: 1500 / 2000 [ 75%]  (Sampling)
Chain 2: Iteration: 1700 / 2000 [ 85%]  (Sampling)
Chain 2: Iteration: 1900 / 2000 [ 95%]  (Sampling)
Chain 2: Iteration: 2000 / 2000 [100%]  (Sampling)
Chain 2: 
Chain 2:  Elapsed Time: 0.014 seconds (Warm-up)
Chain 2:                0.036 seconds (Sampling)
Chain 2:                0.05 seconds (Total)
Chain 2: 

SAMPLING FOR MODEL 'm_cluster_distances_padded' NOW (CHAIN 3).
Chain 3: 
Chain 3: Gradient evaluation took 4e-06 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3: 
Chain 3: 
Chain 3: Iteration:    1 / 2000 [  0%]  (Warmup)
Chain 3: Iteration:  200 / 2000 [ 10%]  (Warmup)
Chain 3: Iteration:  400 / 2000 [ 20%]  (Warmup)
Chain 3: Iteration:  501 / 2000 [ 25%]  (Sampling)
Chain 3: Iteration:  700 / 2000 [ 35%]  (Sampling)
Chain 3: Iteration:  900 / 2000 [ 45%]  (Sampling)
Chain 3: Iteration: 1100 / 2000 [ 55%]  (Sampling)
Chain 3: Iteration: 1300 / 2000 [ 65%]  (Sampling)
Chain 3: Iteration: 1500 / 2000 [ 75%]  (Sampling)
Chain 3: Iteration: 1700 / 2000 [ 85%]  (Sampling)
Chain 3: Iteration: 1900 / 2000 [ 95%]  (Sampling)
Chain 3: Iteration: 2000 / 2000 [100%]  (Sampling)
Chain 3: 
Chain 3:  Elapsed Time: 0.015 seconds (Warm-up)
Chain 3:                0.036 seconds (Sampling)
Chain 3:                0.051 seconds (Total)
Chain 3: 

SAMPLING FOR MODEL 'm_cluster_distances_padded' NOW (CHAIN 4).
Chain 4: 
Chain 4: Gradient evaluation took 4e-06 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4: 
Chain 4: 
Chain 4: Iteration:    1 / 2000 [  0%]  (Warmup)
Chain 4: Iteration:  200 / 2000 [ 10%]  (Warmup)
Chain 4: Iteration:  400 / 2000 [ 20%]  (Warmup)
Chain 4: Iteration:  501 / 2000 [ 25%]  (Sampling)
Chain 4: Iteration:  700 / 2000 [ 35%]  (Sampling)
Chain 4: Iteration:  900 / 2000 [ 45%]  (Sampling)
Chain 4: Iteration: 1100 / 2000 [ 55%]  (Sampling)
Chain 4: Iteration: 1300 / 2000 [ 65%]  (Sampling)
Chain 4: Iteration: 1500 / 2000 [ 75%]  (Sampling)
Chain 4: Iteration: 1700 / 2000 [ 85%]  (Sampling)
Chain 4: Iteration: 1900 / 2000 [ 95%]  (Sampling)
Chain 4: Iteration: 2000 / 2000 [100%]  (Sampling)
Chain 4: 
Chain 4:  Elapsed Time: 0.016 seconds (Warm-up)
Chain 4:                0.03 seconds (Sampling)
Chain 4:                0.046 seconds (Total)
Chain 4: 
Is your data normalized and standardized?
          We recommend normalization by log-transformation.
          Scaling and centering (mean=0, sd=1) should be metabolite and condition specific.

SAMPLING FOR MODEL 'm_ANOVA_partial_pooling' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 8e-06 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:   1 / 1000 [  0%]  (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%]  (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%]  (Warmup)
Chain 1: Iteration: 251 / 1000 [ 25%]  (Sampling)
Chain 1: Iteration: 350 / 1000 [ 35%]  (Sampling)
Chain 1: Iteration: 450 / 1000 [ 45%]  (Sampling)
Chain 1: Iteration: 550 / 1000 [ 55%]  (Sampling)
Chain 1: Iteration: 650 / 1000 [ 65%]  (Sampling)
Chain 1: Iteration: 750 / 1000 [ 75%]  (Sampling)
Chain 1: Iteration: 850 / 1000 [ 85%]  (Sampling)
Chain 1: Iteration: 950 / 1000 [ 95%]  (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.009 seconds (Warm-up)
Chain 1:                0.022 seconds (Sampling)
Chain 1:                0.031 seconds (Total)
Chain 1: 
Is your data normalized and standardized?
          We recommend normalization by log-transformation.
          Scaling and centering (mean=0, sd=1) should be metabolite and condition specific.

