Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:04 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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 308/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cellmig 0.99.16 (landing page) Simo Kitanovski
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
To the developers/maintainers of the cellmig package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellmig.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: cellmig |
Version: 0.99.16 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmig.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmig_0.99.16.tar.gz |
StartedAt: 2025-10-10 20:34:06 -0400 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 20:44:17 -0400 (Fri, 10 Oct 2025) |
EllapsedTime: 610.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cellmig.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmig.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmig_0.99.16.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cellmig.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * 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 ‘cellmig/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cellmig’ version ‘0.99.16’ * 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 ‘cellmig’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.1.sdk’ * checking C++ specification ... OK * checking installed package size ... INFO installed size is 6.5Mb sub-directories of 1Mb or more: extdata 3.2Mb libs 2.9Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘base’ 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 ... NOTE gen_partial: no visible binding for global variable ‘delta’ get_dose_response_profile: no visible binding for global variable ‘isTip’ get_dose_response_profile: no visible binding for global variable ‘label’ get_dose_response_profile: no visible binding for global variable ‘dose’ get_dose_response_profile: no visible binding for global variable ‘X2.5.’ get_dose_response_profile: no visible binding for global variable ‘X97.5.’ get_pairs: no visible binding for global variable ‘group_x’ get_pairs: no visible binding for global variable ‘group_y’ get_pairs: no visible binding for global variable ‘rho_M’ get_pairs: no visible binding for global variable ‘rho_M_exp’ get_ppc_means: no visible binding for global variable ‘v’ get_ppc_means: no visible binding for global variable ‘X2.5.’ get_ppc_means: no visible binding for global variable ‘X97.5.’ get_ppc_violins: no visible binding for global variable ‘dose’ get_ppc_violins: no visible binding for global variable ‘v’ get_ppc_violins: no visible binding for global variable ‘well’ get_ppc_violins: no visible binding for global variable ‘yhat’ get_treatment_profile: no visible binding for global variable ‘isTip’ get_treatment_profile: no visible binding for global variable ‘label’ get_violins: no visible binding for global variable ‘dose’ get_violins: no visible binding for global variable ‘rho’ Undefined global functions or variables: X2.5. X97.5. delta dose group_x group_y isTip label rho rho_M rho_M_exp v well yhat * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in 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 cellmig-package 114.132 3.059 82.109 cellmig 113.504 2.959 82.326 get_dose_response_profile 103.719 2.171 75.525 get_treatment_profile 100.324 2.075 71.335 ppc_violin 32.235 1.405 25.932 get_pairs 27.467 1.133 21.060 get_violins 27.205 1.267 20.482 ppc_means 27.017 1.138 20.210 get_groups 25.924 1.073 19.527 * 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-3.22-bioc/meat/cellmig.Rcheck/00check.log’ for details.
cellmig.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cellmig ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘cellmig’ ... ** this is package ‘cellmig’ version ‘0.99.16’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++17 using SDK: ‘MacOSX11.3.1.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.cc -o stanExports_M.o In file included from stanExports_M.cc:5: In file included from ./stanExports_M.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.cc:5: In file included from ./stanExports_M.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.cc:5: In file included from ./stanExports_M.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.cc:5: In file included from ./stanExports_M.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.cc:5: ./stanExports_M.h:737:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits<int>::min(); ^ 5 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_gen_F.cc -o stanExports_gen_F.o In file included from stanExports_gen_F.cc:5: In file included from ./stanExports_gen_F.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_gen_F.cc:5: In file included from ./stanExports_gen_F.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_gen_F.cc:5: In file included from ./stanExports_gen_F.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_gen_F.cc:5: In file included from ./stanExports_gen_F.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_gen_F.cc:5: ./stanExports_gen_F.h:136:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits<int>::min(); ^ ./stanExports_gen_F.h:330:20: warning: unused variable 'jacobian__' [-Wunused-variable] constexpr bool jacobian__ = false; ^ ./stanExports_gen_F.h:499:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits<int>::min(); ^ ./stanExports_gen_F.h:516:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits<int>::min(); ^ 8 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 cellmig.so RcppExports.o stanExports_M.o stanExports_gen_F.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-cellmig/00new/cellmig/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 (cellmig)
