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Compiled python modules are linking to ubuntu's python library instead of pyenv's python version #82

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ckhoo opened this issue Nov 20, 2013 · 5 comments
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Compiled python modules are linking to ubuntu's python library instead of pyenv's python version #82

ckhoo opened this issue Nov 20, 2013 · 5 comments
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type: question

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@ckhoo
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ckhoo commented Nov 20, 2013

I am trying to "pyenv install 2.7.6" in ubuntu 12.04 (note this is a fresh ubuntu 12.04 install) and I am getting the following error.

ImportError: /opt/pyenv/versions/2.7.6/lib/python2.7/lib-dynload/_sqlite3.so: undefined symbol: _PyInt_AsInt

By doing "ldd _sqlite3.so" found in tmp build directory, I noticed the compiled sqlite3 module is linking to Ubuntu's default python2.7, which does not have _PyInt_AsInt symbol, since it is not python 2.7.6.

ldd /tmp/python-build.20131120202950.5916/Python-2.7.6/build/lib.linux-x86_64-2.7/_sqlite3.so
    linux-vdso.so.1 =>  (0x00007fff00dff000)
    libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 (0x00007f2da67bb000)
    libpython2.7.so.1.0 => /usr/lib/libpython2.7.so.1.0 (0x00007f2da62b8000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f2da609a000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f2da5cda000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f2da5ad6000)
    libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x00007f2da5877000)
    libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x00007f2da549c000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f2da5285000)
    libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f2da5081000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f2da4d85000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f2da4b6f000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f2da6c74000)

Is there some compilation flag I should set such that pyenv will compile sqlite3 module using the correct python library?

I am installing python 2.7.6 using the following:

export CONFIGURE_OPTS="--enable-shared --enable-unicode=ucs4";pyenv install 2.7.6

Thanks.
@yyuu
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yyuu commented Nov 21, 2013

You might need to set LD_LIBRARY_PATH on GNU/Linux if you give --enable-shared as CONFIGURE_OPTS. See also #66.

@ckhoo
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ckhoo commented Nov 25, 2013

Thanks Yuu. Your reference (#66) works for me.

@ckhoo
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ckhoo commented Nov 26, 2013

Adding a note for anyone who wants to --enable-shared like myself,

  1. I had pyenv inside /opt/pyenv. Therefore, I setup my shared library path like this: export LD_LIBRARY_PATH=/opt/pyenv/versions/2.7.6/lib:$LD_LIBRARY_PATH

  2. be sure that LD_LIBRARY_PATH is a permanent entry in ~/.bashrc and not just during pyenv install 2.7.6.

yyuu pushed a commit that referenced this issue Dec 20, 2013
Pass rpath to linker if --enable-shared was given (#65, #66, #82)
43212f6
@yyuu
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yyuu commented Dec 20, 2013

I pushed 43212f6 which will set rpath if --enable-shared was given in PYTHON_CONFIGURE_OPTS. With this fix, just passing --enable-shared will resolve the issue.

$ env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 2.7.5

@yyuu yyuu closed this as completed Dec 20, 2013
@lambdalisue
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👍
this commit saved me a lot. thanks

yyuu pushed a commit to yyuu/homebrew that referenced this issue Jan 10, 2014
pyenv v0.4.0-20140110
037ae9d 
Changes:

* pyenv: Reliably detect parent shell in `pyenv init` (pyenv/pyenv#93)
* pyenv: Import recent changes from rbenv 0.4.0
* pyenv: Import `bats` tests from rbenv 0.4.0
* python-build: Add new CPython releases candidates; 3.4.0b2
* python-build: Add ruby-build style patching feature (pyenv/pyenv#91)
* python-build: Set `RPATH` if `--enable-shared` was given
  (pyenv/pyenv#65, pyenv/pyenv#66, pyenv/pyenv#82)
* python-build: Update default setuptools version (2.0 -> 2.1)
* python-build: Update default pip version (1.4.1 -> 1.5)
* python-build: Activate friendly CPython during build if the one is not
  activated
* python-build: Fix broken install.sh
* python-build: Import recent changes from ruby-build v20131225.1
* version-ext-compat: Removed from default plugin. Please use
  [pyenv-version-ext](https://github.com/yyuu/pyenv-version-ext)
  instead.
yyuu pushed a commit to yyuu/homebrew that referenced this issue Jan 10, 2014
pyenv v0.4.0-20140110.1
333849a 
Changes:

* pyenv: Reliably detect parent shell in `pyenv init` (pyenv/pyenv#93)
* pyenv: Import recent changes from rbenv 0.4.0
* pyenv: Import `bats` tests from rbenv 0.4.0
* python-build: Add new CPython releases candidates; 3.4.0b2
* python-build: Add ruby-build style patching feature (pyenv/pyenv#91)
* python-build: Set `RPATH` if `--enable-shared` was given
  (pyenv/pyenv#65, pyenv/pyenv#66, pyenv/pyenv#82)
* python-build: Update default setuptools version (2.0 -> 2.1)
* python-build: Update default pip version (1.4.1 -> 1.5)
* python-build: Activate friendly CPython during build if the one is not
  activated
* python-build: Fix broken install.sh
* python-build: Import recent changes from ruby-build v20131225.1
* python-build: Fix build error of CPython 2.x on the platform where the
  `gcc` is llvm-gcc.
* version-ext-compat: Removed from default plugin. Please use
  [pyenv-version-ext](https://github.com/yyuu/pyenv-version-ext)
  instead.
@yyuu yyuu mentioned this issue Jan 10, 2014
Closed
yyuu pushed a commit to yyuu/homebrew that referenced this issue Jan 10, 2014
pyenv v0.4.0-20140110.1
28d3fa7 
Changes:

* pyenv: Reliably detect parent shell in `pyenv init` (pyenv/pyenv#93)
* pyenv: Import recent changes from rbenv 0.4.0
* pyenv: Import `bats` tests from rbenv 0.4.0
* python-build: Add new CPython releases candidates; 3.4.0b2
* python-build: Add ruby-build style patching feature (pyenv/pyenv#91)
* python-build: Set `RPATH` if `--enable-shared` was given
  (pyenv/pyenv#65, pyenv/pyenv#66, pyenv/pyenv#82)
* python-build: Update default setuptools version (2.0 -> 2.1)
* python-build: Update default pip version (1.4.1 -> 1.5)
* python-build: Activate friendly CPython during build if the one is not
  activated
* python-build: Fix broken install.sh
* python-build: Import recent changes from ruby-build v20131225.1
* python-build: Fix build error of CPython 2.x on the platform where the
  `gcc` is llvm-gcc.
* version-ext-compat: Removed from default plugin. Please use
  [pyenv-version-ext](https://github.com/yyuu/pyenv-version-ext)
  instead.
yyuu pushed a commit to yyuu/homebrew that referenced this issue Jan 10, 2014
pyenv v0.4.0-20140110.1
8b8bd5a 
Changes:

* pyenv: Reliably detect parent shell in `pyenv init` (pyenv/pyenv#93)
* pyenv: Import recent changes from rbenv 0.4.0
* pyenv: Import `bats` tests from rbenv 0.4.0
* python-build: Add new CPython releases candidates; 3.4.0b2
* python-build: Add ruby-build style patching feature (pyenv/pyenv#91)
* python-build: Set `RPATH` if `--enable-shared` was given
  (pyenv/pyenv#65, pyenv/pyenv#66, pyenv/pyenv#82)
* python-build: Update default setuptools version (2.0 -> 2.1)
* python-build: Update default pip version (1.4.1 -> 1.5)
* python-build: Activate friendly CPython during build if the one is not
  activated
* python-build: Fix broken install.sh
* python-build: Import recent changes from ruby-build v20131225.1
* python-build: Fix build error of CPython 2.x on the platform where the
  `gcc` is llvm-gcc.
* version-ext-compat: Removed from default plugin. Please use
  [pyenv-version-ext](https://github.com/yyuu/pyenv-version-ext)
  instead.
yyuu pushed a commit to yyuu/homebrew that referenced this issue Jan 23, 2014
pyenv v0.4.0-20140110.1
dacd599 
Changes:

* pyenv: Reliably detect parent shell in `pyenv init` (pyenv/pyenv#93)
* pyenv: Import recent changes from rbenv 0.4.0
* pyenv: Import `bats` tests from rbenv 0.4.0
* python-build: Add new CPython releases candidates; 3.4.0b2
* python-build: Add ruby-build style patching feature (pyenv/pyenv#91)
* python-build: Set `RPATH` if `--enable-shared` was given
  (pyenv/pyenv#65, pyenv/pyenv#66, pyenv/pyenv#82)
* python-build: Update default setuptools version (2.0 -> 2.1)
* python-build: Update default pip version (1.4.1 -> 1.5)
* python-build: Activate friendly CPython during build if the one is not
  activated
* python-build: Fix broken install.sh
* python-build: Import recent changes from ruby-build v20131225.1
* python-build: Fix build error of CPython 2.x on the platform where the
  `gcc` is llvm-gcc.
* version-ext-compat: Removed from default plugin. Please use
  [pyenv-version-ext](https://github.com/yyuu/pyenv-version-ext)
  instead.
yyuu pushed a commit to yyuu/homebrew that referenced this issue Jan 23, 2014
pyenv v0.4.0-20140110.1
992d9b9 
Changes:

* pyenv: Reliably detect parent shell in `pyenv init` (pyenv/pyenv#93)
* pyenv: Import recent changes from rbenv 0.4.0
* pyenv: Import `bats` tests from rbenv 0.4.0
* python-build: Add new CPython releases candidates; 3.4.0b2
* python-build: Add ruby-build style patching feature (pyenv/pyenv#91)
* python-build: Set `RPATH` if `--enable-shared` was given
  (pyenv/pyenv#65, pyenv/pyenv#66, pyenv/pyenv#82)
* python-build: Update default setuptools version (2.0 -> 2.1)
* python-build: Update default pip version (1.4.1 -> 1.5)
* python-build: Activate friendly CPython during build if the one is not
  activated
* python-build: Fix broken install.sh
* python-build: Import recent changes from ruby-build v20131225.1
* python-build: Fix build error of CPython 2.x on the platform where the
  `gcc` is llvm-gcc.
* version-ext-compat: Removed from default plugin. Please use
  [pyenv-version-ext](https://github.com/yyuu/pyenv-version-ext)
  instead.
MikeMcQuaid pushed a commit to Homebrew/legacy-homebrew that referenced this issue Jan 24, 2014
@MikeMcQuaid
pyenv 0.4.0-20140110.1
b399f01 
Changes:

* pyenv: Reliably detect parent shell in `pyenv init` (pyenv/pyenv#93)
* pyenv: Import recent changes from rbenv 0.4.0
* pyenv: Import `bats` tests from rbenv 0.4.0
* python-build: Add new CPython releases candidates; 3.4.0b2
* python-build: Add ruby-build style patching feature (pyenv/pyenv#91)
* python-build: Set `RPATH` if `--enable-shared` was given
  (pyenv/pyenv#65, pyenv/pyenv#66, pyenv/pyenv#82)
* python-build: Update default setuptools version (2.0 -> 2.1)
* python-build: Update default pip version (1.4.1 -> 1.5)
* python-build: Activate friendly CPython during build if the one is not
  activated
* python-build: Fix broken install.sh
* python-build: Import recent changes from ruby-build v20131225.1
* python-build: Fix build error of CPython 2.x on the platform where the
  `gcc` is llvm-gcc.
* version-ext-compat: Removed from default plugin. Please use
  [pyenv-version-ext](https://github.com/yyuu/pyenv-version-ext)
  instead.

Closes #25783.

Signed-off-by: Mike McQuaid <mike@mikemcquaid.com>
ehershey pushed a commit to ehershey/homebrew that referenced this issue Apr 4, 2014
@ehershey
pyenv 0.4.0-20140110.1
4634e68 
Changes:

* pyenv: Reliably detect parent shell in `pyenv init` (pyenv/pyenv#93)
* pyenv: Import recent changes from rbenv 0.4.0
* pyenv: Import `bats` tests from rbenv 0.4.0
* python-build: Add new CPython releases candidates; 3.4.0b2
* python-build: Add ruby-build style patching feature (pyenv/pyenv#91)
* python-build: Set `RPATH` if `--enable-shared` was given
  (pyenv/pyenv#65, pyenv/pyenv#66, pyenv/pyenv#82)
* python-build: Update default setuptools version (2.0 -> 2.1)
* python-build: Update default pip version (1.4.1 -> 1.5)
* python-build: Activate friendly CPython during build if the one is not
  activated
* python-build: Fix broken install.sh
* python-build: Import recent changes from ruby-build v20131225.1
* python-build: Fix build error of CPython 2.x on the platform where the
  `gcc` is llvm-gcc.
* version-ext-compat: Removed from default plugin. Please use
  [pyenv-version-ext](https://github.com/yyuu/pyenv-version-ext)
  instead.

Closes Homebrew#25783.

Signed-off-by: Mike McQuaid <mike@mikemcquaid.com>
@IgnacioRubioScola IgnacioRubioScola mentioned this issue May 22, 2017
Closed
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@yyuu @lambdalisue @ckhoo