protoc autogenerated files should not be in the git repository

fsaad commented 9 years ago

When running make, the following error message is thrown

[  6%] Building CXX object
src/CMakeFiles/distributions_shared.dir/io/schema.pb.cc.o In file included from
/distributions/src/io/schema.pb.cc:4:0:
distributions/src/../include/distributions/io/schema.pb.h:17:2: error: #error
This file was generated by an older version of protoc which is
incompatible with your Protocol Buffer headers Please regenerate this
file with a newer version of protoc.

distributions/src/../include/distributions/io/schema.pb.h:18:2: error: #error
This file was generated by an older version of protoc which is
incompatible with your Protocol Buffer headers Please regenerate this
file with a newer version of protoc.

/distributions/src/../include/distributions/io/schema.pb.h:19:2: error: #error
This file was generated by an older version of protoc which is
incompatible with your Protocol Buffer headers Please regenerate this
file with a newer version of protoc.

make[3]: *** [src/CMakeFiles/distributions_shared.dir/io/schema.pb.cc.o] Error 1
make[3]: Leaving directory `distributions/build/python' make[2]: ***
[src/CMakeFiles/distributions_shared.dir/all] Error 2 make[2]: Leaving directory
`distributions/build/python' make[1]: *** [all] Error 2 make[1]: Leaving
directory `distributions/build/python' make: *** [python_cc] Error 2

The solution is to remove the offending file, and rebuild schema.pb.h using make protobuf:

$ rm distributions/include/distributions/io/schema.pb.h
$ make protobuf

Now running make is successful.

fritzo commented 9 years ago

Feel free to submit a pr. You'll probably need to apt-get install protobuf-compiler in .travis.yml to make the build work on travis ci. https://github.com/posterior/distributions/blob/master/.travis.yml#L11

fsaad commented 7 years ago

This issue explains the failures happening on Travis with DISTRIBUTIONS_USE_PROTOBUF=1: https://travis-ci.org/posterior/distributions/jobs/297802278#L654

