Difficulty building on alpine linux

[estechnical]

Hi,

I have just tried to build mavproxy on alpine, eg:

apk update && apk add python-pip python-dev gcc libxml2 libxml2-dev py-lxml libxslt libxslt-dev musl-dev
pip install MAVproxy

But I run into errors about conflicting functions

    mavnative/mavnative.c:322:13: error: conflicting types for '__assert_fail'
     extern void __assert_fail(const char *__assertion, const char *__file, unsigned int __line, const char *__function)
                 ^~~~~~~~~~~~~
    In file included from mavnative/mavnative.c:14:0:
    /usr/include/assert.h:19:16: note: previous declaration of '__assert_fail' was here
     _Noreturn void __assert_fail (const char *, const char *, int, const char *);
                    ^~~~~~~~~~~~~
    error: command 'gcc' failed with exit status 1

Any ideas what I should do to build this?

Many thanks, Ed

[peterbarker]

On Wed, 20 Dec 2017, Ed Simmons wrote:

I have just tried to build mavproxy on alpine, eg:

Which compiler version is this?

[estechnical]

I have tried to build this now with several versions of alpine. My latest attempt gets very similar results.

This time I tried using python 3 instead of 2.7.

    mavnative/mavnative.c: In function 'py_mavlink_parse_char':
    mavnative/mavnative.c:155:5: warning: enumeration value 'MAVLINK_PARSE_STATE_GOT_BAD_CRC1' not handled in switch [-Wswitch]
         switch (status->parse_state)
         ^~~~~~
    mavnative/mavnative.c: At top level:
    mavnative/mavnative.c:322:13: error: conflicting types for '__assert_fail'
     extern void __assert_fail(const char *__assertion, const char *__file, unsigned int __line, const char *__function)
                 ^~~~~~~~~~~~~
    In file included from mavnative/mavnative.c:14:0:
    /usr/include/assert.h:19:16: note: previous declaration of '__assert_fail' was here
     _Noreturn void __assert_fail (const char *, const char *, int, const char *);
                    ^~~~~~~~~~~~~
    mavnative/mavnative.c: In function 'msg_to_py':
    mavnative/mavnative.c:646:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(fnum = 0; fnum < info->num_fields && objValid; fnum++) {
                            ^
    error: command 'gcc' failed with exit status 1

/ # uname -a
Linux cdeffd623252 4.10.0-42-generic #46~16.04.1-Ubuntu SMP Mon Dec 4 15:57:59 UTC 2017 x86_64 Linux
/ # gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-alpine-linux-musl/6.4.0/lto-wrapper
Target: x86_64-alpine-linux-musl
Configured with: /home/buildozer/aports/main/gcc/src/gcc-6.4.0/configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --build=x86_64-alpine-linux-musl --host=x86_64-alpine-linux-musl --target=x86_64-alpine-linux-musl --with-pkgversion='Alpine 6.4.0' --enable-checking=release --disable-fixed-point --disable-libstdcxx-pch --disable-multilib --disable-nls --disable-werror --disable-symvers --enable-__cxa_atexit --enable-default-pie --enable-cloog-backend --enable-languages=c,c++,objc,java,fortran,ada --disable-libssp --disable-libmpx --disable-libmudflap --disable-libsanitizer --enable-shared --enable-threads --enable-tls --with-system-zlib --with-linker-hash-style=gnu
Thread model: posix
gcc version 6.4.0 (Alpine 6.4.0) 

[estechnical]

I think my previous error was just operator error, so I went right back to the start... Here's some more info: Using this basic dockerfile:

FROM python:2.7-alpine3.7
RUN apk update && apk add build-base libxml2-dev libxslt-dev
RUN pip install lxml
RUN pip install MAVproxy

I now get as far as pymavlink failing to build.

