compilation fails on Quantum Mobile (1st attempt only) #11

chrisjsewell · 2020-11-27T15:10:52Z

I didn't notice this before but the compilation is failing, both locally and in the CI (https://github.com/marvel-nccr/quantum-mobile/runs/1287141082?check_suite_focus=true). But weirdly it passes on the second pass.

It looks possibly to do with: /usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'python_requires' which I believe is due to the version of setuptools being too old (but somehow being ok on the second pass!?).
So I will try making a PR to ensure that the setuptools version is up-to-date.

On a related note, the whole bespoke build/installation of pyyaml all feels a bit unnecessary TBH, it would be nice if you could just replace it with pip install pyyaml~=5.1.2

TASK [marvel-nccr.bigdft : Make bigdft executables] ***********************************************************************************************************************************
Friday 27 November 2020  14:32:05 +0100 (0:00:03.683)       1:53:45.092 ******* 
fatal: [vagrant-ssh]: FAILED! => changed=true 
  cmd:
  - /usr/bin/python3
  - ../bundler/jhbuild.py
  - --no-interact
  - --exit-on-error
  - --conditions=+babel
  - -f
  - ./buildrc
  - build
  - spred
  delta: '0:00:35.070966'
  end: '2020-11-27 14:32:28.218468'
  msg: non-zero return code
  rc: 1
  start: '2020-11-27 14:31:53.147502'
  stderr: |-
    configure: WARNING: unrecognized options: --disable-Werror, --with-ext-linalg
    configure: WARNING: unrecognized options: --disable-Werror, --with-ext-linalg
    ar: `u' modifier ignored since `D' is the default (see `U')
    /tmp/bigdft-suite/yaml/tests/run-emitter.c: In function print_output:
    /tmp/bigdft-suite/yaml/tests/run-emitter.c:208:28: warning: format %d expects argument of type int, but argument 2 has type size_t {aka long unsigned int} [-Wformat=]
         printf("#### (length: %d)\n", total_size);
                               ~^
                               %ld
    /tmp/bigdft-suite/yaml/tests/run-emitter.c:209:39: warning: format %d expects argument of type int, but argument 3 has type size_t {aka long unsigned int} [-Wformat=]
         printf("OUTPUT:\n%s#### (length: %d)\n", buffer, size);
                                          ~^
                                          %ld
    /tmp/bigdft-suite/yaml/tests/run-emitter.c: In function main:
    /tmp/bigdft-suite/yaml/tests/run-emitter.c:322:34: warning: format %d expects argument of type int, but argument 2 has type size_t {aka long unsigned int} [-Wformat=]
             printf("PASSED (length: %d)\n", written);
                                     ~^
                                     %ld
    /tmp/bigdft-suite/yaml/tests/run-dumper.c: In function print_output:
    /tmp/bigdft-suite/yaml/tests/run-dumper.c:182:28: warning: format %d expects argument of type int, but argument 2 has type size_t {aka long unsigned int} [-Wformat=]
         printf("#### (length: %d)\n", total_size);
                               ~^
                               %ld
    /tmp/bigdft-suite/yaml/tests/run-dumper.c:183:39: warning: format %d expects argument of type int, but argument 3 has type size_t {aka long unsigned int} [-Wformat=]
         printf("OUTPUT:\n%s#### (length: %d)\n", buffer, size);
                                          ~^
                                          %ld
    /tmp/bigdft-suite/yaml/tests/run-dumper.c: In function main:
    /tmp/bigdft-suite/yaml/tests/run-dumper.c:306:34: warning: format %d expects argument of type int, but argument 2 has type size_t {aka long unsigned int} [-Wformat=]
             printf("PASSED (length: %d)\n", written);
                                     ~^
                                     %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c: In function main:
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:123:60: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Reader error: %s: #%X at %d\n", parser.problem,
                                                               ~^
                                                               %ld
                             parser.problem_value, parser.problem_offset);
                                                   ~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:127:55: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Reader error: %s at %d\n", parser.problem,
                                                          ~^
                                                          %ld
                             parser.problem_offset);
                             ~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:134:61: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                                                ~^
                                                                %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:136:25:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:134:72: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                                                           ~^
                                                                           %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:136:53:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:134:33: warning: format %d expects argument of type int, but argument 7 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:137:41:
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:135:38: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                         ~^
                                         %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:134:33: warning: format %d expects argument of type int, but argument 8 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:138:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:135:49: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                                    ~^
                                                    %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:141:61: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n",
                                                                ~^
                                                                %ld
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:141:72: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n",
                                                                           ~^
                                                                           %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:143:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:149:60: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                                               ~^
                                                               %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:151:25:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:149:71: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                                                          ~^
                                                                          %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:151:53:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:149:33: warning: format %d expects argument of type int, but argument 7 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:152:41:
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:150:38: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                         ~^
                                         %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:149:33: warning: format %d expects argument of type int, but argument 8 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:153:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:150:49: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                                    ~^