SAMPLING FOR MODEL 'm_ANOVA_partial_pooling' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 1.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:   1 / 1000 [  0%]  (Warmup)
Chain 1: Iteration: 100 / 1000 [ 10%]  (Warmup)
Chain 1: Iteration: 200 / 1000 [ 20%]  (Warmup)
Chain 1: Iteration: 251 / 1000 [ 25%]  (Sampling)
Chain 1: Iteration: 350 / 1000 [ 35%]  (Sampling)
Chain 1: Iteration: 450 / 1000 [ 45%]  (Sampling)
Chain 1: Iteration: 550 / 1000 [ 55%]  (Sampling)
Chain 1: Iteration: 650 / 1000 [ 65%]  (Sampling)
Chain 1: Iteration: 750 / 1000 [ 75%]  (Sampling)
Chain 1: Iteration: 850 / 1000 [ 85%]  (Sampling)
Chain 1: Iteration: 950 / 1000 [ 95%]  (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.027 seconds (Warm-up)
Chain 1:                0.034 seconds (Sampling)
Chain 1:                0.061 seconds (Total)
Chain 1: 
Is your data normalized and standardized?
          We recommend normalization by log-transformation.
          Scaling and centering (mean=0, sd=1) should be metabolite and condition specific.
Is your data normalized and standardized?
          We recommend normalization by log-transformation.
          Scaling and centering (mean=0, sd=1) should be metabolite and condition specific.
Is your data normalized and standardized?
          We recommend normalization by log-transformation.
          Scaling and centering (mean=0, sd=1) should be metabolite and condition specific.
Is your data normalized and standardized?
          We recommend normalization by log-transformation.
          Scaling and centering (mean=0, sd=1) should be metabolite and condition specific.
Is your data normalized and standardized?
          We recommend normalization by log-transformation.
          Scaling and centering (mean=0, sd=1) should be metabolite and condition specific.
Is your data normalized and standardized?
          We recommend normalization by log-transformation.
          Scaling and centering (mean=0, sd=1) should be metabolite and condition specific.
Is your data normalized and standardized?
          We recommend normalization by log-transformation.
          Scaling and centering (mean=0, sd=1) should be metabolite and condition specific.

SAMPLING FOR MODEL 'm_ANOVA_partial_pooling' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 8e-06 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1:          three stages of adaptation as currently configured.
Chain 1:          Reducing each adaptation stage to 15%/75%/10% of
Chain 1:          the given number of warmup iterations:
Chain 1:            init_buffer = 3
Chain 1:            adapt_window = 15
Chain 1:            term_buffer = 2
Chain 1: 
Chain 1: Iteration:  1 / 100 [  1%]  (Warmup)
Chain 1: Iteration: 10 / 100 [ 10%]  (Warmup)
Chain 1: Iteration: 20 / 100 [ 20%]  (Warmup)
Chain 1: Iteration: 21 / 100 [ 21%]  (Sampling)
Chain 1: Iteration: 30 / 100 [ 30%]  (Sampling)
Chain 1: Iteration: 40 / 100 [ 40%]  (Sampling)
Chain 1: Iteration: 50 / 100 [ 50%]  (Sampling)
Chain 1: Iteration: 60 / 100 [ 60%]  (Sampling)
Chain 1: Iteration: 70 / 100 [ 70%]  (Sampling)
Chain 1: Iteration: 80 / 100 [ 80%]  (Sampling)
Chain 1: Iteration: 90 / 100 [ 90%]  (Sampling)
Chain 1: Iteration: 100 / 100 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.008 seconds (Warm-up)
Chain 1:                0.015 seconds (Sampling)
Chain 1:                0.023 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'm_ANOVA_partial_pooling' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 7e-06 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1:          three stages of adaptation as currently configured.
Chain 1:          Reducing each adaptation stage to 15%/75%/10% of
Chain 1:          the given number of warmup iterations:
Chain 1:            init_buffer = 3
Chain 1:            adapt_window = 15
Chain 1:            term_buffer = 2
Chain 1: 
Chain 1: Iteration:  1 / 100 [  1%]  (Warmup)
Chain 1: Iteration: 10 / 100 [ 10%]  (Warmup)
Chain 1: Iteration: 20 / 100 [ 20%]  (Warmup)
Chain 1: Iteration: 21 / 100 [ 21%]  (Sampling)
Chain 1: Iteration: 30 / 100 [ 30%]  (Sampling)
Chain 1: Iteration: 40 / 100 [ 40%]  (Sampling)
Chain 1: Iteration: 50 / 100 [ 50%]  (Sampling)
Chain 1: Iteration: 60 / 100 [ 60%]  (Sampling)
Chain 1: Iteration: 70 / 100 [ 70%]  (Sampling)
Chain 1: Iteration: 80 / 100 [ 80%]  (Sampling)
Chain 1: Iteration: 90 / 100 [ 90%]  (Sampling)
Chain 1: Iteration: 100 / 100 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.008 seconds (Warm-up)
Chain 1:                0 seconds (Sampling)
Chain 1:                0.008 seconds (Total)
Chain 1: 
This request may take some time, please be patient.
This request may take some time, please be patient.
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 118 ]

[ FAIL 0 | WARN 10 | SKIP 0 | PASS 118 ]
> 
> proc.time()
   user  system elapsed 
  5.112   0.252   9.476

Example timings

MetaboDynamics.Rcheck/MetaboDynamics-Ex.timings

nameusersystemelapsed
ORA_hypergeometric0.4570.0090.467
compare_dynamics30.268 0.71431.702
compare_metabolites0.0340.0030.037
diagnostics_dynamics0.3500.0200.371
estimates_dynamics0.1710.0070.178
fit_dynamics_model0.1880.0180.207
get_ORA_annotations0.1530.0054.298
heatmap_dynamics29.603 0.61130.453
heatmap_metabolites0.0700.0020.073
plot_ORA0.6110.0250.636
plot_PPC0.3390.0160.356
plot_diagnostics0.4650.0220.489
plot_estimates0.3210.0130.334