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dms-tools2 2.6.6 Uninstalling dms-tools2-2.6.6: Successfully uninstalled dms-tools2-2.6.6 Running setup.py develop for dms-tools2 Successfully installed dms-tools2 ============================= test session starts ============================== platform linux -- Python 3.7.7, pytest-5.4.3, py-1.8.2, pluggy-0.13.1 rootdir: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2, inifile: pytest.ini collected 116 items dms_tools2/barcodes.py ... [ 2%] dms_tools2/compareprefs.py .... [ 6%] dms_tools2/diffsel.py ..... [ 10%] dms_tools2/fracsurvive.py ... [ 12%] dms_tools2/minimap2.py ................. [ 27%] dms_tools2/pacbio.py ..... [ 31%] dms_tools2/parseargs.py . [ 32%] dms_tools2/plot.py ..... [ 37%] dms_tools2/prefs.py ...... [ 42%] dms_tools2/protstruct.py ... [ 44%] dms_tools2/seqnumbering.py . [ 45%] dms_tools2/syn_selection.py . [ 46%] dms_tools2/utils.py .............. [ 58%] tests/test_barcodeInfoToCodonVariantTable.py . [ 59%] tests/test_batch_bcsubamp.py .. [ 61%] tests/test_batch_diffsel.py . [ 62%] tests/test_batch_fracsurvive.py . [ 62%] tests/test_batch_prefs.py F. [ 64%] tests/test_bcsubamp.py ........ [ 71%] tests/test_build_barcode_variant_table.py . [ 72%] tests/test_convertCountsFormat.py . [ 73%] tests/test_diffsel.py ... [ 75%] tests/test_dssp.py . [ 76%] tests/test_fracsurvive.py . [ 77%] tests/test_inferprefsbyratio.py .... [ 81%] tests/test_logoplot_diffsel.py . [ 81%] tests/test_logoplot_fracsurvive.py .. [ 83%] tests/test_logoplot_muteffects.py . [ 84%] tests/test_logoplot_prefs.py . [ 85%] tests/test_minimap2_multi_alignments.py .. [ 87%] tests/test_pacbio.py . [ 87%] tests/test_pacbio_ccs.py ..... [ 92%] tests/test_pacbio_ccs_align.py .... [ 95%] tests/test_pystan_compile.py FFF [ 98%] tests/test_renumbersites.py . [ 99%] tests/test_site_inferprefs.py F [100%] =================================== FAILURES =================================== ____________________ test_batch_prefs.test_dms2_batch_prefs ____________________ self = def test_dms2_batch_prefs(self): """Runs ``dms2_batch_prefs`` on test data.""" batchfile = os.path.join(self.testdir, 'batch.csv') replicates = [1, 2] df = pandas.DataFrame({ 'name':['{0}-replicate-{1}'.format(self.METHOD, r) for r in replicates], 'pre':['mutDNA-{0}_codoncounts.csv'.format(r) for r in replicates], 'post':['mutvirus-{0}_codoncounts.csv'.format(r) for r in replicates], }) df.to_csv(batchfile, index=False) cmds = [ 'dms2_batch_prefs', '--batchfile', batchfile, '--summaryprefix', self.summaryprefix, '--outdir', self.testdir, '--indir', self.indir, '--method', self.METHOD, '--ncpus', '1', ] sys.stderr.write('\nRunning the following command:\n{0}\n'.format( ' '.join(cmds))) subprocess.check_call(cmds) for f in self.outfiles: > self.assertTrue(os.path.isfile(f), "Failed to create {0}".format(f)) E AssertionError: False is not true : Failed to create /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/tests/./test_batch_prefs_files/summary-bayesian_prefscorr.pdf tests/test_batch_prefs.py:75: AssertionError ----------------------------- Captured stderr call ----------------------------- Running the following command: dms2_batch_prefs --batchfile /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/tests/./test_batch_prefs_files/batch.csv --summaryprefix summary-bayesian --outdir /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/tests/./test_batch_prefs_files/ --indir /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/tests/./prefs_input_files/ --method bayesian --ncpus 1 INFO:dms2_batch_prefs:Beginning execution of dms2_batch_prefs in directory /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2 INFO:dms2_batch_prefs:Progress is being logged to /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/tests/./test_batch_prefs_files/summary-bayesian.log INFO:dms2_batch_prefs:Version information: Time and date: Fri Jun 19 04:06:20 2020 Platform: Linux-3.10.0-862.el7.x86_64-x86_64-with-redhat-7.5-Maipo Python version: 3.7.7 (default, May 7 2020, 21:25:33) [GCC 7.3.0] dms_tools2 version: 2.6.6 Bio version: 1.77 pandas version: 0.25.3 numpy version: 1.18.5 IPython version: 7.15.0 jupyter version: 1.0.0 matplotlib version: 3.2.2 plotnine version: 0.6.0 natsort version: 7.0.1 pystan version: 2.19.1.1 scipy version: 1.4.1 seaborn version: 0.10.1 phydmslib version: 2.3.8 statsmodels version: 0.11.1 rpy2 version: 3.3.3 regex version: 2.5.82 umi_tools version: 1.0.1 INFO:dms2_batch_prefs:Parsed the following arguments: outdir = /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/tests/./test_batch_prefs_files/ ncpus = 1 use_existing = no method = bayesian indir = /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/tests/./prefs_input_files/ chartype = codon_to_aa excludestop = yes conc = [1, 1, 1] pseudocount = 1 batchfile = /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/tests/./test_batch_prefs_files/batch.csv summaryprefix = summary-bayesian no_corr = False no_avg = False INFO:dms2_batch_prefs:Parsing info from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/tests/./test_batch_prefs_files/batch.csv INFO:dms2_batch_prefs:Read the following sample information: name,pre,post bayesian-replicate-1,mutDNA-1_codoncounts.csv,mutvirus-1_codoncounts.csv bayesian-replicate-2,mutDNA-2_codoncounts.csv,mutvirus-2_codoncounts.csv INFO:dms2_batch_prefs:Running dms2_prefs on all samples... INFO:dms2_batch_prefs:Completed runs of dms2_prefs. ERROR:dms2_batch_prefs:Terminating dms2_batch_prefs with ERROR Traceback (most recent call last): File "/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/scripts/dms2_batch_prefs", line 140, in main "{1}:\n{2}".format(f, flog, ''.join(lines[-25 : ]))) RuntimeError: Failed to create /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/tests/./test_batch_prefs_files//bayesian-replicate-1_prefs.csv. Here is end of /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/tests/./test_batch_prefs_files//bayesian-replicate-1.log: % (cmd, exit_status)) distutils.errors.DistutilsExecError: command 'gcc' failed with exit status 1 During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/scripts/dms2_prefs", line 204, in main }[error_model])() File "/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/dms_tools2/prefs.py", line 70, in __init__ verbose=verbose) File "/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/model.py", line 378, in __init__ build_extension.run() File "/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/distutils/command/build_ext.py", line 340, in run self.build_extensions() File "/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/distutils/command/build_ext.py", line 449, in build_extensions self._build_extensions_serial() File "/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/distutils/command/build_ext.py", line 474, in _build_extensions_serial self.build_extension(ext) File "/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/distutils/command/build_ext.py", line 534, in build_extension depends=ext.depends) File "/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/distutils/ccompiler.py", line 574, in compile self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts) File "/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/distutils/unixccompiler.py", line 120, in _compile raise CompileError(msg) distutils.errors.CompileError: command 'gcc' failed with exit status 1 __________________ test_pyStanModels.test_pystan_compilation ___________________ self = obj = '/tmp/pystan_jnhv6mdr/tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.o' src = '/tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.cpp' ext = '.cpp' cc_args = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_jnhv6mdr', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] extra_postargs = ['-O2', '-ftemplate-depth-256', '-Wno-unused-function', '-Wno-uninitialized', '-std=c++1y'] pp_opts = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_jnhv6mdr', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts): compiler_so = self.compiler_so if sys.platform == 'darwin': compiler_so = _osx_support.compiler_fixup(compiler_so, cc_args + extra_postargs) try: self.spawn(compiler_so + cc_args + [src, '-o', obj] + > extra_postargs) ../lib/python3.7/distutils/unixccompiler.py:118: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = cmd = ['gcc', '-pthread', '-B', '/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/compiler_compat', '-Wl,--sysroot=/', '-Wsign-compare', ...] def spawn(self, cmd): > spawn(cmd, dry_run=self.dry_run) ../lib/python3.7/distutils/ccompiler.py:910: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cmd = ['gcc', '-pthread', '-B', '/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/compiler_compat', '-Wl,--sysroot=/', '-Wsign-compare', ...] search_path = 1, verbose = 0, dry_run = 0 def spawn(cmd, search_path=1, verbose=0, dry_run=0): """Run another program, specified as a command list 'cmd', in a new process. 