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cleanup of gnu find - #844

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mitzimorris merged 5 commits into
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make_clean_gnu_find
Apr 1, 2020
Merged

cleanup of gnu find#844
mitzimorris merged 5 commits into
developfrom
make_clean_gnu_find

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@rok-cesnovar

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Submisison Checklist

  • Run tests: ./runCmdStanTests.py src/test
  • Declare copyright holder and open-source license: see below

Summary:

Continuing the work in stan-dev/math#1567 to close #786

The issue is that our makefiles rely on the gnu find command that is not available on Windows.

stan-dev/math#1567 introduced a findfiles function that is a recursive version of the makefiles wildcard function.

This PR uses that in stan-dev/cmdstan

Copyright and Licensing

Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company): Rok Češnovar

By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:

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Name Old Result New Result Ratio Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan 4.91 4.83 1.02 1.51% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.02 0.02 1.0 -0.5% slower
eight_schools/eight_schools.stan 0.09 0.09 1.02 2.27% faster
gp_regr/gp_regr.stan 0.22 0.22 0.97 -3.2% slower
irt_2pl/irt_2pl.stan 6.43 6.46 1.0 -0.36% slower
performance.compilation 87.49 86.4 1.01 1.25% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 7.58 7.63 0.99 -0.58% slower
pkpd/one_comp_mm_elim_abs.stan 20.77 20.18 1.03 2.82% faster
sir/sir.stan 94.51 95.24 0.99 -0.78% slower
gp_regr/gen_gp_data.stan 0.05 0.05 0.99 -0.78% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.94 2.94 1.0 0.13% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.31 0.31 0.98 -2.46% slower
arK/arK.stan 1.73 1.74 1.0 -0.19% slower
arma/arma.stan 0.68 0.65 1.05 4.69% faster
garch/garch.stan 0.52 0.52 1.0 0.41% faster
Mean result: 1.00320798218

Jenkins Console Log
Blue Ocean
Commit hash: d55d874


Machine information ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Comment thread makefile
@mitzimorris

mitzimorris commented Mar 16, 2020

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output running make build on develop, followed by make clean-all

--- CmdStan v2.22.1 built ---
~/github/stan-dev/cmdstan (develop)> make clean-all
rm -f -r doc
cd src/docs/cmdstan-guide; rm -f *.brf *.aux *.bbl *.blg *.log *.toc *.pdf *.out *.idx *.ilg *.ind *.cb *.cb2 *.upa
  removing dependency files
  cleaning sundials targets
rm -f stan/lib/stan_math/lib/sundials_5.1.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_5.1.0/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_5.1.0/lib/libsundials_kinsol.a stan/lib/stan_math/lib/sundials_5.1.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodea.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodea_io.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_bandpre.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_bbdpre.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_diag.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_direct.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_io.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_ls.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_nls.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_nls_sim.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_nls_stg.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_nls_stg1.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_spils.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idaa.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idaa_io.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_bbdpre.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_direct.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_ic.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_io.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_ls.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_nls.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_nls_sim.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_nls_stg.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_spils.o stan/lib/stan_math/lib/sundials_5.1.0/src/kinsol/kinsol.o stan/lib/stan_math/lib/sundials_5.1.0/src/kinsol/kinsol_bbdpre.o stan/lib/stan_math/lib/sundials_5.1.0/src/kinsol/kinsol_direct.o stan/lib/stan_math/lib/sundials_5.1.0/src/kinsol/kinsol_io.o stan/lib/stan_math/lib/sundials_5.1.0/src/kinsol/kinsol_ls.o stan/lib/stan_math/lib/sundials_5.1.0/src/kinsol/kinsol_spils.o stan/lib/stan_math/lib/sundials_5.1.0/src/nvector/serial/nvector_serial.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.1.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.1.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.1.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.1.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.1.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o stan/lib/stan_math/lib/sundials_5.1.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o
  cleaning Intel TBB targets
rm -f -rf stan/lib/stan_math/lib/tbb
rm -f -r test
rm -f 
rm -f 
rm -f 
rm -f 
rm -f bin/stanc bin/stanc2 bin/stansummary bin/print bin/diagnose
rm -f -r src/cmdstan/main.o bin/cmdstan
rm -f stan/src/stan/model/model_header.hpp.gch
rm -f examples/bernoulli/bernoulli examples/bernoulli/bernoulli.o examples/bernoulli/bernoulli.d examples/bernoulli/bernoulli.hpp
~/github/stan-dev/cmdstan (develop)> 

on branch make_clean_gnu_find get too many blank lines so you lose track of work done:

--- CmdStan v2.22.1 built ---
~/github/stan-dev/cmdstan (make_clean_gnu_find)> make clean-all
rm -f -r doc
cd src/docs/cmdstan-guide; rm -f *.brf *.aux *.bbl *.blg *.log *.toc *.pdf *.out *.idx *.ilg *.ind *.cb *.cb2 *.upa
  removing dependency files
rm -f                                                                                                                                                                                                                src/cmdstan/stanc.d                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
  cleaning sundials targets
rm -f stan/lib/stan_math/lib/sundials_5.1.0/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_5.1.0/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_5.1.0/lib/libsundials_kinsol.a stan/lib/stan_math/lib/sundials_5.1.0/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodea.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodea_io.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_bandpre.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_bbdpre.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_diag.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_direct.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_io.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_ls.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_nls.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_nls_sim.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_nls_stg.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_nls_stg1.o stan/lib/stan_math/lib/sundials_5.1.0/src/cvodes/cvodes_spils.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idaa.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idaa_io.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_bbdpre.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_direct.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_ic.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_io.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_ls.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_nls.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_nls_sim.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_nls_stg.o stan/lib/stan_math/lib/sundials_5.1.0/src/idas/idas_spils.o stan/lib/stan_math/lib/sundials_5.1.0/src/kinsol/kinsol.o stan/lib/stan_math/lib/sundials_5.1.0/src/kinsol/kinsol_bbdpre.o stan/lib/stan_math/lib/sundials_5.1.0/src/kinsol/kinsol_direct.o stan/lib/stan_math/lib/sundials_5.1.0/src/kinsol/kinsol_io.o stan/lib/stan_math/lib/sundials_5.1.0/src/kinsol/kinsol_ls.o stan/lib/stan_math/lib/sundials_5.1.0/src/kinsol/kinsol_spils.o stan/lib/stan_math/lib/sundials_5.1.0/src/nvector/serial/nvector_serial.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_band.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_dense.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_direct.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_futils.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_iterative.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_linearsolver.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_math.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_matrix.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_nonlinearsolver.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_nvector.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_nvector_senswrapper.o stan/lib/stan_math/lib/sundials_5.1.0/src/sundials/sundials_version.o stan/lib/stan_math/lib/sundials_5.1.0/src/sunlinsol/band/sunlinsol_band.o stan/lib/stan_math/lib/sundials_5.1.0/src/sunlinsol/dense/sunlinsol_dense.o stan/lib/stan_math/lib/sundials_5.1.0/src/sunmatrix/band/sunmatrix_band.o stan/lib/stan_math/lib/sundials_5.1.0/src/sunmatrix/dense/sunmatrix_dense.o stan/lib/stan_math/lib/sundials_5.1.0/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o stan/lib/stan_math/lib/sundials_5.1.0/src/sunnonlinsol/newton/sunnonlinsol_newton.o
rm -f













                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
rm -f    















                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
  cleaning Intel TBB targets
rm -f -rf stan/lib/stan_math/lib/tbb
rm -f -r test
rm -f 
rm -f 
rm -f 
rm -f 
rm -f bin/stanc bin/stanc2 bin/stansummary bin/print bin/diagnose
rm -f -r src/cmdstan/main.o bin/cmdstan
rm -f stan/src/stan/model/model_header.hpp.gch
rm -f examples/bernoulli/bernoulli examples/bernoulli/bernoulli.o examples/bernoulli/bernoulli.d examples/bernoulli/bernoulli.hpp
~/github/stan-dev/cmdstan (make_clean_gnu_find)> 

@mitzimorris

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note number of blank lines in above output is approx - the selection from the terminal lost all blank lines so I had to edit them back in.