                                                    %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:156:60: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n",
                                                               ~^
                                                               %ld
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:156:71: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n",
                                                                          ~^
                                                                          %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter.c:158:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c: In function main:
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:123:60: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Reader error: %s: #%X at %d\n", parser.problem,
                                                               ~^
                                                               %ld
                             parser.problem_value, parser.problem_offset);
                                                   ~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:127:55: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Reader error: %s at %d\n", parser.problem,
                                                          ~^
                                                          %ld
                             parser.problem_offset);
                             ~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:134:61: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                                                ~^
                                                                %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:136:25:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:134:72: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                                                           ~^
                                                                           %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:136:53:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:134:33: warning: format %d expects argument of type int, but argument 7 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:137:41:
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:135:38: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                         ~^
                                         %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:134:33: warning: format %d expects argument of type int, but argument 8 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:138:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:135:49: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                                    ~^
                                                    %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:141:61: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n",
                                                                ~^
                                                                %ld
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:141:72: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n",
                                                                           ~^
                                                                           %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:143:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:149:60: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                                               ~^
                                                               %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:151:25:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:149:71: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                                                          ~^
                                                                          %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:151:53:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:149:33: warning: format %d expects argument of type int, but argument 7 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:152:41:
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:150:38: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                         ~^
                                         %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:149:33: warning: format %d expects argument of type int, but argument 8 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:153:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:150:49: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                                    ~^
                                                    %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:156:60: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n",
                                                               ~^
                                                               %ld
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:156:71: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n",
                                                                          ~^
                                                                          %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:158:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:164:62: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Composer error: %s at line %d, column %d\n"
                                                                 ~^
                                                                 %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:166:25:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:164:73: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Composer error: %s at line %d, column %d\n"
                                                                            ~^
                                                                            %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:166:53:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:164:33: warning: format %d expects argument of type int, but argument 7 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Composer error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:167:41:
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:165:38: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                         ~^
                                         %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:164:33: warning: format %d expects argument of type int, but argument 8 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Composer error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:168:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:165:49: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                                    ~^
                                                    %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:171:62: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Composer error: %s at line %d, column %d\n",
                                                                 ~^
                                                                 %ld
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:171:73: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Composer error: %s at line %d, column %d\n",
                                                                            ~^
                                                                            %ld
    /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c:173:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c: In function main:
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1036:60: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Reader error: %s: #%X at %d\n", parser.problem,