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by key 15866BAFD9BCC4F3C1E0DFC7D69548E1C17EAB57 uses weak digest algorithm (SHA1) travis_fold:start:git.checkout [0Ktravis_time:start:09dca95c [0K$ git clone --depth=50 --branch=2.2.1 https://github.com/posterior/distributions.git posterior/distributions Cloning into 'posterior/distributions'... remote: Counting objects: 1087, done.[K remote: Compressing objects: 0% (1/527) [K remote: Compressing objects: 1% (6/527) [K remote: Compressing objects: 2% (11/527) [K remote: Compressing objects: 3% (16/527) [K remote: Compressing objects: 4% (22/527) [K remote: Compressing objects: 5% (27/527) [K remote: Compressing objects: 6% (32/527) [K remote: Compressing objects: 7% (37/527) [K remote: Compressing objects: 8% (43/527) [K remote: Compressing objects: 9% (48/527) [K remote: Compressing objects: 10% (53/527) [K remote: Compressing objects: 11% (58/527) [K remote: Compressing objects: 12% (64/527) [K remote: Compressing objects: 13% (69/527) [K remote: Compressing objects: 14% (74/527) [K 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Note: checking out '9895f413e96681ff68b1aa4c5693b1385421394e'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b travis_time:end:09dca95c:start=1509942300056845581,finish=1509942300766065593,duration=709220012 [0K$ cd posterior/distributions $ git checkout -qf 2.2.1 travis_fold:end:git.checkout [0K [33;1mSetting environment variables from .travis.yml[0m $ export FLAVOR=_cc $ export DISTRIBUTIONS_USE_PROTOBUF=1 travis_time:start:02d38637 [0K$ source ~/virtualenv/python2.7_with_system_site_packages/bin/activate travis_time:end:02d38637:start=1509942300789750965,finish=1509942300796661104,duration=6910139 [0K$ python --version Python 2.7.6 $ pip --version pip 9.0.1 from /home/travis/virtualenv/python2.7_with_system_site_packages/local/lib/python2.7/site-packages (python 2.7) travis_fold:start:before_install.1 [0Ktravis_time:start:214ed71c [0K$ pip uninstall numpy -y || echo 'numpy not installed' Uninstalling numpy-1.13.1: Successfully uninstalled numpy-1.13.1 travis_time:end:214ed71c:start=1509942301387531675,finish=1509942301914607143,duration=527075468 [0Ktravis_fold:end:before_install.1 [0Ktravis_fold:start:before_install.2 [0Ktravis_time:start:1f0ea6fe [0K$ sudo add-apt-repository -y ppa:cython-dev/master-ppa gpg: keyring `/tmp/tmpbbvsj2tp/secring.gpg' created gpg: keyring `/tmp/tmpbbvsj2tp/pubring.gpg' created gpg: requesting key 6CA77592 from hkp server keyserver.ubuntu.com gpg: /tmp/tmpbbvsj2tp/trustdb.gpg: trustdb created gpg: key 6CA77592: public key "Launchpad PPA for Cython-dev" imported gpg: Total number processed: 1 gpg: imported: 1 (RSA: 1) OK travis_time:end:1f0ea6fe:start=1509942301919284233,finish=1509942304463991089,duration=2544706856 [0Ktravis_fold:end:before_install.2 [0Ktravis_fold:start:before_install.3 [0Ktravis_time:start:1846d640 [0K$ sudo apt-get update -qq W: http://dl.hhvm.com/ubuntu/dists/trusty/InRelease: Signature by key 36AEF64D0207E7EEE352D4875A16E7281BE7A449 uses weak digest algorithm (SHA1) W: http://ppa.launchpad.net/couchdb/stable/ubuntu/dists/trusty/Release.gpg: Signature by key 15866BAFD9BCC4F3C1E0DFC7D69548E1C17EAB57 uses weak digest algorithm (SHA1) travis_time:end:1846d640:start=1509942304468827416,finish=1509942308702620995,duration=4233793579 [0Ktravis_fold:end:before_install.3 [0Ktravis_fold:start:before_install.4 [0Ktravis_time:start:008589b4 [0K$ sudo apt-get install -qq cython python-numpy python-scipy Selecting previously unselected package libamd2.3.1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 92755 files and directories currently installed.) Preparing to unpack .../libamd2.3.1_1%3a4.2.1-3ubuntu1_amd64.deb ... Unpacking libamd2.3.1:amd64 (1:4.2.1-3ubuntu1) ... Selecting previously unselected package