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fix build
This commit is contained in:
sukanka
parent
e992f229c5
commit
ca733a258c
3 changed files with 67 additions and 35 deletions
69
PKGBUILD
69
PKGBUILD
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@ -4,42 +4,58 @@
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pkgname='stanc'
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pkgdesc="A package for obtaining Bayesian inference using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo."
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pkgver=2.35.0
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_mathver=4.9.0
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pkgrel=1
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arch=('i686' 'x86_64' 'aarch64')
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url='https://mc-stan.org/'
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license=('BSD')
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depends=('gcc-libs')
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makedepends=('texlive-bin' 'texlive-core' 'doxygen'
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# needed if compile against system library
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'gtest' 'benchmark' 'sundials' 'boost' 'eigen' 'stanmath'
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'python-cpplint' 'opencl-headers' 'rapidjson'
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'cli11' 'tbb'
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'inetutils'
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makedepends=(
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# needed if compile against system library
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'sundials'
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'eigen'
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'rapidjson'
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'boost'
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'cli11'
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'tbb'
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# needed when making doc
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'doxygen'
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)
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provides=("cmdstan")
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source=("stanc-${pkgver}.tar.gz::https://github.com/stan-dev/cmdstan/archive/refs/tags/v${pkgver}.tar.gz"
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"stan-${pkgver}.tar.gz::https://github.com/stan-dev/stan/archive/refs/tags/v${pkgver}.tar.gz"
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local
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cli11.patch
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"stan-${pkgver}.tar.gz::https://github.com/stan-dev/stan/archive/refs/tags/v${pkgver}.tar.gz"
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"stanmath-${_mathver}.tar.gz::https://github.com/stan-dev/math/archive/refs/tags/v${_mathver}.tar.gz"
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cli11.patch
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local
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)
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sha512sums=('6d4305abcab29bb352530795f32f9a85d6f85dc9373059ea14782272f6ac92dd13cfcb1f13f6af79514d51566c1e7bb64d62ff58d26118d62c53c2df1f3c41d8'
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'36a6694c7fbebb3e7bb659ba754ae7a95703750a23b6ec1a0130cf39d251bae68662da74dd21e687bb81d9d2881cdbc5688973af103ae7fcf769f2c0aeb4eec3'
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'83d164dc8ac6f53980874ee2654dc5a88610ec58763624534cdd169cec0e1639875a2eb470bbf00c4ad5073dc37aea070f87c137c8f080d817fd0983f262acd6'
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'fff32eedf0f2044c3ffdd0e6e83927d1b6b535f7d2f960ff20a2f6e84b5b825ec90ea3db5c7bd5cf67f6b2079fe1a7fac2529d5379af931175cefac44681700b')
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'36a6694c7fbebb3e7bb659ba754ae7a95703750a23b6ec1a0130cf39d251bae68662da74dd21e687bb81d9d2881cdbc5688973af103ae7fcf769f2c0aeb4eec3'
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'43749bbf7504821b56638db56063e4da62a019b93216609c9f6b8e024ba8037a861eb8224dabe46a403e0938df01a97d731158dfb50c5ef8c8096507a4068c8a'
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'c9ad30e8dcb9264315c7078f8f4495417e6937b0207b043776e1fab2acd10704d5518ae04aa535827d17178311014bbe1555692aec0833b7c039e9af1e6c5ad5'
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'SKIP'
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)
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prepare(){
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prepare() {
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cp -rf "${srcdir}/stan-${pkgver/_/-}"/* "${srcdir}/cmdstan-${pkgver/_/-}/stan/"
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sed -i "${srcdir}/math-${_mathver/_/-}"/stan/math/rev/functor/kinsol_data.hpp \
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-e "s|sundials_context.h>|sundials_context.hpp>|"
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sed -i "${srcdir}/math-${_mathver/_/-}"/stan/math/rev/functor/cvodes_integrator{,_adjoint}.hpp \
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-e "s|realtype|sunrealtype|g"
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sed -i "${srcdir}/math-${_mathver/_/-}"/stan/math/rev/functor/idas_service.hpp \
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-e "s|RCONST|SUN_RCONST|g"
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cd "${srcdir}/cmdstan-${pkgver/_/-}"
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patch --strip=1 < ../cli11.patch
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patch --strip=1 <${srcdir}/cli11.patch
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cp -rf "${srcdir}/math-${_mathver/_/-}"/* stan/lib/stan_math
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cp ${srcdir}/local make/local
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cp ${srcdir}/local stan/make/local
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sed -i 's|CLI11/CLI11.hpp|CLI/CLI.hpp|g' src/cmdstan/stansummary.cpp
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}
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build() {
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cd "${srcdir}/cmdstan-${pkgver/_/-}"
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export LDFLAGS="-ltbb"
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export CXXFLAGS="-fPIC -Isrc -Istan/src -I/usr/include/eigen3 -D_REENTRANT -DTBB_INTERFACE_NEW"
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make build
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cd stan
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make doxygen
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}
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package() {
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@ -47,15 +63,18 @@ package() {
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# Stan's makefile doesn't have a make install command...