  running bdist_wheel
  running build
  running build_py
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/tmp/pip-build-meDpBw/pymavlink/setup.py", line 160, in <module>
      ext_modules = extensions
    File "/usr/local/lib/python2.7/site-packages/setuptools/__init__.py", line 129, in setup
      return distutils.core.setup(**attrs)
    File "/usr/local/lib/python2.7/distutils/core.py", line 151, in setup
      dist.run_commands()
    File "/usr/local/lib/python2.7/distutils/dist.py", line 953, in run_commands
      self.run_command(cmd)
    File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/usr/local/lib/python2.7/site-packages/wheel/bdist_wheel.py", line 204, in run
      self.run_command('build')
    File "/usr/local/lib/python2.7/distutils/cmd.py", line 326, in run_command
      self.distribution.run_command(command)
    File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/usr/local/lib/python2.7/distutils/command/build.py", line 127, in run
      self.run_command(cmd_name)
    File "/usr/local/lib/python2.7/distutils/cmd.py", line 326, in run_command
      self.distribution.run_command(command)
    File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-meDpBw/pymavlink/setup.py", line 93, in run
      generate_content()
    File "/tmp/pip-build-meDpBw/pymavlink/setup.py", line 21, in generate_content
      from generator import mavgen, mavparse
    File "generator/mavgen.py", line 12, in <module>
      from future import standard_library
  ImportError: No module named future
  
  ----------------------------------------
  Failed building wheel for pymavlink

And digging through all the logs it looks like the module future HAS been downloaded...

Collecting MAVproxy
  Downloading MAVProxy-1.6.2.tar.gz (6.6MB)
Collecting pymavlink>=1.1.73 (from MAVproxy)
  Downloading pymavlink-2.2.7.tar.gz (2.9MB)
Collecting pyserial>=3.0 (from MAVproxy)
  Downloading pyserial-3.4-py2.py3-none-any.whl (193kB)
Collecting future (from pymavlink>=1.1.73->MAVproxy)
  Downloading future-0.16.0.tar.gz (824kB)

/ # python --version
Python 2.7.14
/ # gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-alpine-linux-musl/6.4.0/lto-wrapper
Target: x86_64-alpine-linux-musl
Configured with: /home/buildozer/aports/main/gcc/src/gcc-6.4.0/configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --build=x86_64-alpine-linux-musl --host=x86_64-alpine-linux-musl --target=x86_64-alpine-linux-musl --with-pkgversion='Alpine 6.4.0' --enable-checking=release --disable-fixed-point --disable-libstdcxx-pch --disable-multilib --disable-nls --disable-werror --disable-symvers --enable-__cxa_atexit --enable-default-pie --enable-cloog-backend --enable-languages=c,c++,objc,java,fortran,ada --disable-libssp --disable-libmpx --disable-libmudflap --disable-libsanitizer --enable-shared --enable-threads --enable-tls --with-system-zlib --with-linker-hash-style=gnu
Thread model: posix
gcc version 6.4.0 (Alpine 6.4.0) 
/ # uname -a
Linux 0ff821c41d67 4.10.0-42-generic #46~16.04.1-Ubuntu SMP Mon Dec 4 15:57:59 UTC 2017 x86_64 Linux

[estechnical]

Does the version >=1.1.73 here

Collecting future (from pymavlink>=1.1.73->MAVproxy)
  Downloading future-0.16.0.tar.gz (824kB)

refer to pymavlink version or future? I'm not familiar with this, but to me it looks like the version of future is too old?

[peterbarker]

On Thu, 21 Dec 2017, Ed Simmons wrote:

Ok, I went right back to the start... Here's some more info: Using this basic dockerfile:

OK, the future thing is weird. Only thing I can currently think of there is some sort of python2 vs python3 issue.

The __assert_fail is happening because the function definitions are different.

The GCC you're using is more recent than any I have here; I'm seeing if artful happens to have the right one installed now....