                                                               ~^
                                                               %ld
                             parser.problem_value, parser.problem_offset);
                                                   ~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1040:55: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Reader error: %s at %d\n", parser.problem,
                                                          ~^
                                                          %ld
                             parser.problem_offset);
                             ~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1047:61: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                                                ~^
                                                                %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1049:25:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1047:72: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                                                           ~^
                                                                           %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1049:53:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1047:33: warning: format %d expects argument of type int, but argument 7 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1050:41:
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1048:38: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                         ~^
                                         %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1047:33: warning: format %d expects argument of type int, but argument 8 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1051:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1048:49: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                                    ~^
                                                    %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1054:61: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n",
                                                                ~^
                                                                %ld
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1054:72: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n",
                                                                           ~^
                                                                           %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1056:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1062:60: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                                               ~^
                                                               %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1064:25:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1062:71: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                                                          ~^
                                                                          %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1064:53:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1062:33: warning: format %d expects argument of type int, but argument 7 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1065:41:
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1063:38: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                         ~^
                                         %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1062:33: warning: format %d expects argument of type int, but argument 8 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1066:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1063:49: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                                    ~^
                                                    %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1069:60: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n",
                                                               ~^
                                                               %ld
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1069:71: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n",
                                                                          ~^
                                                                          %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor.c:1071:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c: In function main:
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:706:60: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Reader error: %s: #%X at %d\n", parser.problem,
                                                               ~^
                                                               %ld
                             parser.problem_value, parser.problem_offset);
                                                   ~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:710:55: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Reader error: %s at %d\n", parser.problem,
                                                          ~^
                                                          %ld
                             parser.problem_offset);
                             ~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:717:61: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                                                ~^
                                                                %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:719:25:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:717:72: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                                                           ~^
                                                                           %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:719:53:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:717:33: warning: format %d expects argument of type int, but argument 7 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:720:41:
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:718:38: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                         ~^
                                         %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:717:33: warning: format %d expects argument of type int, but argument 8 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:721:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:718:49: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                                    ~^
                                                    %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:724:61: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n",
                                                                ~^
                                                                %ld
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:724:72: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Scanner error: %s at line %d, column %d\n",
                                                                           ~^
                                                                           %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:726:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:732:60: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                                               ~^
                                                               %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:734:25:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:732:71: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                                                          ~^