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# Install binaries:
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install -dm755 "${pkgdir}/usr/bin"
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install -m755 bin/stanc "${pkgdir}/usr/bin"
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ln -s /usr/bin/stanc "${pkgdir}/usr/bin/cmdstan"
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install -Tm755 bin/diagnose "${pkgdir}/usr/bin/standiagnose"
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install -Tm755 bin/print "${pkgdir}/usr/bin/stanprint"
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install -Tm755 bin/stansummary "${pkgdir}/usr/bin/stansummary"
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install -dm755 "${pkgdir}/usr/bin"
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install -m755 bin/stanc "${pkgdir}/usr/bin"
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ln -s /usr/bin/stanc "${pkgdir}/usr/bin/cmdstan"
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install -Tm755 bin/diagnose "${pkgdir}/usr/bin/standiagnose"
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install -Tm755 bin/print "${pkgdir}/usr/bin/stanprint"
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install -Tm755 bin/stansummary "${pkgdir}/usr/bin/stansummary"
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install -d ${pkgdir}/usr/share/doc
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install -d "${pkgdir}/usr/include/stan"
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install -d "${pkgdir}/usr/include/cmdstan"
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cp -rf stan/doc ${pkgdir}/usr/share/doc/stan
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install -d "${pkgdir}/usr/include/stan"
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install -d "${pkgdir}/usr/include/cmdstan"
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cd "stan/src"
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find . -iregex './stan.*.hpp$' -type f -exec install -DTm644 "{}" "${pkgdir}/usr/include/{}" \;
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cd ../..
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@ -64,6 +83,6 @@ package() {
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cd ..
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# Install LICENSE file:
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install -dm755 "${pkgdir}/usr/share/licenses/stan"
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install -dm755 "${pkgdir}/usr/share/licenses/stan"
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cp -r "stan/licenses/." "${pkgdir}/usr/share/licenses/stan/."
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}
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21
cli11.patch
21
cli11.patch
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@ -1,9 +1,9 @@
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diff --git a/src/cmdstan/stansummary.cpp b/src/cmdstan/stansummary.cpp
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index eec4f5b2..a5e0b475 100644
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index a0cf2b1..e51b8f8 100644
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--- a/src/cmdstan/stansummary.cpp
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+++ b/src/cmdstan/stansummary.cpp
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@@ -52,18 +52,21 @@ Options:
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std::vector<std::string> filenames;
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@@ -57,21 +57,23 @@ Options:
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std::vector<std::string> requested_params_vec;
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CLI::App app{"Allowed options"};
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- app.add_option("--sig_figs,-s", sig_figs, "Significant figures, default 2.",
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@ -23,9 +23,22 @@ index eec4f5b2..a5e0b475 100644
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->check(CLI::NonexistentPath);
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- app.add_option("--percentiles,-p", percentiles_spec, "Percentiles to report.",
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- true);
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- app.add_option("input_files", filenames, "Sampler csv files.", true)
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+ app.add_option("--percentiles,-p", percentiles_spec, "Percentiles to report.")
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+ ->capture_default_str();
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app.add_option("--include_param,-i", requested_params_vec,
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"Include the named parameter in the output. By default all "
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- "are included.",
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- true)
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+ "are included.")
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+ ->capture_default_str()
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->transform([](auto str) {
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// allow both 'theta.1' and 'theta[1]' style.
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std::string token(str);
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@@ -79,7 +81,8 @@ Options:
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return token;
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})
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->take_all();
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- app.add_option("input_files", filenames, "Sampler csv files.", true)
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+ app.add_option("input_files", filenames, "Sampler csv files.")
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+ ->capture_default_str()
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->required()
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12
local
12
local
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@ -1,11 +1,11 @@
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MATH = /usr/include/stan/
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BOOST = /usr/include/boost
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#MATH = /usr/include/stan/
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BOOST = /usr/include
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EIGEN = /usr/include/eigen3
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OPENCL = /usr/include/CL
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TBB = /usr/include/
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SUNDIALS = /usr/include/sundials
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BENCHMARK = /usr/include/benchmark
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GTEST = /usr/include/gtest
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CPPLINT = /usr/lib/python3.11/site-packages/
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RAPIDJSON = /usr/include/rapidjson/
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CLI11 = /usr/include/
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SUNDIALS_TARGETS =
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TBB_INC = /usr/include
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TBB_LIB = /usr/lib
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CXXFLAGS+=-fPIC -DTBB_INTERFACE_NEW
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