cellmig.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "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. > library(testthat) > library(cellmig) > test_check("cellmig") SAMPLING FOR MODEL 'M' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000153 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.53 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 500 [ 0%] (Warmup) Chain 1: Iteration: 200 / 500 [ 40%] (Warmup) Chain 1: Iteration: 201 / 500 [ 40%] (Sampling) Chain 1: Iteration: 400 / 500 [ 80%] (Sampling) Chain 1: Iteration: 500 / 500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 2.295 seconds (Warm-up) Chain 1: 1.956 seconds (Sampling) Chain 1: 4.251 seconds (Total) Chain 1: SAMPLING FOR MODEL 'M' NOW (CHAIN 1). SAMPLING FOR MODEL 'M' NOW (CHAIN 2). Chain 1: Chain 1: Gradient evaluation took 0.000791 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 7.91 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 2: Chain 2: Gradient evaluation took 0.000513 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 5.13 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 1: Iteration: 1 / 900 [ 0%] (Warmup) Chain 2: Iteration: 1 / 900 [ 0%] (Warmup) Chain 2: Iteration: 200 / 900 [ 22%] (Warmup) Chain 2: Iteration: 201 / 900 [ 22%] (Sampling) Chain 1: Iteration: 200 / 900 [ 22%] (Warmup) Chain 1: Iteration: 201 / 900 [ 22%] (Sampling) Chain 1: Iteration: 400 / 900 [ 44%] (Sampling) Chain 2: Iteration: 400 / 900 [ 44%] (Sampling) Chain 1: Iteration: 600 / 900 [ 66%] (Sampling) Chain 1: Iteration: 800 / 900 [ 88%] (Sampling) Chain 1: Iteration: 900 / 900 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 6.514 seconds (Warm-up) Chain 1: 6.298 seconds (Sampling) Chain 1: 12.812 seconds (Total) Chain 1: Chain 2: Iteration: 600 / 900 [ 66%] (Sampling) Chain 2: Iteration: 800 / 900 [ 88%] (Sampling) Chain 2: Iteration: 900 / 900 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 5.998 seconds (Warm-up) Chain 2: 12.023 seconds (Sampling) Chain 2: 18.021 seconds (Total) Chain 2: SAMPLING FOR MODEL 'M' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000142 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.42 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 500 [ 0%] (Warmup) Chain 1: Iteration: 200 / 500 [ 40%] (Warmup) Chain 1: Iteration: 201 / 500 [ 40%] (Sampling) Chain 1: Iteration: 400 / 500 [ 80%] (Sampling) Chain 1: Iteration: 500 / 500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 2.369 seconds (Warm-up) Chain 1: 1.087 seconds (Sampling) Chain 1: 3.456 seconds (Total) Chain 1: SAMPLING FOR MODEL 'M' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000195 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.95 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 500 [ 0%] (Warmup) Chain 1: Iteration: 200 / 500 [ 40%] (Warmup) Chain 1: Iteration: 201 / 500 [ 40%] (Sampling) Chain 1: Iteration: 400 / 500 [ 80%] (Sampling) Chain 1: Iteration: 500 / 500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 2.116 seconds (Warm-up) Chain 1: 1.007 seconds (Sampling) Chain 1: 3.123 seconds (Total) Chain 1: SAMPLING FOR MODEL 'M' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000126 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.26 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 500 [ 0%] (Warmup) Chain 1: Iteration: 200 / 500 [ 40%] (Warmup) Chain 1: Iteration: 201 / 500 [ 40%] (Sampling) Chain 1: Iteration: 400 / 500 [ 80%] (Sampling) Chain 1: Iteration: 500 / 500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 2.566 seconds (Warm-up) Chain 1: 2.034 seconds (Sampling) Chain 1: 4.6 seconds (Total) Chain 1: SAMPLING FOR MODEL 'M' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 9.8e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.98 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 500 [ 0%] (Warmup) Chain 1: Iteration: 200 / 500 [ 40%] (Warmup) Chain 1: Iteration: 201 / 500 [ 40%] (Sampling) Chain 1: Iteration: 400 / 500 [ 80%] (Sampling) Chain 1: Iteration: 500 / 500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 2.019 seconds (Warm-up) Chain 1: 1.146 seconds (Sampling) Chain 1: 3.165 seconds (Total) Chain 1: SAMPLING FOR MODEL 'M' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000267 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.67 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 500 [ 0%] (Warmup) Chain 1: Iteration: 200 / 500 [ 40%] (Warmup) Chain 1: Iteration: 201 / 500 [ 40%] (Sampling) Chain 1: Iteration: 400 / 500 [ 80%] (Sampling) Chain 1: Iteration: 500 / 500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 2.818 seconds (Warm-up) Chain 1: 1.293 seconds (Sampling) Chain 1: 4.111 seconds (Total) Chain 1: Chain 1: Chain 1: Elapsed Time: 0 seconds (Warm-up) Chain 1: 0.002 seconds (Sampling) Chain 1: 0.002 seconds (Total) Chain 1: [ FAIL 0 | WARN 1 | SKIP 0 | PASS 141 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 141 ] > > proc.time() user system elapsed 100.165 3.047 89.187
cellmig.Rcheck/cellmig-Ex.timings
name | user | system | elapsed | |
cellmig-package | 114.132 | 3.059 | 82.109 | |
cellmig | 113.504 | 2.959 | 82.326 | |
d | 0.018 | 0.003 | 0.021 | |
get_dose_response_profile | 103.719 | 2.171 | 75.525 | |
get_groups | 25.924 | 1.073 | 19.527 | |
get_pairs | 27.467 | 1.133 | 21.060 | |
get_treatment_profile | 100.324 | 2.075 | 71.335 | |
get_violins | 27.205 | 1.267 | 20.482 | |
ppc_means | 27.017 | 1.138 | 20.210 | |
ppc_violin | 32.235 | 1.405 | 25.932 | |
sim_full | 0.044 | 0.006 | 0.050 | |
sim_partial | 0.135 | 0.005 | 0.141 | |