                                                                          %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:734:53:
                             parser.context_mark.line+1, parser.context_mark.column+1,
                                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:732:33: warning: format %d expects argument of type int, but argument 7 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:735:41:
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:733:38: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                         ~^
                                         %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:732:33: warning: format %d expects argument of type int, but argument 8 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n"
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:736:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:733:49: note: format string is defined here
                             "%s at line %d, column %d\n", parser.context,
                                                    ~^
                                                    %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:739:60: warning: format %d expects argument of type int, but argument 4 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n",
                                                               ~^
                                                               %ld
                             parser.problem, parser.problem_mark.line+1,
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:739:71: warning: format %d expects argument of type int, but argument 5 has type size_t {aka long unsigned int} [-Wformat=]
                     fprintf(stderr, "Parser error: %s at line %d, column %d\n",
                                                                          ~^
                                                                          %ld
    /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c:741:25:
                             parser.problem_mark.column+1);
                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    libtool: install: warning: remember to run `libtool --finish /usr/local/lib'
    I: Deleting .la file: '/usr/local/_jhbuild/root-libyaml/usr/local/lib/libyaml.la'
    I: Moving temporary DESTDIR '/usr/local/_jhbuild/root-libyaml' into build prefix
    I: Install complete: 6 files copied
    x86_64-linux-gnu-gcc: error: ext/_yaml.c: No such file or directory
    x86_64-linux-gnu-gcc: fatal error: no input files
    compilation terminated.
    /usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'python_requires'
      warnings.warn(msg)
    Error compiling module, falling back to pure Python
    x86_64-linux-gnu-gcc: error: ext/_yaml.c: No such file or directory
    x86_64-linux-gnu-gcc: fatal error: no input files
    compilation terminated.
    /usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'python_requires'
      warnings.warn(msg)
    Error compiling module, falling back to pure Python
    I: Moving temporary DESTDIR '/usr/local/_jhbuild/root-PyYAML' into build prefix
    I: Install complete: 35 files copied
    configure.ac:42: installing 'config/compile'
    configure.ac:59: installing 'config/config.guess'
    configure.ac:59: installing 'config/config.sub'
    configure.ac:21: installing 'config/install-sh'
    configure.ac:21: installing 'config/missing'
    Makefile.am: installing './INSTALL'
    c-bindings/Makefile.am: installing 'config/depcomp'
    src/python/futile/Makefile.am:1: installing 'config/py-compile'
    wrappers/Makefile.am:16: warning: source file 'dgemmsy/dgemmsy.c' is in a subdirectory,
    wrappers/Makefile.am:16: but option 'subdir-objects' is disabled
    automake: warning: possible forward-incompatibility.
    automake: At least a source file is in a subdirectory, but the 'subdir-objects'
    automake: automake option hasn't been enabled.  For now, the corresponding output
    automake: object file(s) will be placed in the top-level directory.  However,
    automake: this behaviour will change in future Automake versions: they will
    automake: unconditionally cause object files to be placed in the same subdirectory
    automake: of the corresponding sources.
    automake: You are advised to start using 'subdir-objects' option throughout your
    automake: project, to avoid future incompatibilities.
    wrappers/Makefile.am:16: warning: source file 'dgemmsy/gemm_block_c.c' is in a subdirectory,
    wrappers/Makefile.am:16: but option 'subdir-objects' is disabled
    wrappers/Makefile.am:16: warning: source file 'dgemmsy/patterns.c' is in a subdirectory,
    wrappers/Makefile.am:16: but option 'subdir-objects' is disabled
    wrappers/Makefile.am:16: warning: source file 'dgemmsy/dgemmsy_utils.c' is in a subdirectory,
    wrappers/Makefile.am:16: but option 'subdir-objects' is disabled
    wrappers/Makefile.am:16: warning: source file 'dgemmsy/visitors.c' is in a subdirectory,
    wrappers/Makefile.am:16: but option 'subdir-objects' is disabled
    wrappers/Makefile.am:35: warning: source file 'fft/fft2d.f90' is in a subdirectory,
    wrappers/Makefile.am:35: but option 'subdir-objects' is disabled
    wrappers/Makefile.am:35: warning: source file 'fft/fft3d.f90' is in a subdirectory,
    wrappers/Makefile.am:35: but option 'subdir-objects' is disabled
    configure: WARNING: unrecognized options: --disable-Werror
    configure: error: newly created file is older than distributed files!
    Check your system clock
  stderr_lines: <omitted>
  stdout: |-
    patching file include/Makefile.am
    patching file include/Makefile.in
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for a thread-safe mkdir -p... /bin/mkdir -p
    checking for gawk... gawk
    checking whether make sets $(MAKE)... yes
    checking for gcc... gcc
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables...
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking for style of include used by make... GNU
    checking dependency style of gcc... gcc3
    checking how to run the C preprocessor... gcc -E
    checking whether ln -s works... yes
    checking whether make sets $(MAKE)... (cached) yes
    checking build system type... x86_64-unknown-linux-gnu
    checking host system type... x86_64-unknown-linux-gnu
    checking how to print strings... printf
    checking for a sed that does not truncate output... /bin/sed
    checking for grep that handles long lines and -e... /bin/grep
    checking for egrep... /bin/grep -E
    checking for fgrep... /bin/grep -F
    checking for ld used by gcc... /usr/bin/ld
    checking if the linker (/usr/bin/ld) is GNU ld... yes
    checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
    checking the name lister (/usr/bin/nm -B) interface... BSD nm
    checking the maximum length of command line arguments... 1572864
    checking whether the shell understands some XSI constructs... yes
    checking whether the shell understands "+="... yes
    checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
    checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
    checking for /usr/bin/ld option to reload object files... -r
    checking for objdump... objdump
    checking how to recognize dependent libraries... pass_all
    checking for dlltool... no
    checking how to associate runtime and link libraries... printf %s\n
    checking for ar... ar
    checking for archiver @FILE support... @
    checking for strip... strip
    checking for ranlib... ranlib
    checking command to parse /usr/bin/nm -B output from gcc object... ok
    checking for sysroot... no
    checking for mt... mt
    checking if mt is a manifest tool... no
    checking for ANSI C header files... yes
    checking for sys/types.h... yes
