Installing lxml with pip in virtualenv Ubuntu 12.10 error: command 'gcc' failed with exit status 4

Question:

I’m having the following error when trying to run “pip install lxml” into a virtualenv in Ubuntu 12.10 x64. I have Python 2.7.

I have seen other related questions here about the same problem and tried installing python-dev, libxml2-dev and libxslt1-dev.

Please take a look of the traceback from the moment I tip the command to the moment when the error occurs.

Downloading/unpacking lxml
  Running setup.py egg_info for package lxml
    /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'bugtrack_url'
      warnings.warn(msg)
    Building lxml version 3.1.2.
    Building without Cython.
    Using build configuration of libxslt 1.1.26
    Building against libxml2/libxslt in the following directory: /usr/lib

    warning: no files found matching '*.txt' under directory 'src/lxml/tests'
Installing collected packages: lxml
  Running setup.py install for lxml
    /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'bugtrack_url'
      warnings.warn(msg)
    Building lxml version 3.1.2.
    Building without Cython.
    Using build configuration of libxslt 1.1.26
    Building against libxml2/libxslt in the following directory: /usr/lib
    building 'lxml.etree' extension
    gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/libxml2 -I/home/admin/.virtualenvs/dev.actualito.com/build/lxml/src/lxml/includes -I/usr/include/python2.7 -c src/lxml/lxml.etree.c -o build/temp.linux-x86_64-2.7/src/lxml/lxml.etree.o
    src/lxml/lxml.etree.c: In function '__pyx_f_4lxml_5etree__getFilenameForFile':
    src/lxml/lxml.etree.c:26851:7: warning: variable '__pyx_clineno' set but not used [-Wunused-but-set-variable]
    src/lxml/lxml.etree.c:26850:15: warning: variable '__pyx_filename' set but not used [-Wunused-but-set-variable]
    src/lxml/lxml.etree.c:26849:7: warning: variable '__pyx_lineno' set but not used [-Wunused-but-set-variable]
    src/lxml/lxml.etree.c: In function '__pyx_pf_4lxml_5etree_4XSLT_18__call__':
    src/lxml/lxml.etree.c:138273:81: warning: passing argument 1 of '__pyx_f_4lxml_5etree_12_XSLTContext__copy' from incompatible pointer type [enabled by default]
    src/lxml/lxml.etree.c:136229:52: note: expected 'struct __pyx_obj_4lxml_5etree__XSLTContext *' but argument is of type 'struct __pyx_obj_4lxml_5etree__BaseContext *'
    src/lxml/lxml.etree.c: In function '__pyx_f_4lxml_5etree__copyXSLT':
    src/lxml/lxml.etree.c:139667:79: warning: passing argument 1 of '__pyx_f_4lxml_5etree_12_XSLTContext__copy' from incompatible pointer type [enabled by default]
    src/lxml/lxml.etree.c:136229:52: note: expected 'struct __pyx_obj_4lxml_5etree__XSLTContext *' but argument is of type 'struct __pyx_obj_4lxml_5etree__BaseContext *'
    src/lxml/lxml.etree.c: At top level:
    src/lxml/lxml.etree.c:12384:13: warning: '__pyx_f_4lxml_5etree_displayNode' defined but not used [-Wunused-function]
    gcc: internal compiler error: Killed (program cc1)
    Please submit a full bug report,
    with preprocessed source if appropriate.
    See  for instructions.
    error: command 'gcc' failed with exit status 4
    Complete output from command /home/admin/.virtualenvs/dev.actualito.com/bin/python -c "import setuptools;__file__='/home/admin/.virtualenvs/dev.actualito.com/build/lxml/setup.py';exec(compile(open(__file__).read().replace('rn', 'n'), __file__, 'exec'))" install --record /tmp/pip-asDtN5-record/install-record.txt --single-version-externally-managed --install-headers /home/admin/.virtualenvs/dev.actualito.com/include/site/python2.7:
    /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'bugtrack_url'

  warnings.warn(msg)

Building lxml version 3.1.2.

Building without Cython.

Using build configuration of libxslt 1.1.26

Building against libxml2/libxslt in the following directory: /usr/lib

running install

running build

running build_py

copying src/lxml/includes/lxml-version.h -> build/lib.linux-x86_64-2.7/lxml/includes

running build_ext

building 'lxml.etree' extension

gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/libxml2 -I/home/admin/.virtualenvs/dev.actualito.com/build/lxml/src/lxml/includes -I/usr/include/python2.7 -c src/lxml/lxml.etree.c -o build/temp.linux-x86_64-2.7/src/lxml/lxml.etree.o

src/lxml/lxml.etree.c: In function '__pyx_f_4lxml_5etree__getFilenameForFile':

src/lxml/lxml.etree.c:26851:7: warning: variable '__pyx_clineno' set but not used [-Wunused-but-set-variable]