'cmd' is just the argument list for the new process, ie. cmd[0] is the program to run and cmd[1:] are the rest of its arguments. There is no way to run a program with a name different from that of its executable. If 'search_path' is true (the default), the system's executable search path will be used to find the program; otherwise, cmd[0] must be the exact path to the executable. If 'dry_run' is true, the command will not actually be run. Raise DistutilsExecError if running the program fails in any way; just return on success. """ # cmd is documented as a list, but just in case some code passes a tuple # in, protect our %-formatting code against horrible death cmd = list(cmd) if os.name == 'posix': > _spawn_posix(cmd, search_path, dry_run=dry_run) ../lib/python3.7/distutils/spawn.py:36: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cmd = 'gcc', search_path = 1, verbose = 0, dry_run = 0 def _spawn_posix(cmd, search_path=1, verbose=0, dry_run=0): log.info(' '.join(cmd)) if dry_run: return executable = cmd[0] exec_fn = search_path and os.execvp or os.execv env = None if sys.platform == 'darwin': global _cfg_target, _cfg_target_split if _cfg_target is None: _cfg_target = sysconfig.get_config_var( 'MACOSX_DEPLOYMENT_TARGET') or '' if _cfg_target: _cfg_target_split = [int(x) for x in _cfg_target.split('.')] if _cfg_target: # ensure that the deployment target of build process is not less # than that used when the interpreter was built. This ensures # extension modules are built with correct compatibility values cur_target = os.environ.get('MACOSX_DEPLOYMENT_TARGET', _cfg_target) if _cfg_target_split > [int(x) for x in cur_target.split('.')]: my_msg = ('$MACOSX_DEPLOYMENT_TARGET mismatch: ' 'now "%s" but "%s" during configure' % (cur_target, _cfg_target)) raise DistutilsPlatformError(my_msg) env = dict(os.environ, MACOSX_DEPLOYMENT_TARGET=cur_target) exec_fn = search_path and os.execvpe or os.execve pid = os.fork() if pid == 0: # in the child try: if env is None: exec_fn(executable, cmd) else: exec_fn(executable, cmd, env) except OSError as e: if not DEBUG: cmd = executable sys.stderr.write("unable to execute %r: %s\n" % (cmd, e.strerror)) os._exit(1) if not DEBUG: cmd = executable sys.stderr.write("unable to execute %r for unknown reasons" % cmd) os._exit(1) else: # in the parent # Loop until the child either exits or is terminated by a signal # (ie. keep waiting if it's merely stopped) while True: try: pid, status = os.waitpid(pid, 0) except OSError as exc: if not DEBUG: cmd = executable raise DistutilsExecError( "command %r failed: %s" % (cmd, exc.args[-1])) if os.WIFSIGNALED(status): if not DEBUG: cmd = executable raise DistutilsExecError( "command %r terminated by signal %d" % (cmd, os.WTERMSIG(status))) elif os.WIFEXITED(status): exit_status = os.WEXITSTATUS(status) if exit_status == 0: return # hey, it succeeded! else: if not DEBUG: cmd = executable raise DistutilsExecError( "command %r failed with exit status %d" > % (cmd, exit_status)) E distutils.errors.DistutilsExecError: command 'gcc' failed with exit status 1 ../lib/python3.7/distutils/spawn.py:159: DistutilsExecError During handling of the above exception, another exception occurred: self = def test_pystan_compilation(self): """Tests compilation of models.""" > m = self.MODEL(verbose=True) tests/test_pystan_compile.py:15: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ dms_tools2/prefs.py:70: in __init__ verbose=verbose) ../lib/python3.7/site-packages/pystan/model.py:378: in __init__ build_extension.run() ../lib/python3.7/distutils/command/build_ext.py:340: in run self.build_extensions() ../lib/python3.7/distutils/command/build_ext.py:449: in build_extensions self._build_extensions_serial() ../lib/python3.7/distutils/command/build_ext.py:474: in _build_extensions_serial self.build_extension(ext) ../lib/python3.7/distutils/command/build_ext.py:534: in build_extension depends=ext.depends) ../lib/python3.7/distutils/ccompiler.py:574: in compile self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = obj = '/tmp/pystan_jnhv6mdr/tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.o' src = '/tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.cpp' ext = '.cpp' cc_args = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_jnhv6mdr', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] extra_postargs = ['-O2', '-ftemplate-depth-256', '-Wno-unused-function', '-Wno-uninitialized', '-std=c++1y'] pp_opts = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_jnhv6mdr', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts): compiler_so = self.compiler_so if sys.platform == 'darwin': compiler_so = _osx_support.compiler_fixup(compiler_so, cc_args + extra_postargs) try: self.spawn(compiler_so + cc_args + [src, '-o', obj] + extra_postargs) except DistutilsExecError as msg: > raise CompileError(msg) E distutils.errors.CompileError: command 'gcc' failed with exit status 1 ../lib/python3.7/distutils/unixccompiler.py:120: CompileError ----------------------------- Captured stdout call ----------------------------- Compiling /tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.pyx because it changed. [1/1] Cythonizing /tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.pyx building 'stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796' extension creating /tmp/pystan_jnhv6mdr/tmp creating /tmp/pystan_jnhv6mdr/tmp/pystan_jnhv6mdr gcc -pthread -B /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/tmp/pystan_jnhv6mdr -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/eigen_3.3.3 -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0 -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/sundials_4.1.0/include -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/include/python3.7m -c /tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.cpp -o /tmp/pystan_jnhv6mdr/tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.o -O2 -ftemplate-depth-256 -Wno-unused-function -Wno-uninitialized -std=c++1y ----------------------------- Captured stderr call ----------------------------- INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_d3c958b02d8eff9dc447fb55c590fe08 NOW. INFO:pystan:OS: linux, Python: 3.7.7 (default, May 7 2020, 21:25:33) [GCC 7.3.0], Cython 0.29.20 cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.cpp:692: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^ In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat.hpp:336, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/io/dump.hpp:6, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/py_var_context.hpp:12, from /tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.cpp:695: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp: In function ‘typename stan::return_type::type stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:64:59: warning: typedef ‘T_alpha_val’ locally defined but not used [-Wunused-local-typedefs] typename partials_return_type::type>::type T_alpha_val; ^ In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat.hpp:41, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/log_prob_grad.hpp:4, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/test_gradients.hpp:7, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/services/diagnose/diagnose.hpp:10, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan_fit.hpp:23, from /tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.cpp:696: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:32: error: ‘std::index_sequence’ has not been declared std::index_sequence i) { ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:46: error: expected ‘,’ or ‘...’ before ‘<’ token std::index_sequence i) { ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In function ‘constexpr auto stan::math::internal::apply(const F&, const Tuple&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: error: ‘make_index_sequence’ is not a member of ‘std’ return apply_impl(f, t, std::make_index_sequence{}>{}); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: note: suggested alternative: In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/container/vector/vector.hpp:28:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/container/vector/vector10.hpp:25, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/transform_view/transform_view.hpp:22, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/algorithm/transformation/transform.hpp:11, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view/detail/begin_impl.hpp:14, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view/zip_view.hpp:16, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view.hpp:12, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/include/zip_view.hpp:11, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/resize.hpp:26, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/state_wrapper.hpp:26, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint.hpp:25, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/arr.hpp:46, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat.hpp:344, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/io/dump.hpp:6, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/py_var_context.hpp:12, from /tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.cpp:695: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/support/detail/index_sequence.hpp:59:12: note: ‘boost::fusion::detail::make_index_sequence’ struct make_index_sequence ^ In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat.hpp:41, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/log_prob_grad.hpp:4, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/test_gradients.hpp:7, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/services/diagnose/diagnose.hpp:10, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan_fit.hpp:23, from /tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.cpp:696: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected primary-expression before ‘{’ token return apply_impl(f, t, std::make_index_sequence{}>{}); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected ‘)’ before ‘{’ token /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:151:9: error: expected type-specifier = std::result_of_t; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:42: error: ‘FReturnType’ was not declared in this scope std::array::value> M_; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:53: error: template argument 1 is invalid std::array::value> M_; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:61: error: template argument 2 is invalid std::array::value> M_; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘std::vector stan::math::adj_jac_vari::build_return_varis_and_vars(const std::vector&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:349:9: error: invalid types ‘int[int]’ for array subscript M_[0] = val_y.size(); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:350:32: error: invalid types ‘int[int]’ for array subscript std::vector var_y(M_[0]); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘Eigen::Matrix stan::math::adj_jac_vari::build_return_varis_and_vars(const Eigen::Matrix&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:375:9: error: invalid types ‘int[int]’ for array subscript M_[0] = val_y.rows(); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:376:9: error: invalid types ‘int[int]’ for array subscript M_[1] = val_y.cols(); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:40: error: invalid types ‘int[int]’ for array subscript Eigen::Matrix var_y(M_[0], M_[1]); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:47: error: invalid types ‘int[int]’ for array subscript Eigen::Matrix var_y(M_[0], M_[1]); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘void stan::math::adj_jac_vari::chain()’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:5: error: ‘FReturnType’ was not declared in this scope FReturnType y_adj; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:17: error: expected ‘;’ before ‘y_adj’ FReturnType y_adj; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:532:38: error: ‘y_adj’ was not declared in this scope internal::build_y_adj(y_vi_, M_, y_adj); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:26: error: expansion pattern ‘auto&&’ contains no argument packs [this](auto&&... args) { this->accumulate_adjoints(args...); }, ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In lambda function: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:60: error: ‘args’ was not declared in this scope [this](auto&&... args) { this->accumulate_adjoints(args...); }, ^ /tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.cpp: In function ‘PyObject* __pyx_pf_71stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796_2_call_sampler(PyObject*, PyObject*, PyObject*, PyObject*)’: /tmp/pystan_jnhv6mdr/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_7101381945400481796.cpp:9475:71: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] __pyx_t_12 = ((__pyx_t_9 != __pyx_v_fitptr->param_names_oi().size()) != 0); ^ ------------------------------ Captured log call ------------------------------- INFO pystan:model.py:259 COMPILING THE C++ CODE FOR MODEL anon_model_d3c958b02d8eff9dc447fb55c590fe08 NOW. INFO pystan:model.py:264 OS: linux, Python: 3.7.7 (default, May 7 2020, 21:25:33) [GCC 7.3.0], Cython 0.29.20 ________________ test_pyStanModels_Same.test_pystan_compilation ________________ self = obj = '/tmp/pystan_s2e1trz4/tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.o' src = '/tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.cpp' ext = '.cpp' cc_args = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_s2e1trz4', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] extra_postargs = ['-O2', '-ftemplate-depth-256', '-Wno-unused-function', '-Wno-uninitialized', '-std=c++1y'] pp_opts = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_s2e1trz4', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts): compiler_so = self.compiler_so if sys.platform == 'darwin': compiler_so = _osx_support.compiler_fixup(compiler_so, cc_args + extra_postargs) try: self.spawn(compiler_so + cc_args + [src, '-o', obj] + > extra_postargs) ../lib/python3.7/distutils/unixccompiler.py:118: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = cmd = ['gcc', '-pthread', '-B', '/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/compiler_compat', '-Wl,--sysroot=/', '-Wsign-compare', ...] def spawn(self, cmd): > spawn(cmd, dry_run=self.dry_run) ../lib/python3.7/distutils/ccompiler.py:910: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cmd = ['gcc', '-pthread', '-B', '/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/compiler_compat', '-Wl,--sysroot=/', '-Wsign-compare', ...] search_path = 1, verbose = 0, dry_run = 0 def spawn(cmd, search_path=1, verbose=0, dry_run=0): """Run another program, specified as a command list 'cmd', in a new process. 'cmd' is just the argument list for the new process, ie. cmd[0] is the program to run and cmd[1:] are the rest of its arguments. There is no way to run a program with a name different from that of its executable. If 'search_path' is true (the default), the system's executable search path will be used to find the program; otherwise, cmd[0] must be the exact path to the executable. If 'dry_run' is true, the command will not actually be run. Raise DistutilsExecError if running the program fails in any way; just return on success. """ # cmd is documented as a list, but just in case some code passes a tuple # in, protect our %-formatting code against horrible death cmd = list(cmd) if os.name == 'posix': > _spawn_posix(cmd, search_path, dry_run=dry_run) ../lib/python3.7/distutils/spawn.py:36: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cmd = 'gcc', search_path = 1, verbose = 0, dry_run = 0 def _spawn_posix(cmd, search_path=1, verbose=0, dry_run=0): log.info(' '.join(cmd)) if dry_run: return executable = cmd[0] exec_fn = search_path and os.execvp or os.execv env = None if sys.platform == 'darwin': global _cfg_target, _cfg_target_split if _cfg_target is None: _cfg_target = sysconfig.get_config_var( 'MACOSX_DEPLOYMENT_TARGET') or '' if _cfg_target: _cfg_target_split = [int(x) for x in _cfg_target.split('.')] if _cfg_target: # ensure that the deployment target of build process is not less # than that used when the interpreter was built. This ensures # extension modules are built with correct compatibility values cur_target = os.environ.get('MACOSX_DEPLOYMENT_TARGET', _cfg_target) if _cfg_target_split > [int(x) for x in cur_target.split('.')]: my_msg = ('$MACOSX_DEPLOYMENT_TARGET mismatch: ' 'now "%s" but "%s" during configure' % (cur_target, _cfg_target)) raise DistutilsPlatformError(my_msg) env = dict(os.environ, MACOSX_DEPLOYMENT_TARGET=cur_target) exec_fn = search_path and os.execvpe or os.execve pid = os.fork() if pid == 0: # in the child try: if env is None: exec_fn(executable, cmd) else: exec_fn(executable, cmd, env) except OSError as e: if not DEBUG: cmd = executable sys.stderr.write("unable to execute %r: %s\n" % (cmd, e.strerror)) os._exit(1) if not DEBUG: cmd = executable sys.stderr.write("unable to execute %r for unknown reasons" % cmd) os._exit(1) else: # in the parent # Loop until the child either exits or is terminated by a signal # (ie. keep waiting if it's merely stopped) while True: try: pid, status = os.waitpid(pid, 0) except OSError as exc: if not DEBUG: cmd = executable raise DistutilsExecError( "command %r failed: %s" % (cmd, exc.args[-1])) if os.WIFSIGNALED(status): if not DEBUG: cmd = executable raise DistutilsExecError( "command %r terminated by signal %d" % (cmd, os.WTERMSIG(status))) elif os.WIFEXITED(status): exit_status = os.WEXITSTATUS(status) if exit_status == 0: return # hey, it succeeded! else: if not DEBUG: cmd = executable raise DistutilsExecError( "command %r failed with exit status %d" > % (cmd, exit_status)) E distutils.errors.DistutilsExecError: command 'gcc' failed with exit status 1 ../lib/python3.7/distutils/spawn.py:159: DistutilsExecError During handling of the above exception, another exception occurred: self = def test_pystan_compilation(self): """Tests compilation of models.""" > m = self.MODEL(verbose=True) tests/test_pystan_compile.py:26: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ dms_tools2/prefs.py:124: in __init__ verbose=verbose) ../lib/python3.7/site-packages/pystan/model.py:378: in __init__ build_extension.run() ../lib/python3.7/distutils/command/build_ext.py:340: in run self.build_extensions() ../lib/python3.7/distutils/command/build_ext.py:449: in build_extensions self._build_extensions_serial() ../lib/python3.7/distutils/command/build_ext.py:474: in _build_extensions_serial self.build_extension(ext) ../lib/python3.7/distutils/command/build_ext.py:534: in build_extension depends=ext.depends) ../lib/python3.7/distutils/ccompiler.py:574: in compile self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = obj = '/tmp/pystan_s2e1trz4/tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.o' src = '/tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.cpp' ext = '.cpp' cc_args = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_s2e1trz4', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] extra_postargs = ['-O2', '-ftemplate-depth-256', '-Wno-unused-function', '-Wno-uninitialized', '-std=c++1y'] pp_opts = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_s2e1trz4', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts): compiler_so = self.compiler_so if sys.platform == 'darwin': compiler_so = _osx_support.compiler_fixup(compiler_so, cc_args + extra_postargs) try: self.spawn(compiler_so + cc_args + [src, '-o', obj] + extra_postargs) except DistutilsExecError as msg: > raise CompileError(msg) E distutils.errors.CompileError: command 'gcc' failed with exit status 1 ../lib/python3.7/distutils/unixccompiler.py:120: CompileError ----------------------------- Captured stdout call ----------------------------- Compiling /tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.pyx because it changed. [1/1] Cythonizing /tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.pyx building 'stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285' extension creating /tmp/pystan_s2e1trz4/tmp creating /tmp/pystan_s2e1trz4/tmp/pystan_s2e1trz4 gcc -pthread -B /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/tmp/pystan_s2e1trz4 -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/eigen_3.3.3 -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0 -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/sundials_4.1.0/include -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/include/python3.7m -c /tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.cpp -o /tmp/pystan_s2e1trz4/tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.o -O2 -ftemplate-depth-256 -Wno-unused-function -Wno-uninitialized -std=c++1y ----------------------------- Captured stderr call ----------------------------- INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_f7f9e08818ed856dcf6a2c6debccb643 NOW. INFO:pystan:OS: linux, Python: 3.7.7 (default, May 7 2020, 21:25:33) [GCC 7.3.0], Cython 0.29.20 cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.cpp:692: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^ In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat.hpp:336, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/io/dump.hpp:6, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/py_var_context.hpp:12, from /tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.cpp:695: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp: In function ‘typename stan::return_type::type stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:64:59: warning: typedef ‘T_alpha_val’ locally defined but not used [-Wunused-local-typedefs] typename partials_return_type::type>::type T_alpha_val; ^ In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat.hpp:41, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/log_prob_grad.hpp:4, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/test_gradients.hpp:7, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/services/diagnose/diagnose.hpp:10, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan_fit.hpp:23, from /tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.cpp:696: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:32: error: ‘std::index_sequence’ has not been declared std::index_sequence i) { ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:46: error: expected ‘,’ or ‘...’ before ‘<’ token std::index_sequence i) { ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In function ‘constexpr auto stan::math::internal::apply(const F&, const Tuple&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: error: ‘make_index_sequence’ is not a member of ‘std’ return apply_impl(f, t, std::make_index_sequence{}>{}); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: note: suggested alternative: In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/container/vector/vector.hpp:28:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/container/vector/vector10.hpp:25, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/transform_view/transform_view.hpp:22, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/algorithm/transformation/transform.hpp:11, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view/detail/begin_impl.hpp:14, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view/zip_view.hpp:16, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view.hpp:12, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/include/zip_view.hpp:11, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/resize.hpp:26, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/state_wrapper.hpp:26, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint.hpp:25, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/arr.hpp:46, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat.hpp:344, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/io/dump.hpp:6, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/py_var_context.hpp:12, from /tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.cpp:695: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/support/detail/index_sequence.hpp:59:12: note: ‘boost::fusion::detail::make_index_sequence’ struct make_index_sequence ^ In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat.hpp:41, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/log_prob_grad.hpp:4, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/test_gradients.hpp:7, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/services/diagnose/diagnose.hpp:10, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan_fit.hpp:23, from /tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.cpp:696: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected primary-expression before ‘{’ token return apply_impl(f, t, std::make_index_sequence{}>{}); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected ‘)’ before ‘{’ token /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:151:9: error: expected type-specifier = std::result_of_t; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:42: error: ‘FReturnType’ was not declared in this scope std::array::value> M_; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:53: error: template argument 1 is invalid std::array::value> M_; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:61: error: template argument 2 is invalid std::array::value> M_; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘std::vector stan::math::adj_jac_vari::build_return_varis_and_vars(const std::vector&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:349:9: error: invalid types ‘int[int]’ for array subscript M_[0] = val_y.size(); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:350:32: error: invalid types ‘int[int]’ for array subscript std::vector var_y(M_[0]); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘Eigen::Matrix stan::math::adj_jac_vari::build_return_varis_and_vars(const Eigen::Matrix&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:375:9: error: invalid types ‘int[int]’ for array subscript M_[0] = val_y.rows(); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:376:9: error: invalid types ‘int[int]’ for array subscript M_[1] = val_y.cols(); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:40: error: invalid types ‘int[int]’ for array subscript Eigen::Matrix var_y(M_[0], M_[1]); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:47: error: invalid types ‘int[int]’ for array subscript Eigen::Matrix var_y(M_[0], M_[1]); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘void stan::math::adj_jac_vari::chain()’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:5: error: ‘FReturnType’ was not declared