    checking for sys/stat.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for memory.h... yes
    checking for strings.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for unistd.h... yes
    checking for dlfcn.h... yes
    checking for objdir... .libs
    checking if gcc supports -fno-rtti -fno-exceptions... no
    checking for gcc option to produce PIC... -fPIC -DPIC
    checking if gcc PIC flag -fPIC -DPIC works... yes
    checking if gcc static flag -static works... yes
    checking if gcc supports -c -o file.o... yes
    checking if gcc supports -c -o file.o... (cached) yes
    checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
    checking whether -lc should be explicitly linked in... no
    checking dynamic linker characteristics... GNU/Linux ld.so
    checking how to hardcode library paths into programs... immediate
    checking whether stripping libraries is possible... yes
    checking if libtool supports shared libraries... yes
    checking whether to build shared libraries... yes
    checking whether to build static libraries... yes
    checking for doxygen... true
    checking for ANSI C header files... (cached) yes
    checking for stdlib.h... (cached) yes
    checking for an ANSI C-conforming const... yes
    checking for size_t... yes
    configure: creating ./config.status
    config.status: creating yaml-0.1.pc
    config.status: creating include/Makefile
    config.status: creating src/Makefile
    config.status: creating Makefile
    config.status: creating tests/Makefile
    config.status: creating win32/Makefile
    config.status: creating config.h
    config.status: executing depfiles commands
    config.status: executing libtool commands
    make  all-recursive
    make[1]: Entering directory '/tmp/bigdft-suite/build/yaml'
    Making all in include
    make[2]: Entering directory '/tmp/bigdft-suite/build/yaml/include'
    make[2]: Nothing to be done for 'all'.
    make[2]: Leaving directory '/tmp/bigdft-suite/build/yaml/include'
    Making all in src
    make[2]: Entering directory '/tmp/bigdft-suite/build/yaml/src'
    /bin/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT api.lo -MD -MP -MF .deps/api.Tpo -c -o api.lo /tmp/bigdft-suite/yaml/src/api.c
    /bin/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT reader.lo -MD -MP -MF .deps/reader.Tpo -c -o reader.lo /tmp/bigdft-suite/yaml/src/reader.c
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT reader.lo -MD -MP -MF .deps/reader.Tpo -c /tmp/bigdft-suite/yaml/src/reader.c  -fPIC -DPIC -o .libs/reader.o
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT api.lo -MD -MP -MF .deps/api.Tpo -c /tmp/bigdft-suite/yaml/src/api.c  -fPIC -DPIC -o .libs/api.o
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT reader.lo -MD -MP -MF .deps/reader.Tpo -c /tmp/bigdft-suite/yaml/src/reader.c -o reader.o >/dev/null 2>&1
    mv -f .deps/reader.Tpo .deps/reader.Plo
    /bin/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT scanner.lo -MD -MP -MF .deps/scanner.Tpo -c -o scanner.lo /tmp/bigdft-suite/yaml/src/scanner.c
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT scanner.lo -MD -MP -MF .deps/scanner.Tpo -c /tmp/bigdft-suite/yaml/src/scanner.c  -fPIC -DPIC -o .libs/scanner.o
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT api.lo -MD -MP -MF .deps/api.Tpo -c /tmp/bigdft-suite/yaml/src/api.c -o api.o >/dev/null 2>&1
    mv -f .deps/api.Tpo .deps/api.Plo
    /bin/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c -o parser.lo /tmp/bigdft-suite/yaml/src/parser.c
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c /tmp/bigdft-suite/yaml/src/parser.c  -fPIC -DPIC -o .libs/parser.o
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c /tmp/bigdft-suite/yaml/src/parser.c -o parser.o >/dev/null 2>&1
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT scanner.lo -MD -MP -MF .deps/scanner.Tpo -c /tmp/bigdft-suite/yaml/src/scanner.c -o scanner.o >/dev/null 2>&1
    mv -f .deps/parser.Tpo .deps/parser.Plo
    /bin/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT loader.lo -MD -MP -MF .deps/loader.Tpo -c -o loader.lo /tmp/bigdft-suite/yaml/src/loader.c
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT loader.lo -MD -MP -MF .deps/loader.Tpo -c /tmp/bigdft-suite/yaml/src/loader.c  -fPIC -DPIC -o .libs/loader.o
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT loader.lo -MD -MP -MF .deps/loader.Tpo -c /tmp/bigdft-suite/yaml/src/loader.c -o loader.o >/dev/null 2>&1
    mv -f .deps/loader.Tpo .deps/loader.Plo
    /bin/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT writer.lo -MD -MP -MF .deps/writer.Tpo -c -o writer.lo /tmp/bigdft-suite/yaml/src/writer.c
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT writer.lo -MD -MP -MF .deps/writer.Tpo -c /tmp/bigdft-suite/yaml/src/writer.c  -fPIC -DPIC -o .libs/writer.o
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT writer.lo -MD -MP -MF .deps/writer.Tpo -c /tmp/bigdft-suite/yaml/src/writer.c -o writer.o >/dev/null 2>&1
    mv -f .deps/writer.Tpo .deps/writer.Plo
    /bin/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT emitter.lo -MD -MP -MF .deps/emitter.Tpo -c -o emitter.lo /tmp/bigdft-suite/yaml/src/emitter.c
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT emitter.lo -MD -MP -MF .deps/emitter.Tpo -c /tmp/bigdft-suite/yaml/src/emitter.c  -fPIC -DPIC -o .libs/emitter.o
    mv -f .deps/scanner.Tpo .deps/scanner.Plo
    /bin/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT dumper.lo -MD -MP -MF .deps/dumper.Tpo -c -o dumper.lo /tmp/bigdft-suite/yaml/src/dumper.c
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT dumper.lo -MD -MP -MF .deps/dumper.Tpo -c /tmp/bigdft-suite/yaml/src/dumper.c  -fPIC -DPIC -o .libs/dumper.o
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT dumper.lo -MD -MP -MF .deps/dumper.Tpo -c /tmp/bigdft-suite/yaml/src/dumper.c -o dumper.o >/dev/null 2>&1
    libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/src -I.. -I/tmp/bigdft-suite/yaml/include -g -O2 -MT emitter.lo -MD -MP -MF .deps/emitter.Tpo -c /tmp/bigdft-suite/yaml/src/emitter.c -o emitter.o >/dev/null 2>&1
    mv -f .deps/dumper.Tpo .deps/dumper.Plo
    mv -f .deps/emitter.Tpo .deps/emitter.Plo
    /bin/bash ../libtool --tag=CC   --mode=link gcc  -g -O2 -release 0 -version-info 2:4:0 -L/usr/local/lib -L/usr/local/lib  -o libyaml.la -rpath /usr/local/lib api.lo reader.lo scanner.lo parser.lo loader.lo writer.lo emitter.lo dumper.lo
    libtool: link: gcc -shared  -fPIC -DPIC  .libs/api.o .libs/reader.o .libs/scanner.o .libs/parser.o .libs/loader.o .libs/writer.o .libs/emitter.o .libs/dumper.o   -L/usr/local/lib  -O2   -Wl,-soname -Wl,libyaml-0.so.2 -o .libs/libyaml-0.so.2.0.4
    libtool: link: (cd ".libs" && rm -f "libyaml-0.so.2" && ln -s "libyaml-0.so.2.0.4" "libyaml-0.so.2")
    libtool: link: (cd ".libs" && rm -f "libyaml.so" && ln -s "libyaml-0.so.2.0.4" "libyaml.so")
    libtool: link: ar cru .libs/libyaml.a  api.o reader.o scanner.o parser.o loader.o writer.o emitter.o dumper.o
    libtool: link: ranlib .libs/libyaml.a
    libtool: link: ( cd ".libs" && rm -f "libyaml.la" && ln -s "../libyaml.la" "libyaml.la" )
    make[2]: Leaving directory '/tmp/bigdft-suite/build/yaml/src'
    Making all in .
    make[2]: Entering directory '/tmp/bigdft-suite/build/yaml'
    make[2]: Leaving directory '/tmp/bigdft-suite/build/yaml'
    Making all in tests
    make[2]: Entering directory '/tmp/bigdft-suite/build/yaml/tests'
    gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/tests -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT run-scanner.o -MD -MP -MF .deps/run-scanner.Tpo -c -o run-scanner.o /tmp/bigdft-suite/yaml/tests/run-scanner.c
    gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/tests -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT run-parser.o -MD -MP -MF .deps/run-parser.Tpo -c -o run-parser.o /tmp/bigdft-suite/yaml/tests/run-parser.c
