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pip install fails on Ubuntu 18.04 under freshly installed Anaconda3 #40

@johann-petrak

Description

@johann-petrak

After installing Anaconda3-2019.07-Linux-x86_64.sh for a new user, directly running pip install DAWG fails with the following:

  Building wheel for DAWG (setup.py) ... error
  ERROR: Complete output from command /home/conda/anaconda3/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-_lu0pouq/DAWG/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-k8u1ivdk --python-tag cp37:
  ERROR: running bdist_wheel
  running build
  running build_ext
  building 'dawg' extension
  creating build
  creating build/temp.linux-x86_64-3.7
  creating build/temp.linux-x86_64-3.7/src
  creating build/temp.linux-x86_64-3.7/lib
  creating build/temp.linux-x86_64-3.7/lib/b64
  gcc -pthread -B /home/conda/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ilib -I/home/conda/anaconda3/include/python3.7m -c src/dawg.cpp -o build/temp.linux-x86_64-3.7/src/dawg.o
  cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
  In file included from src/dawg.cpp:266:0:
  src/../lib/dawgdic/dictionary-builder.h: In member function ‘bool dawgdic::DictionaryBuilder::BuildDictionary(dawgdic::BaseType, dawgdic::BaseType)’:
  src/../lib/dawgdic/dictionary-builder.h:138:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
       if (dawg_.is_merging(dawg_child_index))
       ^~
  src/../lib/dawgdic/dictionary-builder.h:139:53: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
         link_table_.Insert(dawg_child_index, offset); {
                                                       ^
  src/dawg.cpp: In function ‘PyObject* __pyx_f_4dawg_9BytesDAWG_items(__pyx_obj_4dawg_BytesDAWG*, int, __pyx_opt_args_4dawg_9BytesDAWG_items*)’:
  src/dawg.cpp:11011:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (__pyx_t_10 = 0; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) {
                            ~~~~~~~~~~~^~~~~~~~~~~
  src/dawg.cpp: In function ‘PyObject* __pyx_gb_4dawg_9BytesDAWG_24generator2(__pyx_GeneratorObject*, PyObject*)’:
  src/dawg.cpp:11485:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
                           ~~~~~~~~~~^~~~~~~~~~~
  src/dawg.cpp: In function ‘PyObject* __pyx_f_4dawg_9BytesDAWG_keys(__pyx_obj_4dawg_BytesDAWG*, int, __pyx_opt_args_4dawg_9BytesDAWG_keys*)’:
  src/dawg.cpp:11814:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (__pyx_t_10 = 0; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) {
                            ~~~~~~~~~~~^~~~~~~~~~~
  src/dawg.cpp: In function ‘PyObject* __pyx_gb_4dawg_9BytesDAWG_29generator3(__pyx_GeneratorObject*, PyObject*)’:
  src/dawg.cpp:12222:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
                           ~~~~~~~~~~^~~~~~~~~~~
  src/dawg.cpp: In function ‘int __Pyx_GetException(PyObject**, PyObject**, PyObject**)’:
  src/dawg.cpp:21523:24: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
       tmp_type = tstate->exc_type;
                          ^~~~~~~~
                          curexc_type
  src/dawg.cpp:21524:25: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
       tmp_value = tstate->exc_value;
                           ^~~~~~~~~
                           curexc_value
  src/dawg.cpp:21525:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
       tmp_tb = tstate->exc_traceback;
                        ^~~~~~~~~~~~~
                        curexc_traceback
  src/dawg.cpp:21526:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
       tstate->exc_type = local_type;
               ^~~~~~~~
               curexc_type
  src/dawg.cpp:21527:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
       tstate->exc_value = local_value;
               ^~~~~~~~~
               curexc_value
  src/dawg.cpp:21528:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
       tstate->exc_traceback = local_tb;
               ^~~~~~~~~~~~~
               curexc_traceback
  src/dawg.cpp: In function ‘void __Pyx_ExceptionSwap(PyObject**, PyObject**, PyObject**)’:
  src/dawg.cpp:21550:24: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
       tmp_type = tstate->exc_type;
                          ^~~~~~~~
                          curexc_type
  src/dawg.cpp:21551:25: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
       tmp_value = tstate->exc_value;
                           ^~~~~~~~~
                           curexc_value
  src/dawg.cpp:21552:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
       tmp_tb = tstate->exc_traceback;
                        ^~~~~~~~~~~~~
                        curexc_traceback
  src/dawg.cpp:21553:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
       tstate->exc_type = *type;
               ^~~~~~~~
               curexc_type
