##############################################################################
##############################################################################
###
### 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_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MetaboDynamics.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaboDynamics/DESCRIPTION’ ... OK
* this is package ‘MetaboDynamics’ version ‘1.1.1’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘KEGGREST’ ‘stringr’
  All declared Imports should be used.
* 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
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 135.912  1.872 138.399
heatmap_dynamics 134.230  1.569 136.597
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/MetaboDynamics.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘MetaboDynamics’ ...
** this is package ‘MetaboDynamics’ version ‘1.1.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/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-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/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-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -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-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/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 ('std::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-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/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 ('std::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-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/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-x86_64/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-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/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:518:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
6 warnings generated.


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/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-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -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-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/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 ('std::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-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/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 ('std::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-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/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-x86_64/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-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/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();
          ^
6 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-MetaboDynamics/00new/MetaboDynamics/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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.

> # 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")
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.
 ..cutHeight not given, setting it to 2.99  ===>  99% of the (truncated) height range in dendro.
 ..done.
 ..cutHeight not given, setting it to 2.99  ===>  99% of the (truncated) height range in dendro.
 ..done.

SAMPLING FOR MODEL 'm_cluster_distances_padded' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 3.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.37 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: 0.048 seconds (Warm-up)
Chain 1:                0.153 seconds (Sampling)
Chain 1:                0.201 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'm_cluster_distances_padded' NOW (CHAIN 2).
Chain 2: 
Chain 2: Gradient evaluation took 1.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.11 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: 0.053 seconds (Warm-up)
Chain 2:                0.12 seconds (Sampling)
Chain 2:                0.173 seconds (Total)
Chain 2: 

SAMPLING FOR MODEL 'm_cluster_distances_padded' NOW (CHAIN 3).
Chain 3: 
Chain 3: Gradient evaluation took 1.7e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.17 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3: 
Chain 3: 
Chain 3: Iteration:    1 / 2000 [  0%]  (Warmup)
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Chain 3: 
Chain 3:  Elapsed Time: 0.064 seconds (Warm-up)
Chain 3:                0.183 seconds (Sampling)
Chain 3:                0.247 seconds (Total)
Chain 3: 

SAMPLING FOR MODEL 'm_cluster_distances_padded' NOW (CHAIN 4).
Chain 4: 
Chain 4: Gradient evaluation took 1.5e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.15 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)
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Chain 4: Iteration: 1900 / 2000 [ 95%]  (Sampling)
Chain 4: Iteration: 2000 / 2000 [100%]  (Sampling)
Chain 4: 
Chain 4:  Elapsed Time: 0.083 seconds (Warm-up)
Chain 4:                0.148 seconds (Sampling)
Chain 4:                0.231 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 2.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.22 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)
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Chain 1: Iteration: 950 / 1000 [ 95%]  (Sampling)
Chain 1: Iteration: 1000 / 1000 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.058 seconds (Warm-up)
Chain 1:                0.187 seconds (Sampling)
Chain 1:                0.245 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 1.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.16 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)
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Chain 1: Iteration: 1000 / 1000 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.046 seconds (Warm-up)
Chain 1:                0.122 seconds (Sampling)
Chain 1:                0.168 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 1.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.15 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)
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Chain 1: Iteration: 100 / 100 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.027 seconds (Warm-up)
Chain 1:                0.002 seconds (Sampling)
Chain 1:                0.029 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'm_ANOVA_partial_pooling' 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: 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)
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Chain 1: Iteration: 100 / 100 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.02 seconds (Warm-up)
Chain 1:                0.003 seconds (Sampling)
Chain 1:                0.023 seconds (Total)
Chain 1: 
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 121 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 121 ]
> 
> proc.time()
   user  system elapsed 
 14.922   0.816  15.560