    mv -f .deps/run-scanner.Tpo .deps/run-scanner.Po
    mv -f .deps/run-parser.Tpo .deps/run-parser.Po
    gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/tests -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT run-loader.o -MD -MP -MF .deps/run-loader.Tpo -c -o run-loader.o /tmp/bigdft-suite/yaml/tests/run-loader.c
    gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/tests -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT run-emitter.o -MD -MP -MF .deps/run-emitter.Tpo -c -o run-emitter.o /tmp/bigdft-suite/yaml/tests/run-emitter.c
    mv -f .deps/run-loader.Tpo .deps/run-loader.Po
    gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/tests -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT run-dumper.o -MD -MP -MF .deps/run-dumper.Tpo -c -o run-dumper.o /tmp/bigdft-suite/yaml/tests/run-dumper.c
    mv -f .deps/run-emitter.Tpo .deps/run-emitter.Po
    gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/tests -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT example-reformatter.o -MD -MP -MF .deps/example-reformatter.Tpo -c -o example-reformatter.o /tmp/bigdft-suite/yaml/tests/example-reformatter.c
    mv -f .deps/run-dumper.Tpo .deps/run-dumper.Po
    mv -f .deps/example-reformatter.Tpo .deps/example-reformatter.Po
    gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/tests -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT example-reformatter-alt.o -MD -MP -MF .deps/example-reformatter-alt.Tpo -c -o example-reformatter-alt.o /tmp/bigdft-suite/yaml/tests/example-reformatter-alt.c
    gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/tests -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT example-deconstructor.o -MD -MP -MF .deps/example-deconstructor.Tpo -c -o example-deconstructor.o /tmp/bigdft-suite/yaml/tests/example-deconstructor.c
    mv -f .deps/example-reformatter-alt.Tpo .deps/example-reformatter-alt.Po
    gcc -DHAVE_CONFIG_H -I. -I/tmp/bigdft-suite/yaml/tests -I..  -I/tmp/bigdft-suite/yaml/include   -g -O2 -MT example-deconstructor-alt.o -MD -MP -MF .deps/example-deconstructor-alt.Tpo -c -o example-deconstructor-alt.o /tmp/bigdft-suite/yaml/tests/example-deconstructor-alt.c
    mv -f .deps/example-deconstructor.Tpo .deps/example-deconstructor.Po
    /bin/bash ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib -L/usr/local/lib  -o run-scanner run-scanner.o ../src/libyaml.la
    mv -f .deps/example-deconstructor-alt.Tpo .deps/example-deconstructor-alt.Po
    /bin/bash ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib -L/usr/local/lib  -o run-parser run-parser.o ../src/libyaml.la
    libtool: link: gcc -g -O2 -o .libs/run-scanner run-scanner.o  -L/usr/local/lib ../src/.libs/libyaml.so
    /bin/bash ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib -L/usr/local/lib  -o run-loader run-loader.o ../src/libyaml.la
    libtool: link: gcc -g -O2 -o .libs/run-parser run-parser.o  -L/usr/local/lib ../src/.libs/libyaml.so
    /bin/bash ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib -L/usr/local/lib  -o run-emitter run-emitter.o ../src/libyaml.la
    libtool: link: gcc -g -O2 -o .libs/run-loader run-loader.o  -L/usr/local/lib ../src/.libs/libyaml.so
    /bin/bash ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib -L/usr/local/lib  -o run-dumper run-dumper.o ../src/libyaml.la
    libtool: link: gcc -g -O2 -o .libs/run-emitter run-emitter.o  -L/usr/local/lib ../src/.libs/libyaml.so
    /bin/bash ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib -L/usr/local/lib  -o example-reformatter example-reformatter.o ../src/libyaml.la
    libtool: link: gcc -g -O2 -o .libs/run-dumper run-dumper.o  -L/usr/local/lib ../src/.libs/libyaml.so
    /bin/bash ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib -L/usr/local/lib  -o example-reformatter-alt example-reformatter-alt.o ../src/libyaml.la
    libtool: link: gcc -g -O2 -o .libs/example-reformatter example-reformatter.o  -L/usr/local/lib ../src/.libs/libyaml.so
    /bin/bash ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib -L/usr/local/lib  -o example-deconstructor example-deconstructor.o ../src/libyaml.la
    libtool: link: gcc -g -O2 -o .libs/example-reformatter-alt example-reformatter-alt.o  -L/usr/local/lib ../src/.libs/libyaml.so
    libtool: link: gcc -g -O2 -o .libs/example-deconstructor example-deconstructor.o  -L/usr/local/lib ../src/.libs/libyaml.so
    /bin/bash ../libtool --tag=CC   --mode=link gcc  -g -O2  -L/usr/local/lib -L/usr/local/lib  -o example-deconstructor-alt example-deconstructor-alt.o ../src/libyaml.la
    libtool: link: gcc -g -O2 -o .libs/example-deconstructor-alt example-deconstructor-alt.o  -L/usr/local/lib ../src/.libs/libyaml.so
    make[2]: Leaving directory '/tmp/bigdft-suite/build/yaml/tests'
    Making all in win32
    make[2]: Entering directory '/tmp/bigdft-suite/build/yaml/win32'
    make[2]: Nothing to be done for 'all'.
    make[2]: Leaving directory '/tmp/bigdft-suite/build/yaml/win32'
    make[1]: Leaving directory '/tmp/bigdft-suite/build/yaml'
    Making install in include
    make[1]: Entering directory '/tmp/bigdft-suite/build/yaml/include'
    make[2]: Entering directory '/tmp/bigdft-suite/build/yaml/include'
    make[2]: Nothing to be done for 'install-exec-am'.
    test -z "/usr/local/include" || /bin/mkdir -p "/usr/local/_jhbuild/root-libyaml/usr/local/include"
     /usr/bin/install -c -m 644  /tmp/bigdft-suite/yaml/include/yaml.h '/usr/local/_jhbuild/root-libyaml/usr/local/include/.'
    make[2]: Leaving directory '/tmp/bigdft-suite/build/yaml/include'
    make[1]: Leaving directory '/tmp/bigdft-suite/build/yaml/include'
    Making install in src
    make[1]: Entering directory '/tmp/bigdft-suite/build/yaml/src'
    make[2]: Entering directory '/tmp/bigdft-suite/build/yaml/src'
    test -z "/usr/local/lib" || /bin/mkdir -p "/usr/local/_jhbuild/root-libyaml/usr/local/lib"
     /bin/bash ../libtool   --mode=install /usr/bin/install -c   libyaml.la '/usr/local/_jhbuild/root-libyaml/usr/local/lib'
    libtool: install: /usr/bin/install -c .libs/libyaml-0.so.2.0.4 /usr/local/_jhbuild/root-libyaml/usr/local/lib/libyaml-0.so.2.0.4
    libtool: install: (cd /usr/local/_jhbuild/root-libyaml/usr/local/lib && { ln -s -f libyaml-0.so.2.0.4 libyaml-0.so.2 || { rm -f libyaml-0.so.2 && ln -s libyaml-0.so.2.0.4 libyaml-0.so.2; }; })
    libtool: install: (cd /usr/local/_jhbuild/root-libyaml/usr/local/lib && { ln -s -f libyaml-0.so.2.0.4 libyaml.so || { rm -f libyaml.so && ln -s libyaml-0.so.2.0.4 libyaml.so; }; })
    libtool: install: /usr/bin/install -c .libs/libyaml.lai /usr/local/_jhbuild/root-libyaml/usr/local/lib/libyaml.la
    libtool: install: /usr/bin/install -c .libs/libyaml.a /usr/local/_jhbuild/root-libyaml/usr/local/lib/libyaml.a
    libtool: install: chmod 644 /usr/local/_jhbuild/root-libyaml/usr/local/lib/libyaml.a
    libtool: install: ranlib /usr/local/_jhbuild/root-libyaml/usr/local/lib/libyaml.a
    make[2]: Nothing to be done for 'install-data-am'.
    make[2]: Leaving directory '/tmp/bigdft-suite/build/yaml/src'
    make[1]: Leaving directory '/tmp/bigdft-suite/build/yaml/src'
    Making install in .
    make[1]: Entering directory '/tmp/bigdft-suite/build/yaml'
    make[2]: Entering directory '/tmp/bigdft-suite/build/yaml'
    make[2]: Nothing to be done for 'install-exec-am'.
    test -z "/usr/local/lib/pkgconfig" || /bin/mkdir -p "/usr/local/_jhbuild/root-libyaml/usr/local/lib/pkgconfig"
     /usr/bin/install -c -m 644 yaml-0.1.pc '/usr/local/_jhbuild/root-libyaml/usr/local/lib/pkgconfig'
    make[2]: Leaving directory '/tmp/bigdft-suite/build/yaml'
    make[1]: Leaving directory '/tmp/bigdft-suite/build/yaml'
    Making install in tests
    make[1]: Entering directory '/tmp/bigdft-suite/build/yaml/tests'
    make[2]: Entering directory '/tmp/bigdft-suite/build/yaml/tests'
    make[2]: Nothing to be done for 'install-exec-am'.
