Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:44 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 1226/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MetaboDynamics 1.0.2 (landing page) Katja Danielzik
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. |
Package: MetaboDynamics |
Version: 1.0.2 |
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_1.0.2.tar.gz |
StartedAt: 2025-08-01 05:52:26 -0400 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 06:05:14 -0400 (Fri, 01 Aug 2025) |
EllapsedTime: 768.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MetaboDynamics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.0.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MetaboDynamics.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * 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 ‘1.0.2’ * 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 ... INFO installed size is 5.6Mb sub-directories of 1Mb or more: help 2.1Mb libs 2.8Mb * 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 ... 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 148.410 3.257 175.203 heatmap_dynamics 147.995 1.642 167.087 * 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-3.21-bioc/meat/MetaboDynamics.Rcheck/00check.log’ for details.
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-x86_64/Resources/library’ * installing *source* package ‘MetaboDynamics’ ... ** this is package ‘MetaboDynamics’ version ‘1.0.2’ ** 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)
MetaboDynamics.Rcheck/tests/testthat.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "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 5.1e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.51 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: 0.081 seconds (Warm-up) Chain 1: 0.234 seconds (Sampling) Chain 1: 0.315 seconds (Total) Chain 1: SAMPLING FOR MODEL 'm_cluster_distances_padded' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.2 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: 0.067 seconds (Warm-up) Chain 2: 0.18 seconds (Sampling) Chain 2: 0.247 seconds (Total) Chain 2: SAMPLING FOR MODEL 'm_cluster_distances_padded' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 1.8e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.18 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: 0.068 seconds (Warm-up) Chain 3: 0.184 seconds (Sampling) Chain 3: 0.252 seconds (Total) Chain 3: SAMPLING FOR MODEL 'm_cluster_distances_padded' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 1.9e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.19 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: 0.07 seconds (Warm-up) Chain 4: 0.137 seconds (Sampling) Chain 4: 0.207 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 2.1e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.21 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: 0.068 seconds (Warm-up) Chain 1: 0.133 seconds (Sampling) Chain 1: 0.201 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) 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: 0.051 seconds (Warm-up) Chain 1: 0.159 seconds (Sampling) Chain 1: 0.21 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 2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.2 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: 0.067 seconds (Warm-up) Chain 1: 0.006 seconds (Sampling) Chain 1: 0.073 seconds (Total) Chain 1: SAMPLING FOR MODEL 'm_ANOVA_partial_pooling' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 1.8e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.18 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: 0.044 seconds (Warm-up) Chain 1: 0.007 seconds (Sampling) Chain 1: 0.051 seconds (Total) Chain 1: [ FAIL 0 | WARN 12 | SKIP 0 | PASS 121 ] [ FAIL 0 | WARN 12 | SKIP 0 | PASS 121 ] > > proc.time() user system elapsed 23.005 1.287 24.674
MetaboDynamics.Rcheck/MetaboDynamics-Ex.timings
name | user | system | elapsed | |
ORA_hypergeometric | 1.204 | 0.048 | 1.446 | |
cluster_dynamics | 2.666 | 0.159 | 3.686 | |
compare_dynamics | 148.410 | 3.257 | 175.203 | |
compare_metabolites | 0.220 | 0.021 | 0.278 | |
diagnostics_dynamics | 0.741 | 0.025 | 0.860 | |
estimates_dynamics | 0.704 | 0.016 | 0.827 | |
fit_dynamics_model | 0.689 | 0.039 | 0.837 | |
heatmap_dynamics | 147.995 | 1.642 | 167.087 | |
heatmap_metabolites | 0.454 | 0.013 | 0.479 | |
plot_ORA | 3.429 | 0.056 | 3.980 | |
plot_PPC | 1.628 | 0.047 | 1.860 | |
plot_cluster | 3.556 | 0.035 | 4.031 | |
plot_diagnostics | 2.728 | 0.073 | 2.925 | |
plot_estimates | 1.348 | 0.025 | 1.464 | |