in this scope FReturnType y_adj; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:17: error: expected ‘;’ before ‘y_adj’ FReturnType y_adj; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:532:38: error: ‘y_adj’ was not declared in this scope internal::build_y_adj(y_vi_, M_, y_adj); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:26: error: expansion pattern ‘auto&&’ contains no argument packs [this](auto&&... args) { this->accumulate_adjoints(args...); }, ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In lambda function: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:60: error: ‘args’ was not declared in this scope [this](auto&&... args) { this->accumulate_adjoints(args...); }, ^ /tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.cpp: In function ‘PyObject* __pyx_pf_71stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285_2_call_sampler(PyObject*, PyObject*, PyObject*, PyObject*)’: /tmp/pystan_s2e1trz4/stanfit4anon_model_f7f9e08818ed856dcf6a2c6debccb643_4415851057653176285.cpp:9475:71: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] __pyx_t_12 = ((__pyx_t_9 != __pyx_v_fitptr->param_names_oi().size()) != 0); ^ ------------------------------ Captured log call ------------------------------- INFO pystan:model.py:259 COMPILING THE C++ CODE FOR MODEL anon_model_f7f9e08818ed856dcf6a2c6debccb643 NOW. INFO pystan:model.py:264 OS: linux, Python: 3.7.7 (default, May 7 2020, 21:25:33) [GCC 7.3.0], Cython 0.29.20 _____________ test_pyStanModels_Different.test_pystan_compilation ______________ self = obj = '/tmp/pystan_upbic9c4/tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.o' src = '/tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.cpp' ext = '.cpp' cc_args = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_upbic9c4', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] extra_postargs = ['-O2', '-ftemplate-depth-256', '-Wno-unused-function', '-Wno-uninitialized', '-std=c++1y'] pp_opts = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_upbic9c4', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts): compiler_so = self.compiler_so if sys.platform == 'darwin': compiler_so = _osx_support.compiler_fixup(compiler_so, cc_args + extra_postargs) try: self.spawn(compiler_so + cc_args + [src, '-o', obj] + > extra_postargs) ../lib/python3.7/distutils/unixccompiler.py:118: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = cmd = ['gcc', '-pthread', '-B', '/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/compiler_compat', '-Wl,--sysroot=/', '-Wsign-compare', ...] def spawn(self, cmd): > spawn(cmd, dry_run=self.dry_run) ../lib/python3.7/distutils/ccompiler.py:910: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cmd = ['gcc', '-pthread', '-B', '/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/compiler_compat', '-Wl,--sysroot=/', '-Wsign-compare', ...] search_path = 1, verbose = 0, dry_run = 0 def spawn(cmd, search_path=1, verbose=0, dry_run=0): """Run another program, specified as a command list 'cmd', in a new process. 'cmd' is just the argument list for the new process, ie. cmd[0] is the program to run and cmd[1:] are the rest of its arguments. There is no way to run a program with a name different from that of its executable. If 'search_path' is true (the default), the system's executable search path will be used to find the program; otherwise, cmd[0] must be the exact path to the executable. If 'dry_run' is true, the command will not actually be run. Raise DistutilsExecError if running the program fails in any way; just return on success. """ # cmd is documented as a list, but just in case some code passes a tuple # in, protect our %-formatting code against horrible death cmd = list(cmd) if os.name == 'posix': > _spawn_posix(cmd, search_path, dry_run=dry_run) ../lib/python3.7/distutils/spawn.py:36: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cmd = 'gcc', search_path = 1, verbose = 0, dry_run = 0 def _spawn_posix(cmd, search_path=1, verbose=0, dry_run=0): log.info(' '.join(cmd)) if dry_run: return executable = cmd[0] exec_fn = search_path and os.execvp or os.execv env = None if sys.platform == 'darwin': global _cfg_target, _cfg_target_split if _cfg_target is None: _cfg_target = sysconfig.get_config_var( 'MACOSX_DEPLOYMENT_TARGET') or '' if _cfg_target: _cfg_target_split = [int(x) for x in _cfg_target.split('.')] if _cfg_target: # ensure that the deployment target of build process is not less # than that used when the interpreter was built. This ensures # extension modules are built with correct compatibility values cur_target = os.environ.get('MACOSX_DEPLOYMENT_TARGET', _cfg_target) if _cfg_target_split > [int(x) for x in cur_target.split('.')]: my_msg = ('$MACOSX_DEPLOYMENT_TARGET mismatch: ' 'now "%s" but "%s" during configure' % (cur_target, _cfg_target)) raise DistutilsPlatformError(my_msg) env = dict(os.environ, MACOSX_DEPLOYMENT_TARGET=cur_target) exec_fn = search_path and os.execvpe or os.execve pid = os.fork() if pid == 0: # in the child try: if env is None: exec_fn(executable, cmd) else: exec_fn(executable, cmd, env) except OSError as e: if not DEBUG: cmd = executable sys.stderr.write("unable to execute %r: %s\n" % (cmd, e.strerror)) os._exit(1) if not DEBUG: cmd = executable sys.stderr.write("unable to execute %r for unknown reasons" % cmd) os._exit(1) else: # in the parent # Loop until the child either exits or is terminated by a signal # (ie. keep waiting if it's merely stopped) while True: try: pid, status = os.waitpid(pid, 0) except OSError as exc: if not DEBUG: cmd = executable raise DistutilsExecError( "command %r failed: %s" % (cmd, exc.args[-1])) if os.WIFSIGNALED(status): if not DEBUG: cmd = executable raise DistutilsExecError( "command %r terminated by signal %d" % (cmd, os.WTERMSIG(status))) elif os.WIFEXITED(status): exit_status = os.WEXITSTATUS(status) if exit_status == 0: return # hey, it succeeded! else: if not DEBUG: cmd = executable raise DistutilsExecError( "command %r failed with exit status %d" > % (cmd, exit_status)) E distutils.errors.DistutilsExecError: command 'gcc' failed with exit status 1 ../lib/python3.7/distutils/spawn.py:159: DistutilsExecError During handling of the above exception, another exception occurred: self = def test_pystan_compilation(self): """Tests compilation of models.""" > m = self.MODEL(verbose=True) tests/test_pystan_compile.py:37: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ dms_tools2/prefs.py:183: in __init__ verbose=verbose) ../lib/python3.7/site-packages/pystan/model.py:378: in __init__ build_extension.run() ../lib/python3.7/distutils/command/build_ext.py:340: in run self.build_extensions() ../lib/python3.7/distutils/command/build_ext.py:449: in build_extensions self._build_extensions_serial() ../lib/python3.7/distutils/command/build_ext.py:474: in _build_extensions_serial self.build_extension(ext) ../lib/python3.7/distutils/command/build_ext.py:534: in build_extension depends=ext.depends) ../lib/python3.7/distutils/ccompiler.py:574: in compile self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = obj = '/tmp/pystan_upbic9c4/tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.o' src = '/tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.cpp' ext = '.cpp' cc_args = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_upbic9c4', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] extra_postargs = ['-O2', '-ftemplate-depth-256', '-Wno-unused-function', '-Wno-uninitialized', '-std=c++1y'] pp_opts = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_upbic9c4', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts): compiler_so = self.compiler_so if sys.platform == 'darwin': compiler_so = _osx_support.compiler_fixup(compiler_so, cc_args + extra_postargs) try: self.spawn(compiler_so + cc_args + [src, '-o', obj] + extra_postargs) except DistutilsExecError as msg: > raise CompileError(msg) E distutils.errors.CompileError: command 'gcc' failed with exit status 1 ../lib/python3.7/distutils/unixccompiler.py:120: CompileError ----------------------------- Captured stdout call ----------------------------- Compiling /tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.pyx because it changed. [1/1] Cythonizing /tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.pyx building 'stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827' extension creating /tmp/pystan_upbic9c4/tmp creating /tmp/pystan_upbic9c4/tmp/pystan_upbic9c4 gcc -pthread -B /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/tmp/pystan_upbic9c4 -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/eigen_3.3.3 -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0 -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/sundials_4.1.0/include -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include -I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/include/python3.7m -c /tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.cpp -o /tmp/pystan_upbic9c4/tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.o -O2 -ftemplate-depth-256 -Wno-unused-function -Wno-uninitialized -std=c++1y ----------------------------- Captured stderr call ----------------------------- INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_f45c400d882edcb41dc18afdf977fa57 NOW. INFO:pystan:OS: linux, Python: 3.7.7 (default, May 7 2020, 21:25:33) [GCC 7.3.0], Cython 0.29.20 cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.cpp:692: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^ In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat.hpp:336, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/io/dump.hpp:6, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/py_var_context.hpp:12, from /tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.cpp:695: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp: In function ‘typename stan::return_type::type stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:64:59: warning: typedef ‘T_alpha_val’ locally defined but not used [-Wunused-local-typedefs] typename partials_return_type::type>::type T_alpha_val; ^ In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat.hpp:41, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/log_prob_grad.hpp:4, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/test_gradients.hpp:7, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/services/diagnose/diagnose.hpp:10, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan_fit.hpp:23, from /tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.cpp:696: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:32: error: ‘std::index_sequence’ has not been declared std::index_sequence i) { ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:46: error: expected ‘,’ or ‘...’ before ‘<’ token std::index_sequence i) { ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In function ‘constexpr auto stan::math::internal::apply(const F&, const Tuple&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: error: ‘make_index_sequence’ is not a member of ‘std’ return apply_impl(f, t, std::make_index_sequence{}>{}); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: note: suggested alternative: In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/container/vector/vector.hpp:28:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/container/vector/vector10.hpp:25, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/transform_view/transform_view.hpp:22, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/algorithm/transformation/transform.hpp:11, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view/detail/begin_impl.hpp:14, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view/zip_view.hpp:16, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view.hpp:12, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/include/zip_view.hpp:11, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/resize.hpp:26, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/state_wrapper.hpp:26, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint.hpp:25, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/arr.hpp:46, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat.hpp:344, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/io/dump.hpp:6, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/py_var_context.hpp:12, from /tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.cpp:695: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/support/detail/index_sequence.hpp:59:12: note: ‘boost::fusion::detail::make_index_sequence’ struct make_index_sequence ^ In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat.hpp:41, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/log_prob_grad.hpp:4, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/test_gradients.hpp:7, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/services/diagnose/diagnose.hpp:10, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan_fit.hpp:23, from /tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.cpp:696: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected primary-expression before ‘{’ token return apply_impl(f, t, std::make_index_sequence{}>{}); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected ‘)’ before ‘{’ token /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:151:9: error: expected type-specifier = std::result_of_t; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:42: error: ‘FReturnType’ was not declared in this scope std::array::value> M_; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:53: error: template argument 1 is invalid std::array::value> M_; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:61: error: template argument 2 is invalid std::array::value> M_; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘std::vector stan::math::adj_jac_vari::build_return_varis_and_vars(const std::vector&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:349:9: error: invalid types ‘int[int]’ for array subscript M_[0] = val_y.size(); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:350:32: error: invalid types ‘int[int]’ for array subscript std::vector var_y(M_[0]); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘Eigen::Matrix stan::math::adj_jac_vari::build_return_varis_and_vars(const Eigen::Matrix&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:375:9: error: invalid types ‘int[int]’ for array subscript M_[0] = val_y.rows(); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:376:9: error: invalid types ‘int[int]’ for array subscript M_[1] = val_y.cols(); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:40: error: invalid types ‘int[int]’ for array subscript Eigen::Matrix var_y(M_[0], M_[1]); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:47: error: invalid types ‘int[int]’ for array subscript Eigen::Matrix var_y(M_[0], M_[1]); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘void stan::math::adj_jac_vari::chain()’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:5: error: ‘FReturnType’ was not declared in this scope FReturnType y_adj; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:17: error: expected ‘;’ before ‘y_adj’ FReturnType y_adj; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:532:38: error: ‘y_adj’ was not declared in this scope internal::build_y_adj(y_vi_, M_, y_adj); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:26: error: expansion pattern ‘auto&&’ contains no argument packs [this](auto&&... args) { this->accumulate_adjoints(args...); }, ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In lambda function: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:60: error: ‘args’ was not declared in this scope [this](auto&&... args) { this->accumulate_adjoints(args...); }, ^ /tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.cpp: In function ‘PyObject* __pyx_pf_70stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827_2_call_sampler(PyObject*, PyObject*, PyObject*, PyObject*)’: /tmp/pystan_upbic9c4/stanfit4anon_model_f45c400d882edcb41dc18afdf977fa57_578730941479601827.cpp:9475:71: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] __pyx_t_12 = ((__pyx_t_9 != __pyx_v_fitptr->param_names_oi().size()) != 0); ^ ------------------------------ Captured log call ------------------------------- INFO pystan:model.py:259 COMPILING THE C++ CODE FOR MODEL anon_model_f45c400d882edcb41dc18afdf977fa57 NOW. INFO pystan:model.py:264 OS: linux, Python: 3.7.7 (default, May 7 2020, 21:25:33) [GCC 7.3.0], Cython 0.29.20 _________________ TestInferSitePreferences.test_inferSitePrefs _________________ self = obj = '/tmp/pystan_6yuob5ai/tmp/pystan_6yuob5ai/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_6776682967519156809.o' src = '/tmp/pystan_6yuob5ai/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_6776682967519156809.cpp' ext = '.cpp' cc_args = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_6yuob5ai', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] extra_postargs = ['-O2', '-ftemplate-depth-256', '-Wno-unused-function', '-Wno-uninitialized', '-std=c++1y'] pp_opts = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_6yuob5ai', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts): compiler_so = self.compiler_so if sys.platform == 'darwin': compiler_so = _osx_support.compiler_fixup(compiler_so, cc_args + extra_postargs) try: self.spawn(compiler_so + cc_args + [src, '-o', obj] + > extra_postargs) ../lib/python3.7/distutils/unixccompiler.py:118: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = cmd = ['gcc', '-pthread', '-B', '/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/compiler_compat', '-Wl,--sysroot=/', '-Wsign-compare', ...] def spawn(self, cmd): > spawn(cmd, dry_run=self.dry_run) ../lib/python3.7/distutils/ccompiler.py:910: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cmd = ['gcc', '-pthread', '-B', '/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/compiler_compat', '-Wl,--sysroot=/', '-Wsign-compare', ...] search_path = 1, verbose = 0, dry_run = 0 def spawn(cmd, search_path=1, verbose=0, dry_run=0): """Run another program, specified as a command list 'cmd', in a new process. 