  src/dawg.cpp:21554:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
       tstate->exc_value = *value;
               ^~~~~~~~~
               curexc_value
  src/dawg.cpp:21555:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
       tstate->exc_traceback = *tb;
               ^~~~~~~~~~~~~
               curexc_traceback
  src/dawg.cpp: In function ‘void __Pyx_ExceptionSave(PyObject**, PyObject**, PyObject**)’:
  src/dawg.cpp:21568:21: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
       *type = tstate->exc_type;
                       ^~~~~~~~
                       curexc_type
  src/dawg.cpp:21569:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
       *value = tstate->exc_value;
                        ^~~~~~~~~
                        curexc_value
  src/dawg.cpp:21570:19: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
       *tb = tstate->exc_traceback;
                     ^~~~~~~~~~~~~
                     curexc_traceback
  src/dawg.cpp: In function ‘void __Pyx_ExceptionReset(PyObject*, PyObject*, PyObject*)’:
  src/dawg.cpp:21582:24: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
       tmp_type = tstate->exc_type;
                          ^~~~~~~~
                          curexc_type
  src/dawg.cpp:21583:25: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
       tmp_value = tstate->exc_value;
                           ^~~~~~~~~
                           curexc_value
  src/dawg.cpp:21584:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
       tmp_tb = tstate->exc_traceback;
                        ^~~~~~~~~~~~~
                        curexc_traceback
  src/dawg.cpp:21585:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
       tstate->exc_type = type;
               ^~~~~~~~
               curexc_type
  src/dawg.cpp:21586:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
       tstate->exc_value = value;
               ^~~~~~~~~
               curexc_value
  src/dawg.cpp:21587:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
       tstate->exc_traceback = tb;
               ^~~~~~~~~~~~~
               curexc_traceback
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for DAWG
  Running setup.py clean for DAWG
Failed to build DAWG
Installing collected packages: DAWG
  Running setup.py install for DAWG ... error
    ERROR: Complete output from command /home/conda/anaconda3/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-_lu0pouq/DAWG/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-6jwkhmli/install-record.txt --single-version-externally-managed --compile:
    ERROR: running install
    running build
    running build_ext
    building 'dawg' extension
    creating build
    creating build/temp.linux-x86_64-3.7
    creating build/temp.linux-x86_64-3.7/src
    creating build/temp.linux-x86_64-3.7/lib
    creating build/temp.linux-x86_64-3.7/lib/b64
    gcc -pthread -B /home/conda/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ilib -I/home/conda/anaconda3/include/python3.7m -c src/dawg.cpp -o build/temp.linux-x86_64-3.7/src/dawg.o
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    In file included from src/dawg.cpp:266:0:
    src/../lib/dawgdic/dictionary-builder.h: In member function ‘bool dawgdic::DictionaryBuilder::BuildDictionary(dawgdic::BaseType, dawgdic::BaseType)’:
    src/../lib/dawgdic/dictionary-builder.h:138:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if (dawg_.is_merging(dawg_child_index))
         ^~
    src/../lib/dawgdic/dictionary-builder.h:139:53: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
           link_table_.Insert(dawg_child_index, offset); {
                                                         ^
    src/dawg.cpp: In function ‘PyObject* __pyx_f_4dawg_9BytesDAWG_items(__pyx_obj_4dawg_BytesDAWG*, int, __pyx_opt_args_4dawg_9BytesDAWG_items*)’:
    src/dawg.cpp:11011:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (__pyx_t_10 = 0; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) {
                              ~~~~~~~~~~~^~~~~~~~~~~
    src/dawg.cpp: In function ‘PyObject* __pyx_gb_4dawg_9BytesDAWG_24generator2(__pyx_GeneratorObject*, PyObject*)’:
    src/dawg.cpp:11485:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
                             ~~~~~~~~~~^~~~~~~~~~~
    src/dawg.cpp: In function ‘PyObject* __pyx_f_4dawg_9BytesDAWG_keys(__pyx_obj_4dawg_BytesDAWG*, int, __pyx_opt_args_4dawg_9BytesDAWG_keys*)’:
    src/dawg.cpp:11814:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (__pyx_t_10 = 0; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) {
                              ~~~~~~~~~~~^~~~~~~~~~~
    src/dawg.cpp: In function ‘PyObject* __pyx_gb_4dawg_9BytesDAWG_29generator3(__pyx_GeneratorObject*, PyObject*)’:
    src/dawg.cpp:12222:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