    make[2]: Nothing to be done for 'install-data-am'.
    make[2]: Leaving directory '/tmp/bigdft-suite/build/yaml/tests'
    make[1]: Leaving directory '/tmp/bigdft-suite/build/yaml/tests'
    Making install in win32
    make[1]: Entering directory '/tmp/bigdft-suite/build/yaml/win32'
    make[2]: Entering directory '/tmp/bigdft-suite/build/yaml/win32'
    make[2]: Nothing to be done for 'install-exec-am'.
    make[2]: Nothing to be done for 'install-data-am'.
    make[2]: Leaving directory '/tmp/bigdft-suite/build/yaml/win32'
    make[1]: Leaving directory '/tmp/bigdft-suite/build/yaml/win32'
    running build
    running build_py
    creating /tmp/bigdft-suite/build/PyYAML
    creating /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6
    creating /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/error.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/events.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/scanner.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/reader.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/loader.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/serializer.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/cyaml.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/dumper.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/tokens.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/parser.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/resolver.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/composer.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/emitter.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/nodes.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/__init__.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/representer.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    copying lib3/yaml/constructor.py -> /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml
    running build_ext
    building '_yaml' extension
    creating /tmp/bigdft-suite/build/PyYAML/temp.linux-x86_64-3.6
    creating /tmp/bigdft-suite/build/PyYAML/temp.linux-x86_64-3.6/ext
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/bigdft-suite/build/install/include -I/usr/include/python3.6m -c ext/_yaml.c -o /tmp/bigdft-suite/build/PyYAML/temp.linux-x86_64-3.6/ext/_yaml.o
    running build
    running build_py
    running build_ext
    building '_yaml' extension
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c ext/_yaml.c -o /tmp/bigdft-suite/build/PyYAML/temp.linux-x86_64-3.6/ext/_yaml.o
    running install
    running install_lib
    creating /usr/local/_jhbuild/root-PyYAML/usr
    creating /usr/local/_jhbuild/root-PyYAML/usr/local
    creating /usr/local/_jhbuild/root-PyYAML/usr/local/lib
    creating /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6
    creating /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages
    creating /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/error.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/events.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/scanner.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/reader.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/loader.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/serializer.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/cyaml.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/dumper.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/tokens.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/parser.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/resolver.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/composer.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/emitter.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/nodes.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/__init__.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/representer.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    copying /tmp/bigdft-suite/build/PyYAML/lib.linux-x86_64-3.6/yaml/constructor.py -> /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/error.py to error.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/events.py to events.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/scanner.py to scanner.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/reader.py to reader.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/loader.py to loader.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/serializer.py to serializer.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/cyaml.py to cyaml.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/dumper.py to dumper.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/tokens.py to tokens.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/parser.py to parser.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/resolver.py to resolver.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/composer.py to composer.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/emitter.py to emitter.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/nodes.py to nodes.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/__init__.py to __init__.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/representer.py to representer.cpython-36.pyc
    byte-compiling /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/yaml/constructor.py to constructor.cpython-36.pyc
    running install_egg_info
    Writing /usr/local/_jhbuild/root-PyYAML/usr/local/lib/python3.6/dist-packages/PyYAML-5.1.2-py3.6.egg-info
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... *** Checking out libyaml *** [1/14]
    gzip -dc "/tmp/bigdft-suite/yaml-0.1.6.tar.gz" | tar xf -
    *** Applying patch yaml-doxygen.patch *** [1/14]
    patch -p0 < "/tmp/bigdft-suite/yaml-doxygen.patch"
    *** Applying patch yaml-doxygen-in.patch *** [1/14]
    patch -p0 < "/tmp/bigdft-suite/yaml-doxygen-in.patch"
    *** Configuring libyaml *** [1/14]
    /tmp/bigdft-suite/yaml/configure --prefix /usr/local --disable-Werror   "FC=mpifort" "CC=gcc" "FCFLAGS=-O2 -Wno-error -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow -fopenmp -m64 -g -Wl,--no-as-needed -ldl" "--with-ext-linalg=-lblacs-openmpi -lblacsF77init-openmpi -llapack -lblas -lyaml -lrt -lblacs-openmpi -lblacsF77init-openmpi -llapack -lblas -Wl,--no-as-needed -ldl"   LDFLAGS="-L/usr/local/lib -L/usr/local/lib " C_INCLUDE_PATH="/usr/local/include" PKG_CONFIG_PATH="/usr/local/lib/pkgconfig:/usr/local/share/pkgconfig:/usr/lib/pkgconfig:/usr/share/pkgconfig"
    *** Building libyaml *** [1/14]
    make -j 2
    *** Installing libyaml *** [1/14]
    make DESTDIR=/usr/local/_jhbuild/root-libyaml install
    *** Checking out PyYAML *** [2/14]
    gzip -dc "/tmp/bigdft-suite/PyYAML-5.1.2.tar.gz" | tar xf -
    *** Building PyYAML *** [2/14]
    python3 setup.py build --build-base /tmp/bigdft-suite/build/PyYAML build_ext -I/tmp/bigdft-suite/build/install/include -L/tmp/bigdft-suite/build/install/lib --rpath=/tmp/bigdft-suite/build/install/lib
    *** Installing PyYAML *** [2/14]
    python3 setup.py build --build-base /tmp/bigdft-suite/build/PyYAML install --prefix /usr/local --root /usr/local/_jhbuild/root-PyYAML
    *** Checking out futile *** [3/14]
    *** Configuring futile *** [3/14]
    autoreconf -fi
    /tmp/bigdft-suite/futile/configure --prefix /usr/local --disable-Werror   "FC=mpifort" "CC=gcc" "FCFLAGS=-O2 -Wno-error -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow -fopenmp -m64 -g -Wl,--no-as-needed -ldl" "--with-ext-linalg=-lblacs-openmpi -lblacsF77init-openmpi -llapack -lblas -lyaml -lrt -lblacs-openmpi -lblacsF77init-openmpi -llapack -lblas -Wl,--no-as-needed -ldl"   LDFLAGS="-L/usr/local/lib -L/usr/local/lib " C_INCLUDE_PATH="/usr/local/include" PKG_CONFIG_PATH="/usr/local/lib/pkgconfig:/usr/local/share/pkgconfig:/usr/lib/pkgconfig:/usr/share/pkgconfig"
  stdout_lines: <omitted>