@rok-cesnovar

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Should be fixed by stan-dev/math#1784

@rok-cesnovar
rok-cesnovar requested review from mitzimorris and removed request for mitzimorris March 23, 2020 20:13
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Name Old Result New Result Ratio Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan 4.92 4.88 1.01 0.7% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.02 0.02 0.98 -1.74% slower
eight_schools/eight_schools.stan 0.09 0.09 1.03 3.38% faster
gp_regr/gp_regr.stan 0.22 0.21 1.03 2.53% faster
irt_2pl/irt_2pl.stan 6.5 6.44 1.01 0.85% faster
performance.compilation 87.57 86.66 1.01 1.04% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 7.62 7.55 1.01 0.93% faster
pkpd/one_comp_mm_elim_abs.stan 20.75 20.81 1.0 -0.28% slower
sir/sir.stan 93.25 93.6 1.0 -0.37% slower
gp_regr/gen_gp_data.stan 0.05 0.05 1.01 0.65% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.95 2.96 1.0 -0.38% slower
pkpd/sim_one_comp_mm_elim_abs.stan 0.31 0.32 0.98 -2.36% slower
arK/arK.stan 1.74 1.73 1.0 0.32% faster
arma/arma.stan 0.66 0.66 1.01 0.68% faster
garch/garch.stan 0.52 0.52 1.0 -0.08% slower
Mean result: 1.00412053668

Jenkins Console Log
Blue Ocean
Commit hash: 2be05f8


Machine information ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

@stan-buildbot

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Name Old Result New Result Ratio Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan 4.94 4.81 1.03 2.6% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.02 0.02 0.98 -1.77% slower
eight_schools/eight_schools.stan 0.09 0.09 0.97 -2.96% slower
gp_regr/gp_regr.stan 0.22 0.22 0.97 -3.07% slower
irt_2pl/irt_2pl.stan 6.44 6.46 1.0 -0.41% slower
performance.compilation 87.98 86.68 1.01 1.48% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 7.58 7.61 1.0 -0.37% slower
pkpd/one_comp_mm_elim_abs.stan 21.04 21.1 1.0 -0.32% slower
sir/sir.stan 95.03 93.66 1.01 1.43% faster
gp_regr/gen_gp_data.stan 0.05 0.05 1.01 1.03% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.96 2.95 1.0 0.17% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.32 0.32 1.0 0.18% faster
arK/arK.stan 1.74 1.74 1.0 -0.3% slower
arma/arma.stan 0.66 0.67 0.99 -1.42% slower
garch/garch.stan 0.51 0.51 1.01 0.51% faster
Mean result: 0.99808180656

Jenkins Console Log
Blue Ocean
Commit hash: bd45115


Machine information ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

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Name Old Result New Result Ratio Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan 4.84 4.88 0.99 -0.97% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.02 0.02 0.98 -2.52% slower
eight_schools/eight_schools.stan 0.1 0.09 1.06 5.57% faster
gp_regr/gp_regr.stan 0.22 0.22 1.02 2.39% faster
irt_2pl/irt_2pl.stan 6.47 6.46 1.0 0.11% faster
performance.compilation 88.45 87.08 1.02 1.56% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 7.57 7.56 1.0 0.15% faster
pkpd/one_comp_mm_elim_abs.stan 21.84 20.92 1.04 4.2% faster
sir/sir.stan 90.65 90.92 1.0 -0.3% slower
gp_regr/gen_gp_data.stan 0.05 0.05 0.98 -1.97% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.94 2.95 1.0 -0.17% slower
pkpd/sim_one_comp_mm_elim_abs.stan 0.31 0.31 1.0 -0.18% slower
arK/arK.stan 1.73 1.75 0.99 -1.46% slower
arma/arma.stan 0.65 0.67 0.98 -2.26% slower
garch/garch.stan 0.51 0.51 1.0 -0.09% slower
Mean result: 1.00321927017

Jenkins Console Log
Blue Ocean
Commit hash: cae09bb


Machine information ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

@mitzimorris mitzimorris left a comment

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lgtm - thanks!

@mitzimorris
mitzimorris merged commit b3ff19b into develop Apr 1, 2020
@mitzimorris

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@rok-cesnovar - in the future, please follow the branch naming conventions described here: https://github.com/stan-dev/stan/wiki/Developer-process-overview#2-create-a-branch-for-the-issue

thanks!

@rok-cesnovar
rok-cesnovar deleted the make_clean_gnu_find branch April 1, 2020 16:55
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Deal! I keep forgetting.

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Cleanup build warnings on Windows

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