'cmd' is just the argument list for the new process, ie. cmd[0] is the program to run and cmd[1:] are the rest of its arguments. There is no way to run a program with a name different from that of its executable. If 'search_path' is true (the default), the system's executable search path will be used to find the program; otherwise, cmd[0] must be the exact path to the executable. If 'dry_run' is true, the command will not actually be run. Raise DistutilsExecError if running the program fails in any way; just return on success. """ # cmd is documented as a list, but just in case some code passes a tuple # in, protect our %-formatting code against horrible death cmd = list(cmd) if os.name == 'posix': > _spawn_posix(cmd, search_path, dry_run=dry_run) ../lib/python3.7/distutils/spawn.py:36: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cmd = 'gcc', search_path = 1, verbose = 0, dry_run = 0 def _spawn_posix(cmd, search_path=1, verbose=0, dry_run=0): log.info(' '.join(cmd)) if dry_run: return executable = cmd[0] exec_fn = search_path and os.execvp or os.execv env = None if sys.platform == 'darwin': global _cfg_target, _cfg_target_split if _cfg_target is None: _cfg_target = sysconfig.get_config_var( 'MACOSX_DEPLOYMENT_TARGET') or '' if _cfg_target: _cfg_target_split = [int(x) for x in _cfg_target.split('.')] if _cfg_target: # ensure that the deployment target of build process is not less # than that used when the interpreter was built. This ensures # extension modules are built with correct compatibility values cur_target = os.environ.get('MACOSX_DEPLOYMENT_TARGET', _cfg_target) if _cfg_target_split > [int(x) for x in cur_target.split('.')]: my_msg = ('$MACOSX_DEPLOYMENT_TARGET mismatch: ' 'now "%s" but "%s" during configure' % (cur_target, _cfg_target)) raise DistutilsPlatformError(my_msg) env = dict(os.environ, MACOSX_DEPLOYMENT_TARGET=cur_target) exec_fn = search_path and os.execvpe or os.execve pid = os.fork() if pid == 0: # in the child try: if env is None: exec_fn(executable, cmd) else: exec_fn(executable, cmd, env) except OSError as e: if not DEBUG: cmd = executable sys.stderr.write("unable to execute %r: %s\n" % (cmd, e.strerror)) os._exit(1) if not DEBUG: cmd = executable sys.stderr.write("unable to execute %r for unknown reasons" % cmd) os._exit(1) else: # in the parent # Loop until the child either exits or is terminated by a signal # (ie. keep waiting if it's merely stopped) while True: try: pid, status = os.waitpid(pid, 0) except OSError as exc: if not DEBUG: cmd = executable raise DistutilsExecError( "command %r failed: %s" % (cmd, exc.args[-1])) if os.WIFSIGNALED(status): if not DEBUG: cmd = executable raise DistutilsExecError( "command %r terminated by signal %d" % (cmd, os.WTERMSIG(status))) elif os.WIFEXITED(status): exit_status = os.WEXITSTATUS(status) if exit_status == 0: return # hey, it succeeded! else: if not DEBUG: cmd = executable raise DistutilsExecError( "command %r failed with exit status %d" > % (cmd, exit_status)) E distutils.errors.DistutilsExecError: command 'gcc' failed with exit status 1 ../lib/python3.7/distutils/spawn.py:159: DistutilsExecError During handling of the above exception, another exception occurred: self = def test_inferSitePrefs(self): """Inference with with correct priors.""" # rates drawn uniformly from following ranges after dividing by nchars mutrate = (0.005, 0.025) errorratepre = (0.0001, 0.0003) errorratepost = (0.0002, 0.0005) # prefs drawn uniformly from this range and adjusted to sum to one pidist = (1e-5, 0.6) random.seed(self.SEED) numpy.random.seed(self.SEED) wtchar = random.choice(self.CHARLIST) iwtchar = self.CHARLIST.index(wtchar) nchars = len(self.CHARLIST) mur = [] pir = [] epsilonr = [] rhor = [] for i in range(nchars): mur.append(random.uniform(mutrate[0] / float(nchars), mutrate[1] / float(nchars))) epsilonr.append(random.uniform(errorratepre[0] / float(nchars), errorratepre[1] / float(nchars))) rhor.append(random.uniform(errorratepost[0] / float(nchars), errorratepost[1] / float(nchars))) pir.append(random.uniform(pidist[0], pidist[1])) mur[iwtchar] = 1.0 - sum([mur[i] for i in range(nchars) if i != iwtchar]) epsilonr[iwtchar] = 1.0 - sum([epsilonr[i] for i in range(nchars) if i != iwtchar]) rhor[iwtchar] = 1.0 - sum([rhor[i] for i in range(nchars) if i != iwtchar]) pir[iwtchar] = 1.0 pir = numpy.array(pir) pir /= pir.sum() mur = numpy.array(mur) epsilonr = numpy.array(epsilonr) rhor = numpy.array(rhor) deltar = numpy.zeros(nchars) deltar[iwtchar] = 1.0 priors = { 'pir_prior_params':dict([(char, pir[i] * nchars) for (i, char) in enumerate(self.CHARLIST)]), 'mur_prior_params':dict([(char, mur[i] * nchars) for (i, char) in enumerate(self.CHARLIST)]), 'epsilonr_prior_params':dict([(char, epsilonr[i] * nchars) for (i, char) in enumerate(self.CHARLIST)]), 'rhor_prior_params':dict([(char, rhor[i] * nchars) for (i, char) in enumerate(self.CHARLIST)]), } difflist = [] for (depth, maxdiffsum) in [(1e9, 0.01)]: # first with no errors nrpre = numpy.random.multinomial(depth, mur) nrpost = numpy.random.multinomial(depth, mur * pir / numpy.dot(mur, pir)) counts = { 'pre':dict([(char, nrpre[i]) for (i, char) in enumerate(self.CHARLIST)]), 'post':dict([(char, nrpost[i]) for (i, char) in enumerate(self.CHARLIST)]), } (converged, pi_means, pi_95credint, logstring) = \ dms_tools2.prefs.inferSitePrefs(self.CHARLIST, wtchar, > 'none', counts, priors, n_jobs=self.n_jobs) tests/test_site_inferprefs.py:102: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ dms_tools2/prefs.py:608: in inferSitePrefs sm = StanModelNoneErr().model dms_tools2/prefs.py:70: in __init__ verbose=verbose) ../lib/python3.7/site-packages/pystan/model.py:378: in __init__ build_extension.run() ../lib/python3.7/distutils/command/build_ext.py:340: in run self.build_extensions() ../lib/python3.7/distutils/command/build_ext.py:449: in build_extensions self._build_extensions_serial() ../lib/python3.7/distutils/command/build_ext.py:474: in _build_extensions_serial self.build_extension(ext) ../lib/python3.7/distutils/command/build_ext.py:534: in build_extension depends=ext.depends) ../lib/python3.7/distutils/ccompiler.py:574: in compile self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = obj = '/tmp/pystan_6yuob5ai/tmp/pystan_6yuob5ai/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_6776682967519156809.o' src = '/tmp/pystan_6yuob5ai/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_6776682967519156809.cpp' ext = '.cpp' cc_args = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_6yuob5ai', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] extra_postargs = ['-O2', '-ftemplate-depth-256', '-Wno-unused-function', '-Wno-uninitialized', '-std=c++1y'] pp_opts = ['-DBOOST_RESULT_OF_USE_TR1', '-DBOOST_NO_DECLTYPE', '-DBOOST_DISABLE_ASSERTS', '-I/tmp/pystan_6yuob5ai', '-I/rugpfs/f... '-I/rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src', ...] def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts): compiler_so = self.compiler_so if sys.platform == 'darwin': compiler_so = _osx_support.compiler_fixup(compiler_so, cc_args + extra_postargs) try: self.spawn(compiler_so + cc_args + [src, '-o', obj] + extra_postargs) except DistutilsExecError as msg: > raise CompileError(msg) E distutils.errors.CompileError: command 'gcc' failed with exit status 1 ../lib/python3.7/distutils/unixccompiler.py:120: CompileError ----------------------------- Captured stderr call ----------------------------- INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_d3c958b02d8eff9dc447fb55c590fe08 NOW. cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/pystan_6yuob5ai/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_6776682967519156809.cpp:692: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^ In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat.hpp:336, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/io/dump.hpp:6, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/py_var_context.hpp:12, from /tmp/pystan_6yuob5ai/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_6776682967519156809.cpp:695: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp: In function ‘typename stan::return_type::type stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:64:59: warning: typedef ‘T_alpha_val’ locally defined but not used [-Wunused-local-typedefs] typename partials_return_type::type>::type T_alpha_val; ^ In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat.hpp:41, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/log_prob_grad.hpp:4, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/test_gradients.hpp:7, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/services/diagnose/diagnose.hpp:10, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan_fit.hpp:23, from /tmp/pystan_6yuob5ai/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_6776682967519156809.cpp:696: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:32: error: ‘std::index_sequence’ has not been declared std::index_sequence i) { ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:31:46: error: expected ‘,’ or ‘...’ before ‘<’ token std::index_sequence i) { ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In function ‘constexpr auto stan::math::internal::apply(const F&, const Tuple&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: error: ‘make_index_sequence’ is not a member of ‘std’ return apply_impl(f, t, std::make_index_sequence{}>{}); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:27: note: suggested alternative: In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/container/vector/vector.hpp:28:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/container/vector/vector10.hpp:25, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/transform_view/transform_view.hpp:22, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/algorithm/transformation/transform.hpp:11, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view/detail/begin_impl.hpp:14, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view/zip_view.hpp:16, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/view/zip_view.hpp:12, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/include/zip_view.hpp:11, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/resize.hpp:26, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/state_wrapper.hpp:26, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/numeric/odeint.hpp:25, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/arr.hpp:46, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/prim/mat.hpp:344, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/io/dump.hpp:6, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/py_var_context.hpp:12, from /tmp/pystan_6yuob5ai/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_6776682967519156809.cpp:695: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/lib/boost_1.69.0/boost/fusion/support/detail/index_sequence.hpp:59:12: note: ‘boost::fusion::detail::make_index_sequence’ struct make_index_sequence ^ In file included from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/fun/ordered_constrain.hpp:6:0, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat.hpp:41, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/log_prob_grad.hpp:4, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/model/test_gradients.hpp:7, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/src/stan/services/diagnose/diagnose.hpp:10, from /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan_fit.hpp:23, from /tmp/pystan_6yuob5ai/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_6776682967519156809.cpp:696: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected primary-expression before ‘{’ token return apply_impl(f, t, std::make_index_sequence{}>{}); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:49:77: error: expected ‘)’ before ‘{’ token /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: At global scope: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:151:9: error: expected type-specifier = std::result_of_t; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:42: error: ‘FReturnType’ was not declared in this scope std::array::value> M_; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:53: error: template argument 1 is invalid std::array::value> M_; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:156:61: error: template argument 2 is invalid std::array::value> M_; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘std::vector stan::math::adj_jac_vari::build_return_varis_and_vars(const std::vector&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:349:9: error: invalid types ‘int[int]’ for array subscript M_[0] = val_y.size(); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:350:32: error: invalid types ‘int[int]’ for array subscript std::vector var_y(M_[0]); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘Eigen::Matrix stan::math::adj_jac_vari::build_return_varis_and_vars(const Eigen::Matrix&)’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:375:9: error: invalid types ‘int[int]’ for array subscript M_[0] = val_y.rows(); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:376:9: error: invalid types ‘int[int]’ for array subscript M_[1] = val_y.cols(); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:40: error: invalid types ‘int[int]’ for array subscript Eigen::Matrix var_y(M_[0], M_[1]); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:377:47: error: invalid types ‘int[int]’ for array subscript Eigen::Matrix var_y(M_[0], M_[1]); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In member function ‘void stan::math::adj_jac_vari::chain()’: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:5: error: ‘FReturnType’ was not declared in this scope FReturnType y_adj; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:530:17: error: expected ‘;’ before ‘y_adj’ FReturnType y_adj; ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:532:38: error: ‘y_adj’ was not declared in this scope internal::build_y_adj(y_vi_, M_, y_adj); ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:26: error: expansion pattern ‘auto&&’ contains no argument packs [this](auto&&... args) { this->accumulate_adjoints(args...); }, ^ /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp: In lambda function: /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/pystan/stan/lib/stan_math/stan/math/rev/mat/functor/adj_jac_apply.hpp:536:60: error: ‘args’ was not declared in this scope [this](auto&&... args) { this->accumulate_adjoints(args...); }, ^ /tmp/pystan_6yuob5ai/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_6776682967519156809.cpp: In function ‘PyObject* __pyx_pf_71stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_6776682967519156809_2_call_sampler(PyObject*, PyObject*, PyObject*, PyObject*)’: /tmp/pystan_6yuob5ai/stanfit4anon_model_d3c958b02d8eff9dc447fb55c590fe08_6776682967519156809.cpp:9475:71: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] __pyx_t_12 = ((__pyx_t_9 != __pyx_v_fitptr->param_names_oi().size()) != 0); ^ ------------------------------ Captured log call ------------------------------- INFO pystan:model.py:259 COMPILING THE C++ CODE FOR MODEL anon_model_d3c958b02d8eff9dc447fb55c590fe08 NOW. =============================== warnings summary =============================== /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/Bio/Alphabet/__init__.py:27 /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/Bio/Alphabet/__init__.py:27: PendingDeprecationWarning: We intend to remove or replace Bio.Alphabet in 2020, ideally avoid using it explicitly in your code. Please get in touch if you will be adversely affected by this. https://github.com/biopython/biopython/issues/2046 PendingDeprecationWarning, /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/patsy/constraint.py:13 /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/patsy/constraint.py:13: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working from collections import Mapping /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/Cython/Build/Inline.py:4 /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/Cython/Build/Inline.py:4: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses import imp dms_tools2/minimap2.py::dms_tools2.minimap2.Mapper /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/dms_tools2/minimap2.py:2257: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working elif not isinstance(paf_file, collections.Iterable): dms_tools2/plot.py::dms_tools2.plot.findSigSel dms_tools2/plot.py::dms_tools2.plot.findSigSel dms_tools2/plot.py::dms_tools2.plot.findSigSel /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/dms_tools2/dms_tools2/plot.py:1154: UserWarning: tight_layout: falling back to Agg renderer plt.tight_layout() tests/test_pacbio_ccs.py::test_pacbio_CCS::test_plotColCorrs /rugpfs/fs0/marr_lab/store/jmath97/softwares/miniconda/envs/test/lib/python3.7/site-packages/seaborn/axisgrid.py:1342: UserWarning: tight_layout: falling back to Agg renderer fig.tight_layout(pad=layout_pad) -- Docs: https://docs.pytest.org/en/latest/warnings.html =========================== short test summary info ============================ FAILED tests/test_batch_prefs.py::test_batch_prefs::test_dms2_batch_prefs - A... FAILED tests/test_pystan_compile.py::test_pyStanModels::test_pystan_compilation FAILED tests/test_pystan_compile.py::test_pyStanModels_Same::test_pystan_compilation FAILED tests/test_pystan_compile.py::test_pyStanModels_Different::test_pystan_compilation FAILED tests/test_site_inferprefs.py::TestInferSitePreferences::test_inferSitePrefs ============ 5 failed, 111 passed, 8 warnings in 1407.73s (0:23:27) ============ done