The text was updated successfully, but these errors were encountered:

adegomme · 2020-11-28T11:30:00Z

Actually this error on yaml should be harmless I think, it keeps going with the python version it found (but yes, it might still be better with setuptools).

Checking quickly in the logs of the linked build, I see that messages
make: Warning: File '/tmp/bigdft-suite/futile/Makefile.in' has modification time 5.3 s in the future
configure: error: newly created file is older than distributed files!

This seems to be the failing point ...
It looks like there is some time discrepancy in the clocks of the guest vm and the host ? so make is confused and does not know which files to build or not... And I guess that at the second attempt, it's more than 5s later when it reaches this point, so it's fine this time ?

I found some sources saying that virtualbox is subject to drifts, for example when the host is suspended for a while, the guest time is out of sync.
It looks like virtualbox resynchronizes the time every 20 minutes by default, but this setting can be changed to something like 10 seconds, there are some options here for vagrant as well https://stackoverflow.com/questions/19490652/how-to-sync-time-on-host-wake-up-within-virtualbox

I'll see if I can reproduce this behaviour elsewhere

chrisjsewell · 2020-11-28T11:35:40Z

Thanks for the analysis, I guess as at least a temporary fix we can add a retry to the make task

adegomme · 2020-11-28T13:56:55Z

I published v1.3.5 with a retry attempt if the build fails.

chrisjsewell · 2020-11-28T14:02:39Z

Thanks but... I'm going to be a bit of a stickler here and ask can you please adhere to the formal PR and review process for making these changes 😬

In #11 it was found that the compilation can fail on VirtualBox, potentially due to a discrepancy in clocks (when checking modified times of files). As a preliminary fix, we add a retry to the compilation.

adegomme · 2020-11-30T08:46:30Z

Indeed, I'll try to do it properly from now on. Thanks for the other changes.

adegomme added a commit that referenced this issue Nov 28, 2020

add retries in bigdft build to see if it helps with #11

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compilation fails on Quantum Mobile (1st attempt only) #11

compilation fails on Quantum Mobile (1st attempt only) #11

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compilation fails on Quantum Mobile (1st attempt only) #11

compilation fails on Quantum Mobile (1st attempt only) #11

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