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This page was generated on 2024-03-04 11:37:49 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1864/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sccomp 1.6.0  (landing page)
Stefano Mangiola
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/sccomp
git_branch: RELEASE_3_18
git_last_commit: a9c2d70
git_last_commit_date: 2023-10-24 11:38:27 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

BUILD BIN results for sccomp on lconway


To the developers/maintainers of the sccomp package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sccomp.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: sccomp
Version: 1.6.0
Command: rm -rf sccomp.buildbin-libdir && mkdir sccomp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sccomp_1.6.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sccomp.buildbin-libdir
StartedAt: 2024-03-04 01:02:53 -0500 (Mon, 04 Mar 2024)
EndedAt: 2024-03-04 01:10:10 -0500 (Mon, 04 Mar 2024)
EllapsedTime: 436.5 seconds
RetCode: 0
Status:   OK  
PackageFile: sccomp_1.6.0.tgz
PackageFileSize: 3.913 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf sccomp.buildbin-libdir && mkdir sccomp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sccomp_1.6.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sccomp.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=sccomp.buildbin-libdir sccomp_1.6.0.tar.gz'
>>>>>>> 

* installing *source* package ‘sccomp’ ...
** 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/4.3-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/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c stanExports_glm_multi_beta_binomial.cc -o stanExports_glm_multi_beta_binomial.o
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.3-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, const 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 'const int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.3-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, const 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 'const int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.3-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_glm_multi_beta_binomial.cc:5:
./stanExports_glm_multi_beta_binomial.h:2286:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable]
      const T x_extrema = 1 / (1 + a);
              ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here
      temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2);
      ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
               x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol);
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
   rx = detail::ibeta_inv_imp(
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here
   return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol);
          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here
  return boost::math::ibeta_inv(a, b, p, boost_policy_t<>());
                      ^
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/4.3-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/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c stanExports_glm_multi_beta_binomial_generate_date.cc -o stanExports_glm_multi_beta_binomial_generate_date.o
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.3-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, const 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 'const int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.3-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, const 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 'const int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.3-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_glm_multi_beta_binomial_generate_date.cc:5:
./stanExports_glm_multi_beta_binomial_generate_date.h:566:20: warning: unused variable 'jacobian__' [-Wunused-variable]
    constexpr bool jacobian__ = false;
                   ^
./stanExports_glm_multi_beta_binomial_generate_date.h:784:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable]
      const T x_extrema = 1 / (1 + a);
              ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here
      temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2);
      ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
               x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol);
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
   rx = detail::ibeta_inv_imp(
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here
   return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol);
          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here
  return boost::math::ibeta_inv(a, b, p, boost_policy_t<>());
                      ^
7 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/4.3-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/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c stanExports_glm_multi_beta_binomial_simulate_data.cc -o stanExports_glm_multi_beta_binomial_simulate_data.o
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.3-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, const 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 'const int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.3-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, const 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 'const int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.3-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_glm_multi_beta_binomial_simulate_data.cc:5:
./stanExports_glm_multi_beta_binomial_simulate_data.h:534:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
./stanExports_glm_multi_beta_binomial_simulate_data.h:568:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable]
      const T x_extrema = 1 / (1 + a);
              ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here
      temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2);
      ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
               x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol);
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
   rx = detail::ibeta_inv_imp(
                ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here
   return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol);
          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here
  return boost::math::ibeta_inv(a, b, p, boost_policy_t<>());
                      ^
7 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 sccomp.so RcppExports.o stanExports_glm_multi_beta_binomial.o stanExports_glm_multi_beta_binomial_generate_date.o stanExports_glm_multi_beta_binomial_simulate_data.o -L/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc/meat/sccomp.buildbin-libdir/00LOCK-sccomp/00new/sccomp/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (sccomp)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR sccomp.buildbin-libdir/sccomp/libs/sccomp.so
>>>>>>> 

>>>>>>> Paths before fix:
sccomp.buildbin-libdir/sccomp/libs/sccomp.so:
	sccomp.so (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libtbb.dylib (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libtbbmalloc.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.2)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "sccomp.buildbin-libdir/sccomp/libs/sccomp.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "sccomp.buildbin-libdir/sccomp/libs/sccomp.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "sccomp.buildbin-libdir/sccomp/libs/sccomp.so"

>>>>>>> Paths after fix:
sccomp.buildbin-libdir/sccomp/libs/sccomp.so:
	sccomp.so (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libtbb.dylib (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libtbbmalloc.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.2)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)