libcamd2.3.1:amd64. Preparing to unpack .../libcamd2.3.1_1%3a4.2.1-3ubuntu1_amd64.deb ... Unpacking libcamd2.3.1:amd64 (1:4.2.1-3ubuntu1) ... Selecting previously unselected package libccolamd2.8.0:amd64. Preparing to unpack .../libccolamd2.8.0_1%3a4.2.1-3ubuntu1_amd64.deb ... Unpacking libccolamd2.8.0:amd64 (1:4.2.1-3ubuntu1) ... Selecting previously unselected package libblas3. Preparing to unpack .../libblas3_1.2.20110419-7_amd64.deb ... Unpacking libblas3 (1.2.20110419-7) ... Selecting previously unselected package libcolamd2.8.0:amd64. Preparing to unpack .../libcolamd2.8.0_1%3a4.2.1-3ubuntu1_amd64.deb ... Unpacking libcolamd2.8.0:amd64 (1:4.2.1-3ubuntu1) ... Selecting previously unselected package libgfortran3:amd64. Preparing to unpack .../libgfortran3_4.8.4-2ubuntu1~14.04.3_amd64.deb ... Unpacking libgfortran3:amd64 (4.8.4-2ubuntu1~14.04.3) ... Selecting previously unselected package liblapack3. Preparing to unpack .../liblapack3_3.5.0-2ubuntu1_amd64.deb ... Unpacking liblapack3 (3.5.0-2ubuntu1) ... Selecting previously unselected package libcholmod2.1.2:amd64. Preparing to unpack .../libcholmod2.1.2_1%3a4.2.1-3ubuntu1_amd64.deb ... Unpacking libcholmod2.1.2:amd64 (1:4.2.1-3ubuntu1) ... Selecting previously unselected package libumfpack5.6.2:amd64. Preparing to unpack .../libumfpack5.6.2_1%3a4.2.1-3ubuntu1_amd64.deb ... Unpacking libumfpack5.6.2:amd64 (1:4.2.1-3ubuntu1) ... Selecting previously unselected package libwebp5:amd64. Preparing to unpack .../libwebp5_0.4.0-4_amd64.deb ... Unpacking libwebp5:amd64 (0.4.0-4) ... Selecting previously unselected package libwebpmux1:amd64. Preparing to unpack .../libwebpmux1_0.4.0-4_amd64.deb ... Unpacking libwebpmux1:amd64 (0.4.0-4) ... Selecting previously unselected package cython. Preparing to unpack .../cython_0.20.1+git90-g0e6e38e-1ubuntu2_amd64.deb ... Unpacking cython (0.20.1+git90-g0e6e38e-1ubuntu2) ... Selecting previously unselected package python-decorator. Preparing to unpack .../python-decorator_3.4.0-2build1_all.deb ... Unpacking python-decorator (3.4.0-2build1) ... Selecting previously unselected package python-pil. Preparing to unpack .../python-pil_2.3.0-1ubuntu3.4_amd64.deb ... Unpacking python-pil (2.3.0-1ubuntu3.4) ... Selecting previously unselected package python-imaging. Preparing to unpack .../python-imaging_2.3.0-1ubuntu3.4_all.deb ... Unpacking python-imaging (2.3.0-1ubuntu3.4) ... Selecting previously unselected package python-numpy. Preparing to unpack .../python-numpy_1%3a1.8.2-0ubuntu0.1_amd64.deb ... Unpacking python-numpy (1:1.8.2-0ubuntu0.1) ... Selecting previously unselected package python-scipy. Preparing to unpack .../python-scipy_0.13.3-1build1_amd64.deb ... Unpacking python-scipy (0.13.3-1build1) ... Processing triggers for man-db (2.6.7.1-1ubuntu1) ... Setting up libamd2.3.1:amd64 (1:4.2.1-3ubuntu1) ... Setting up libcamd2.3.1:amd64 (1:4.2.1-3ubuntu1) ... Setting up libccolamd2.8.0:amd64 (1:4.2.1-3ubuntu1) ... Setting up libblas3 (1.2.20110419-7) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libcolamd2.8.0:amd64 (1:4.2.1-3ubuntu1) ... Setting up libgfortran3:amd64 (4.8.4-2ubuntu1~14.04.3) ... Setting up liblapack3 (3.5.0-2ubuntu1) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libcholmod2.1.2:amd64 (1:4.2.1-3ubuntu1) ... Setting up libumfpack5.6.2:amd64 (1:4.2.1-3ubuntu1) ... Setting up libwebp5:amd64 (0.4.0-4) ... Setting up libwebpmux1:amd64 (0.4.0-4) ... Setting up cython (0.20.1+git90-g0e6e38e-1ubuntu2) ... Setting up python-decorator (3.4.0-2build1) ... Setting up python-pil (2.3.0-1ubuntu3.4) ... Setting up python-imaging (2.3.0-1ubuntu3.4) ... Setting up python-numpy (1:1.8.2-0ubuntu0.1) ... Setting up python-scipy (0.13.3-1build1) ... Processing triggers for libc-bin (2.19-0ubuntu6.13) ... travis_time:end:008589b4:start=1509942308706983081,finish=1509942316566287592,duration=7859304511 [0Ktravis_fold:end:before_install.4 [0Ktravis_fold:start:before_install.5 [0Ktravis_time:start:076f0e50 [0K$ sudo apt-get install libprotobuf-dev libeigen3-dev Reading package lists... 