Peter

[estechnical]

I also tried this dockerfile:

FROM python:2.7-alpine3.7
RUN apk update && apk add build-base libxml2-dev libxslt-dev
RUN apk add git
RUN cd /tmp && git clone https://github.com/ArduPilot/MAVProxy.git && cd MAVProxy && python setup.py install

also resulting in an error about future:

ImportError: No module named future

[peterbarker]

On Thu, 21 Dec 2017, Ed Simmons wrote:

FROM python:2.7-alpine3.7 RUN apk update && apk add build-base libxml2-dev libxslt-dev RUN apk add git RUN cd /tmp && git clone https://github.com/ArduPilot/MAVProxy.git && cd MA VProxy && python setup.py install

also resulting in an error about future:

ImportError: No module named future

Throw a "pip install future" and "pip install lxml" into that mix.

[estechnical]

I was trying that as your message arrived :)

FROM python:2.7-alpine3.6
RUN apk update && apk add build-base libxml2-dev libxslt-dev
RUN pip install future
RUN apk add git
RUN cd /tmp && git clone https://github.com/ArduPilot/MAVProxy.git && cd MAVProxy && python setup.py install

Gives this (the XML validation message repeats a lot!)

WARNING: Unable to load XML validator libraries. XML validation will not be performed
WARNING: Unable to load XML validator libraries. XML validation will not be performed
WARNING: Unable to load XML validator libraries. XML validation will not be performed
mavnative/mavnative.c: In function 'py_mavlink_parse_char':
mavnative/mavnative.c:155:5: warning: enumeration value 'MAVLINK_PARSE_STATE_GOT_BAD_CRC1' not handled in switch [-Wswitch]
     switch (status->parse_state)
     ^~~~~~
mavnative/mavnative.c: At top level:
mavnative/mavnative.c:322:13: error: conflicting types for '__assert_fail'
 extern void __assert_fail(const char *__assertion, const char *__file, unsigned int __line, const char *__function)
             ^~~~~~~~~~~~~
In file included from mavnative/mavnative.c:14:0:
/usr/include/assert.h:19:16: note: previous declaration of '__assert_fail' was here
 _Noreturn void __assert_fail (const char *, const char *, int, const char *);
                ^~~~~~~~~~~~~
error: Setup script exited with error: command 'gcc' failed with exit status 1

Can't be far off now, I will also try jumping back a version with the alpine base image.

[estechnical]

I think I'm stuck here, because of this:

mavnative/mavnative.c: In function 'py_mavlink_parse_char':
mavnative/mavnative.c:155:5: warning: enumeration value 'MAVLINK_PARSE_STATE_GOT_BAD_CRC1' not handled in switch [-Wswitch]
     switch (status->parse_state)
     ^~~~~~
mavnative/mavnative.c: At top level:
mavnative/mavnative.c:322:13: error: conflicting types for '__assert_fail'
 extern void __assert_fail(const char *__assertion, const char *__file, unsigned int __line, const char *__function)
             ^~~~~~~~~~~~~
In file included from mavnative/mavnative.c:14:0:
/usr/include/assert.h:19:16: note: previous declaration of '__assert_fail' was here
 _Noreturn void __assert_fail (const char *, const char *, int, const char *);
                ^~~~~~~~~~~~~
error: Setup script exited with error: command 'gcc' failed with exit status 1

The difference in assert_fail is puzzling...

[estechnical]

I should clarify, just in case it wasn't clear above, that all my recent testing has been using python 2.7.

Thanks for your help :)

[estechnical]

Turns out it is possible to build... no idea if this is a good idea but I found the inspiration here: https://github.com/gmyoungblood-parc/docker-alpine-ardupilot/blob/master/Dockerfile#L81

[russkel]

I ran into this as well. This is an apparent incompat issue with musl libc vs glibc. Anything prefixed with underscores is considered internal/private and not meant to be used as an external interface. Or this is what I am led to believe.

With out knowing anything about this call specifically, is there an actual documented call that can be used rather than this private one?

[sanmai-NL]

See https://alex-robenko.gitbook.io/bare_metal_cpp/basic_needs/assertion.