                             ~~~~~~~~~~^~~~~~~~~~~
    src/dawg.cpp: In function ‘int __Pyx_GetException(PyObject**, PyObject**, PyObject**)’:
    src/dawg.cpp:21523:24: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
         tmp_type = tstate->exc_type;
                            ^~~~~~~~
                            curexc_type
    src/dawg.cpp:21524:25: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
         tmp_value = tstate->exc_value;
                             ^~~~~~~~~
                             curexc_value
    src/dawg.cpp:21525:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
         tmp_tb = tstate->exc_traceback;
                          ^~~~~~~~~~~~~
                          curexc_traceback
    src/dawg.cpp:21526:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
         tstate->exc_type = local_type;
                 ^~~~~~~~
                 curexc_type
    src/dawg.cpp:21527:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
         tstate->exc_value = local_value;
                 ^~~~~~~~~
                 curexc_value
    src/dawg.cpp:21528:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
         tstate->exc_traceback = local_tb;
                 ^~~~~~~~~~~~~
                 curexc_traceback
    src/dawg.cpp: In function ‘void __Pyx_ExceptionSwap(PyObject**, PyObject**, PyObject**)’:
    src/dawg.cpp:21550:24: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
         tmp_type = tstate->exc_type;
                            ^~~~~~~~
                            curexc_type
    src/dawg.cpp:21551:25: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
         tmp_value = tstate->exc_value;
                             ^~~~~~~~~
                             curexc_value
    src/dawg.cpp:21552:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
         tmp_tb = tstate->exc_traceback;
                          ^~~~~~~~~~~~~
                          curexc_traceback
    src/dawg.cpp:21553:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
         tstate->exc_type = *type;
                 ^~~~~~~~
                 curexc_type
    src/dawg.cpp:21554:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
         tstate->exc_value = *value;
                 ^~~~~~~~~
                 curexc_value
    src/dawg.cpp:21555:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
         tstate->exc_traceback = *tb;
                 ^~~~~~~~~~~~~
                 curexc_traceback
    src/dawg.cpp: In function ‘void __Pyx_ExceptionSave(PyObject**, PyObject**, PyObject**)’:
    src/dawg.cpp:21568:21: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
         *type = tstate->exc_type;
                         ^~~~~~~~
                         curexc_type
    src/dawg.cpp:21569:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
         *value = tstate->exc_value;
                          ^~~~~~~~~
                          curexc_value
    src/dawg.cpp:21570:19: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
         *tb = tstate->exc_traceback;
                       ^~~~~~~~~~~~~
                       curexc_traceback
    src/dawg.cpp: In function ‘void __Pyx_ExceptionReset(PyObject*, PyObject*, PyObject*)’:
    src/dawg.cpp:21582:24: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
         tmp_type = tstate->exc_type;
                            ^~~~~~~~
                            curexc_type
    src/dawg.cpp:21583:25: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
         tmp_value = tstate->exc_value;
                             ^~~~~~~~~
                             curexc_value
    src/dawg.cpp:21584:22: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
         tmp_tb = tstate->exc_traceback;
                          ^~~~~~~~~~~~~
                          curexc_traceback
    src/dawg.cpp:21585:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_type’; did you mean ‘curexc_type’?
         tstate->exc_type = type;
                 ^~~~~~~~
                 curexc_type
    src/dawg.cpp:21586:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_value’; did you mean ‘curexc_value’?
         tstate->exc_value = value;
                 ^~~~~~~~~
                 curexc_value
    src/dawg.cpp:21587:13: error: ‘PyThreadState {aka struct _ts}’ has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
         tstate->exc_traceback = tb;
                 ^~~~~~~~~~~~~
                 curexc_traceback
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command "/home/conda/anaconda3/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-_lu0pouq/DAWG/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-6jwkhmli/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-_lu0pouq/DAWG/

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