search

pymc-devs / pymc2

THIS IS THE **OLD** PYMC PROJECT (VERSION 2). PLEASE USE PYMC INSTEAD:
http://pymc-devs.github.com/pymc/
Other
879 stars 229 forks source link

Can not build pymc on Mac OS Darwin #119

Closed khuevu closed 8 years ago

khuevu commented 8 years ago

Hi, I tried building pymc from source code. I have the following error when running: python setup.py config_fc --fcompiler gfortran build

error: Command "/usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O2 -march=x86-64 -DMS_WIN64 -mtune=generic -msse2 -DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-10.11-x86_64-2.7 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c -c pymc/flib.f -o build/temp.macosx-10.11-x86_64-2.7/pymc/flib.o" failed with exit status 1

I then tried executing the above command directly but the output does not give any error but warning. The output:

Using built-in specs. COLLECT_GCC=/usr/local/bin/gfortran Target: x86_64-apple-darwin15.0.0 Configured with: ../configure --build=x86_64-apple-darwin15.0.0 --prefix=/usr/local/Cellar/gcc/5.3.0 --libdir=/usr/local/Cellar/gcc/5.3.0/lib/gcc/5 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-5 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --with-build-config=bootstrap-debug --disable-werror --with-pkgversion='Homebrew gcc 5.3.0' --with-bugurl=https://github.com/Homebrew/homebrew/issues --enable-plugin --disable-nls --enable-multilib Thread model: posix gcc version 5.3.0 (Homebrew gcc 5.3.0) COLLECT_GCC_OPTIONS='-mmacosx-version-min=10.11.2' '-v' '-Wall' '-g' '-ffixed-form' '-fno-second-underscore' '-fPIC' '-O2' '-march=x86-64' '-D' 'MS_WIN64' '-mtune=generic' '-msse2' '-D' 'NO_ATLAS_INFO=3' '-D' 'HAVE_CBLAS' '-I' 'build/src.macosx-10.11-x86_64-2.7' '-I' '/usr/local/lib/python2.7/site-packages/numpy/core/include' '-I' '/usr/local/include' '-I' '/usr/local/opt/openssl/include' '-I' '/usr/local/opt/sqlite/include' '-I' '/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/include/python2.7' '-c' '-c' '-o' 'build/temp.macosx-10.11-x86_64-2.7/pymc/flib.o' /usr/local/Cellar/gcc/5.3.0/libexec/gcc/x86_64-apple-darwin15.0.0/5.3.0/f951 pymc/flib.f -ffixed-form -I build/src.macosx-10.11-x86_64-2.7 -I /usr/local/lib/python2.7/site-packages/numpy/core/include -I /usr/local/include -I /usr/local/opt/openssl/include -I /usr/local/opt/sqlite/include -I /usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/include/python2.7 -fPIC -feliminate-unused-debug-symbols -quiet -dumpbase flib.f -mmacosx-version-min=10.11.2 -march=x86-64 -mtune=generic -msse2 -auxbase-strip build/temp.macosx-10.11-x86_64-2.7/pymc/flib.o -g -O2 -Wall -version -ffixed-form -fno-second-underscore -fPIC -fintrinsic-modules-path /usr/local/Cellar/gcc/5.3.0/lib/gcc/5/gcc/x86_64-apple-darwin15.0.0/5.3.0/finclude -o /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s GNU Fortran (Homebrew gcc 5.3.0) version 5.3.0 (x86_64-apple-darwin15.0.0) compiled by GNU C version 5.3.0, GMP version 6.1.0, MPFR version 3.1.3-p2, MPC version 1.0.3 warning: MPFR header version 3.1.3-p2 differs from library version 3.1.4-p1. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU Fortran2008 (Homebrew gcc 5.3.0) version 5.3.0 (x86_64-apple-darwin15.0.0) compiled by GNU C version 5.3.0, GMP version 6.1.0, MPFR version 3.1.3-p2, MPC version 1.0.3 warning: MPFR header version 3.1.3-p2 differs from library version 3.1.4-p1. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 f951: Warning: Nonconforming tab character in column 1 of line 509 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 510 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 511 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 512 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 513 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 557 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 558 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 559 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 560 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 561 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 707 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 711 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 715 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 723 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 775 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 779 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 783 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 791 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 849 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 853 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 857 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 865 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 921 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 925 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 929 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 937 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 991 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 995 [-Wtabs] f951: Warning: Nonconforming tab character in column 6 of line 999 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1007 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1195 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1196 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1197 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1200 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1201 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1408 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1409 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1412 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1420 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1421 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1422 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1423 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1424 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1425 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1452 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1454 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1457 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1465 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1466 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1467 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1469 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1470 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1471 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1472 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1473 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1478 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1499 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1501 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1504 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1512 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1513 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1514 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1515 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1516 [-Wtabs] f951: Warning: Nonconforming tab character in column 5 of line 1517 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1740 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1743 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1746 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1755 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1783 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1786 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1789 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1798 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1800 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1832 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1835 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1838 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1847 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1849 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1977 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 1978 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2030 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2031 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2079 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2080 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2168 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2174 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2218 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2224 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2339 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2395 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2692 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2693 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2694 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2696 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2697 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2756 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2820 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 2881 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3191 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3192 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3656 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3657 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3658 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3660 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3661 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3662 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3664 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3665 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3666 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3716 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3717 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3718 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3720 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3721 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3722 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3724 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3725 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3726 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3732 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3846 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3847 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3849 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3851 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3875 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3876 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3877 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 3878 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4286 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4287 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4288 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4290 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4291 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4292 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4294 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4295 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4296 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4298 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4299 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4300 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4352 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4353 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4354 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4356 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4357 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4358 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4360 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4361 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4362 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4364 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4365 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4366 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4630 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4632 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4633 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4634 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4636 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4638 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4640 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4642 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4643 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4644 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4645 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4647 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4648 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4649 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4650 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4652 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4653 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4654 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4655 [-Wtabs] f951: Warning: Nonconforming tab character in column 1 of line 4656 [-Wtabs] pymc/flib.f:316:55:

   DOUBLE PRECISION mu_now, tau_now, alph_now, d_now, like
                                                   1

Warning: Unused variable 'd_now' declared at (1) [-Wunused-variable] pymc/flib.f:314:42:

   INTEGER i, nx, nalph, nmu, ntau, tnx
                                      1

Warning: Unused variable 'tnx' declared at (1) [-Wunused-variable] pymc/flib.f:442:71:

   subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
                                                                   1

Warning: Unused dummy argument 'gradxlike' at (1) [-Wunused-dummy-argument] pymc/flib.f:461:40:

     DOUBLE PRECISION like, low, high
                                    1

Warning: Unused variable 'high' declared at (1) [-Wunused-variable] pymc/flib.f:458:36:

     INTEGER n, nlower, nupper, i
                                1

Warning: Unused variable 'i' declared at (1) [-Wunused-variable] pymc/flib.f:461:29:

     DOUBLE PRECISION like, low, high
                         1

Warning: Unused variable 'like' declared at (1) [-Wunused-variable] pymc/flib.f:461:34:

     DOUBLE PRECISION like, low, high
                              1

Warning: Unused variable 'low' declared at (1) [-Wunused-variable] pymc/flib.f:442:39:

   subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
                                   1

Warning: Unused dummy argument 'lower' at (1) [-Wunused-dummy-argument] pymc/flib.f:442:45:

   subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
                                         1

Warning: Unused dummy argument 'upper' at (1) [-Wunused-dummy-argument] pymc/flib.f:442:33:

   subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
                             1

Warning: Unused dummy argument 'x' at (1) [-Wunused-dummy-argument] pymc/flib.f:692:41:

   DOUBLE PRECISION aa, cc, sigma, pdf
                                     1

Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable] pymc/flib.f:760:41:

   DOUBLE PRECISION aa, cc, sigma, pdf
                                     1

Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable] pymc/flib.f:834:41:

   DOUBLE PRECISION aa, cc, sigma, pdf
                                     1

Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable] pymc/flib.f:906:41:

   DOUBLE PRECISION aa, cc, sigma, pdf
                                     1

Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable] pymc/flib.f:976:41:

   DOUBLE PRECISION aa, cc, sigma, pdf
                                     1

Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable] pymc/flib.f:1186:29:

   DOUBLE PRECISION factln
                         1

Warning: Unused variable 'factln' declared at (1) [-Wunused-variable] pymc/flib.f:1185:51:

   DOUBLE PRECISION sumx, mut, infinity, sumfact
                                               1

Warning: Unused variable 'sumfact' declared at (1) [-Wunused-variable] pymc/flib.f:1185:27:

   DOUBLE PRECISION sumx, mut, infinity, sumfact
                       1

Warning: Unused variable 'sumx' declared at (1) [-Wunused-variable] pymc/flib.f:1300:55:

   DOUBLE PRECISION mu(nmu), gradlike(nmu),grad, cdf
                                                   1

Warning: Unused variable 'cdf' declared at (1) [-Wunused-variable] pymc/flib.f:1302:29:

   DOUBLE PRECISION factln, gammq
                         1

Warning: Unused variable 'factln' declared at (1) [-Wunused-variable] pymc/flib.f:1302:36:

   DOUBLE PRECISION factln, gammq
                                1

Warning: Unused variable 'gammq' declared at (1) [-Wunused-variable] pymc/flib.f:1301:59:

   DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
                                                       1

Warning: Unused variable 'sumcdf' declared at (1) [-Wunused-variable] pymc/flib.f:1301:51:

   DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
                                               1

Warning: Unused variable 'sumfact' declared at (1) [-Wunused-variable] pymc/flib.f:1301:27:

   DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
                       1

Warning: Unused variable 'sumx' declared at (1) [-Wunused-variable] pymc/flib.f:1402:29:

   DOUBLE PRECISION gammln
                         1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable] pymc/flib.f:2154:40:

   DOUBLE PRECISION gradlike(n), grad
                                    1

Warning: Unused variable 'grad' declared at (1) [-Wunused-variable] pymc/flib.f:2665:29:

   DOUBLE PRECISION gammln
                         1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable] pymc/flib.f:2728:29:

   DOUBLE PRECISION gammln, psi
                         1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable] pymc/flib.f:2793:29:

   DOUBLE PRECISION gammln
                         1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable] pymc/flib.f:2903:29:

   DOUBLE PRECISION gammln
                         1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable] pymc/flib.f:2959:29:

   DOUBLE PRECISION gammln, psi
                         1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable] pymc/flib.f:3021:29:

   DOUBLE PRECISION gammln
                         1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable] pymc/flib.f:3396:58:

   DOUBLE PRECISION gradlike(nx), atmp, btmp, PI, glike
                                                      1

Warning: Unused variable 'glike' declared at (1) [-Wunused-variable] pymc/flib.f:3646:37:

   DOUBLE PRECISION gammln, factln
                                 1

Warning: Unused variable 'factln' declared at (1) [-Wunused-variable] pymc/flib.f:3646:29:

   DOUBLE PRECISION gammln, factln
                         1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable] pymc/flib.f:3706:37:

   DOUBLE PRECISION gammln, factln, psi
                                 1

Warning: Unused variable 'factln' declared at (1) [-Wunused-variable] pymc/flib.f:3706:29:

   DOUBLE PRECISION gammln, factln, psi
                         1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable] pymc/flib.f:3836:29:

   DOUBLE PRECISION factln
                         1

Warning: Unused variable 'factln' declared at (1) [-Wunused-variable] pymc/flib.f:4039:26:

   DOUBLE PRECISION psi
                      1

Warning: Unused variable 'psi' declared at (1) [-Wunused-variable] pymc/flib.f:4276:29:

   DOUBLE PRECISION gammln, psi
                         1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable] pymc/flib.f:4342:29:

   DOUBLE PRECISION gammln, psi
                         1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable] pymc/flib.f:5194:35:

   DOUBLE PRECISION like, factln, infinity, sump
                               1

Warning: Unused variable 'factln' declared at (1) [-Wunused-variable] pymc/flib.f:5196:23:

   INTEGER i,j,n_tmp
                   1

Warning: Unused variable 'n_tmp' declared at (1) [-Wunused-variable] pymc/flib.f:5444:26:

   DOUBLE PRECISION tmp
                      1

Warning: Unused variable 'tmp' declared at (1) [-Wunused-variable] pymc/flib.f:5498:25:

   DOUBLE PRECISION i0
                     1

Warning: Unused variable 'i0' declared at (1) [-Wunused-variable] pymc/flib.f:5491:26:

   DOUBLE PRECISION tmp
                      1

Warning: Unused variable 'tmp' declared at (1) [-Wunused-variable] pymc/flib.f:5545:25:

   DOUBLE PRECISION i0
                     1

Warning: Unused variable 'i0' declared at (1) [-Wunused-variable] pymc/flib.f:5538:26:

   DOUBLE PRECISION tmp
                      1

Warning: Unused variable 'tmp' declared at (1) [-Wunused-variable] pymc/flib.f:4892:0:

         K   = I

^ Warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized] pymc/flib.f:778:0:

   do i = 1,nc

^ Warning: 'nc' may be used uninitialized in this function [-Wmaybe-uninitialized] pymc/flib.f:994:0:

   do i = 1,nc

^ Warning: 'nc' may be used uninitialized in this function [-Wmaybe-uninitialized] COLLECT_GCC_OPTIONS='-mmacosx-version-min=10.11.2' '-v' '-Wall' '-g' '-ffixed-form' '-fno-second-underscore' '-fPIC' '-O2' '-march=x86-64' '-D' 'MS_WIN64' '-mtune=generic' '-msse2' '-D' 'NO_ATLAS_INFO=3' '-D' 'HAVE_CBLAS' '-I' 'build/src.macosx-10.11-x86_64-2.7' '-I' '/usr/local/lib/python2.7/site-packages/numpy/core/include' '-I' '/usr/local/include' '-I' '/usr/local/opt/openssl/include' '-I' '/usr/local/opt/sqlite/include' '-I' '/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/include/python2.7' '-c' '-c' '-o' 'build/temp.macosx-10.11-x86_64-2.7/pymc/flib.o' as -arch x86_64 -force_cpusubtype_ALL -o build/temp.macosx-10.11-x86_64-2.7/pymc/flib.o /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:64:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:147:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:496:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:1488:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:2166:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:2169:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:2282:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:2397:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:2484:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:2931:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:3259:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:3408:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:3481:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:3552:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:3651:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:3722:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:6546:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:6597:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:6837:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:6922:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:7552:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:7632:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:9903:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:10008:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:10057:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:10109:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:10159:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:10239:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:10422:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:10482:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:10531:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:10636:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:12679:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:13110:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:13259:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:13487:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:13604:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:13906:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:14048:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:14469:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:14564:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:15190:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:15251:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:15300:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:15403:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:15469:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:16031:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:16184:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:17077:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:17400:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:17470:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:17513:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:20012:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:20015:expecting string instruction afterrep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:20362:expecting string instruction after rep' /var/folders/9s/s5hl5w4x7zjdjkdljw9cnsrm0000gn/T//ccAaMvv3.s:20716:expecting string instruction afterrep'

fonnesbeck commented 8 years ago

These sorts of errors typically arise when your gfortran compiler is not compatible with your gcc. Where did you get yours from?

mgorjis commented 8 years ago

I have similar issue. My fortran compiler is a part of gcc gcc-4.9.2_1. How can I change it?!

gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.3.0 (clang-703.0.31)
Target: x86_64-apple-darwin15.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
khuevu commented 8 years ago

I have clang gcc: Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn).

I saw the problem with my gfortran which was compiled by Homebrew gcc 5.30. I replaced it by using the binary version for El capitan from here: https://gcc.gnu.org/wiki/GFortranBinaries. So now I have gfortran compiled by gcc 6.1.0. Unfortunately the same error happens when building.

fonnesbeck commented 8 years ago

One thing you should try is rebuilding your Numpy with your current setup. There can sometimes be build incompatibilities.

maxpagels commented 8 years ago

I have the exact same issue. GCC version: Apple LLVM version 7.3.0 (clang-703.0.31). I installed gfortran using homebrew (brew install gcc).

fonnesbeck commented 8 years ago

Was numpy built using that compiler? Also, if you use the gfortran from brew, you should also use that gcc.

maxpagels commented 8 years ago

Numpy was installed using pip, not built from source. Numpy itself is working just fine.

The problem (at least for me) seems to be that that the following install procedure won't work even though it should (?):

  1. pip install numpy (works)
  2. brew install gcc (includes gfortran)
  3. pip install pymc (fails with the errors mentioned at the start of this thread).

Is there a specific version of Homebrew's gcc & gfortran that is known to work?

maxpagels commented 8 years ago

pip install pymc outputs the following (attached):

out.txt

fonnesbeck commented 8 years ago

pip should always be building from source unless a cached build is being installed.

fonnesbeck commented 8 years ago

You said above you were using Apple's clang compiler, not homebrew's gcc. You either need to use Apple's clang and a gfortran that is compatible with it, or use both the homebrew compilers. Make sure the compilers on your path are those you think you are using.

maxpagels commented 8 years ago

Yeah, I already installed numpy successfully without using the cache:

Lynx:~ maxpagels$ pip install --no-cache-dir numpy
Collecting numpy
  Downloading numpy-1.11.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.9MB)
    100% |████████████████████████████████| 3.9MB 5.2MB/s 
Installing collected packages: numpy
Successfully installed numpy-1.11.1
maxpagels commented 8 years ago

Thanks, I'll give that a try.

fonnesbeck commented 8 years ago

Ah, a wheel is being installed. Try the following:

pip install -U git+https://github.com/numpy/numpy.git
maxpagels commented 8 years ago

Fixed the problem by installing a version of gfortran compatible with my clang version (i.e. brew install homebrew/dupes/apple-gcc42).

fonnesbeck commented 8 years ago

That makes sense. I am going to close this for now; if the above does not fix the issue for others, please re-open.