0% Reading package lists... 100% Reading package lists... Done Building dependency tree... 0% Building dependency tree... 0% Building dependency tree... 50% Building dependency tree... 50% Building dependency tree Reading state information... 0% Reading state information... 0% Reading state information... Done The following additional packages will be installed: libprotobuf-lite8 libprotobuf8 Suggested packages: libeigen3-doc libmrpt-dev The following NEW packages will be installed: libeigen3-dev libprotobuf-dev libprotobuf-lite8 libprotobuf8 0 upgraded, 4 newly installed, 0 to remove and 106 not upgraded. Need to get 1,264 kB of archives. After this operation, 8,447 kB of additional disk space will be used. 0% [Working] Get:1 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libprotobuf-lite8 amd64 2.5.0-9ubuntu1 [52.7 kB] 1% [1 libprotobuf-lite8 8,192 B/52.7 kB 16%] 8% [Working] Get:2 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libprotobuf8 amd64 2.5.0-9ubuntu1 [296 kB] 9% [2 libprotobuf8 8,042 B/296 kB 3%] 32% [Working] Get:3 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/universe amd64 libeigen3-dev all 3.2.0-8 [494 kB] 33% [3 libeigen3-dev 12.3 kB/494 kB 2%] 68% [Working] Get:4 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libprotobuf-dev amd64 2.5.0-9ubuntu1 [421 kB] 69% [4 libprotobuf-dev 7,496 B/421 kB 2%] 100% [Working] Fetched 1,264 kB in 0s (38.6 MB/s) Selecting previously unselected package libprotobuf-lite8:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 94736 files and directories currently installed.) Preparing to unpack .../libprotobuf-lite8_2.5.0-9ubuntu1_amd64.deb ... Unpacking libprotobuf-lite8:amd64 (2.5.0-9ubuntu1) ... Selecting previously unselected package libprotobuf8:amd64. Preparing to unpack .../libprotobuf8_2.5.0-9ubuntu1_amd64.deb ... Unpacking libprotobuf8:amd64 (2.5.0-9ubuntu1) ... Selecting previously unselected package libeigen3-dev. Preparing to unpack .../libeigen3-dev_3.2.0-8_all.deb ... Unpacking libeigen3-dev (3.2.0-8) ... Selecting previously unselected package libprotobuf-dev:amd64. Preparing to unpack .../libprotobuf-dev_2.5.0-9ubuntu1_amd64.deb ... Unpacking libprotobuf-dev:amd64 (2.5.0-9ubuntu1) ... Setting up libprotobuf-lite8:amd64 (2.5.0-9ubuntu1) ... Setting up libprotobuf8:amd64 (2.5.0-9ubuntu1) ... Setting up libeigen3-dev (3.2.0-8) ... Setting up libprotobuf-dev:amd64 (2.5.0-9ubuntu1) ... Processing triggers for libc-bin (2.19-0ubuntu6.13) ... travis_time:end:076f0e50:start=1509942316570843531,finish=1509942318067147477,duration=1496303946 [0Ktravis_fold:end:before_install.5 [0Ktravis_fold:start:before_install.6 [0Ktravis_time:start:1c600c2c [0K$ pip install cpplint Collecting cpplint /home/travis/virtualenv/python2.7_with_system_site_packages/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:318: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#snimissingwarning. SNIMissingWarning /home/travis/virtualenv/python2.7_with_system_site_packages/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning. InsecurePlatformWarning Downloading cpplint-1.3.0.tar.gz (71kB) [?25l [K 14% |████▋ | 10kB 3.8MB/s eta 0:00:01 [K 28% |█████████▏ | 20kB 1.9MB/s eta 0:00:01 [K 42% |█████████████▊ | 30kB 2.3MB/s eta 0:00:01 [K 57% |██████████████████▎ | 40kB 2.1MB/s eta 0:00:01 [K 71% |██████████████████████▉ | 51kB 2.3MB/s eta 0:00:01 [K 85% |███████████████████████████▍ | 61kB 2.7MB/s eta 0:00:01 [K 99% |████████████████████████████████| 71kB 3.0MB/s eta 0:00:01 [K 100% |████████████████████████████████| 81kB 2.7MB/s [?25hBuilding wheels for collected packages: cpplint Running setup.py bdist_wheel for cpplint ... [?25l- done [?25h Stored in directory: /home/travis/.cache/pip/wheels/f5/ba/81/00c14f0d4606c2f5de5273d2c35efa6355bb6fa6e5fa8ca104 Successfully built cpplint Installing collected packages: cpplint Successfully installed cpplint-1.3.0 travis_time:end:1c600c2c:start=1509942318071501283,finish=1509942319353283188,duration=1281781905 [0Ktravis_fold:end:before_install.6 [0Ktravis_fold:start:install.1 [0Ktravis_time:start:146a5d84 [0K$ make install$FLAVOR mkdir -p lib mkdir -p build/python cd build/python && cmake -DCMAKE_BUILD_TYPE=Python -DCMAKE_INSTALL_PREFIX=/home/travis/virtualenv/python2.7_with_system_site_packages ../.. -- The C compiler identification is GNU 4.8.4 -- The CXX compiler identification is GNU 4.8.4 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done CXX_FLAGS = -mfpmath=sse -fPIC -std=c++0x -Wall -Wextra -Werror -Wno-unused-parameter -Wno-strict-aliasing -O3 -msse4.1 -ffast-math -funsafe-math-optimizations -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Finding YEPPP library locate: can not stat () `/var/lib/mlocate/mlocate.db': No such file or directory -- missing YEPPP library -- Finding AMD LibM library locate: can not stat () `/var/lib/mlocate/mlocate.db': No such file or directory -- missing AMD LibM -- Finding Intel MKL library locate: can not stat () `/var/lib/mlocate/mlocate.db': No such file or directory -- missing Intel MKL -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found PROTOBUF: /usr/lib/x86_64-linux-gnu/libprotobuf.so -- Using Google Protocol Buffers -- Configuring done -- Generating done -- Build files have been written to: /home/travis/build/posterior/distributions/build/python cd build/python && make make[1]: Entering directory `/home/travis/build/posterior/distributions/build/python' make[2]: Entering directory `/home/travis/build/posterior/distributions/build/python' make[3]: Entering directory `/home/travis/build/posterior/distributions/build/python' [35m[1mScanning dependencies of target distributions_shared [0mmake[3]: Leaving directory `/home/travis/build/posterior/distributions/build/python' make[3]: Entering directory `/home/travis/build/posterior/distributions/build/python' [ 6%] [32mBuilding CXX object src/CMakeFiles/distributions_shared.dir/io/schema.pb.cc.o [0mIn file included from /home/travis/build/posterior/distributions/src/io/schema.pb.cc:4:0: /home/travis/build/posterior/distributions/src/../include/distributions/io/schema.pb.h:17:2: error: #error This file was generated by an older version of protoc which is #error This file was generated by an older version of protoc which is ^ /home/travis/build/posterior/distributions/src/../include/distributions/io/schema.pb.h:18:2: error: #error incompatible with your Protocol Buffer headers. Please #error incompatible with your Protocol Buffer headers. Please ^ /home/travis/build/posterior/distributions/src/../include/distributions/io/schema.pb.h:19:2: error: #error regenerate this file with a newer version of protoc. #error regenerate this file with a newer version of protoc. ^ make[3]: *** [src/CMakeFiles/distributions_shared.dir/io/schema.pb.cc.o] Error 1 make[3]: Leaving directory `/home/travis/build/posterior/distributions/build/python' make[2]: *** [src/CMakeFiles/distributions_shared.dir/all] Error 2 make[2]: Leaving directory `/home/travis/build/posterior/distributions/build/python' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/travis/build/posterior/distributions/build/python' make: *** [python_cc] Error 2 travis_time:end:146a5d84:start=1509942319357795598,finish=1509942321608630892,duration=2250835294 [0K [31;1mThe command "make install$FLAVOR" failed and exited with 2 during .[0m Your build has been stopped.

posterior / distributions

protoc autogenerated files should not be in the git repository #10