src/lxml/lxml.etree.c:26850:15: warning: variable '__pyx_filename' set but not used [-Wunused-but-set-variable]

src/lxml/lxml.etree.c:26849:7: warning: variable '__pyx_lineno' set but not used [-Wunused-but-set-variable]

src/lxml/lxml.etree.c: In function '__pyx_pf_4lxml_5etree_4XSLT_18__call__':

src/lxml/lxml.etree.c:138273:81: warning: passing argument 1 of '__pyx_f_4lxml_5etree_12_XSLTContext__copy' from incompatible pointer type [enabled by default]

src/lxml/lxml.etree.c:136229:52: note: expected 'struct __pyx_obj_4lxml_5etree__XSLTContext *' but argument is of type 'struct __pyx_obj_4lxml_5etree__BaseContext *'

src/lxml/lxml.etree.c: In function '__pyx_f_4lxml_5etree__copyXSLT':

src/lxml/lxml.etree.c:139667:79: warning: passing argument 1 of '__pyx_f_4lxml_5etree_12_XSLTContext__copy' from incompatible pointer type [enabled by default]

src/lxml/lxml.etree.c:136229:52: note: expected 'struct __pyx_obj_4lxml_5etree__XSLTContext *' but argument is of type 'struct __pyx_obj_4lxml_5etree__BaseContext *'

src/lxml/lxml.etree.c: At top level:

src/lxml/lxml.etree.c:12384:13: warning: '__pyx_f_4lxml_5etree_displayNode' defined but not used [-Wunused-function]

gcc: internal compiler error: Killed (program cc1)

Please submit a full bug report,

with preprocessed source if appropriate.

See  for instructions.

error: command 'gcc' failed with exit status 4

----------------------------------------
Command /home/admin/.virtualenvs/dev.actualito.com/bin/python -c "import setuptools;__file__='/home/admin/.virtualenvs/dev.actualito.com/build/lxml/setup.py';exec(compile(open(__file__).read().replace('rn', 'n'), __file__, 'exec'))" install --record /tmp/pip-asDtN5-record/install-record.txt --single-version-externally-managed --install-headers /home/admin/.virtualenvs/dev.actualito.com/include/site/python2.7 failed with error code 1 in /home/admin/.virtualenvs/dev.actualito.com/build/lxml
Storing complete log in /home/admin/.pip/pip.log
Asked By: Cristian Rojas

||
Source

Answers:

Here is the my saved note.

sudo apt-get install libxml2
sudo apt-get install libxslt1.1
sudo apt-get install libxml2-dev
sudo apt-get install libxslt1-dev
sudo apt-get install python-libxml2
sudo apt-get install python-libxslt1
sudo apt-get install python-dev
sudo apt-get install python-setuptools

easy_install lxml

It has worked for my ubuntu 12.10

Answered By: Delgermurun

Make sure you have enough memory. Try dmesg | tail to see if it outputs something like:

...
[3778136.277570] Out of memory: Kill process 21267 (cc1) score 557 or sacrifice child
[3778136.277587] Killed process 21267 (cc1) total-vm:365836kB, anon-rss:336228kB, file-rss:0kB
Answered By: Matmas

I’ve stumbled with this trouble a couple of times.

Short answer

Python2: $ python2.7 setup.py clean build --with-cython install
Python3: $ pip-3.3 install lxml

Long answer

The hypothesis is that pip install lxml should work in every environment, regardless if you are using Python2 or Python3.

There’s also Cython to be considered: You will certainly enjoy lxml compiled with Cython due to relevant performance gains.

For reasons unknown to me, the compilation on Python2 does not find Cython.
To be more precise and absolutely explicit about this matter, both commands below DO NOT employ Cython:

# DO NOT use these commands. I repeat: DO NOT use these commands.
$ pip-2.7 install lxml
$ easy_install-2.7 install lxml

So, when using Python2 you have only one alternative, as far as I know, which is: compile from sources, Luke!

# install build environment and dependencies
$ kernel_release=$( uname -r )
$ sudo apt-get install linux-headers-${kernel_release} build-essential -y
$ sudo apt-get install libxml2-dev libxslt1-dev -y

# Download from github and compile from sources
$ git clone --branch lxml-3.2.4 https://github.com/lxml/lxml
$ python2.7 setup.py clean build --with-cython install
Answered By: Richard Gomes

According to lxml site you could use such construction:

CFLAGS="-O0"  pip install lxml

installation guide

Note for those installing globally: The proper way to pass environment variables with sudo is after sudo:

sudo CFLAGS="-O0" pip install lxml
Answered By: TenaciousRaptor

I met the similar question(error: command ‘gcc’ failed with exit status 4) this morning. It seems you need check your machine’s memory. If the memory is lower than 512M,that may be the cause.Try to close some services temporarily,like apache server,and try “pip install lxml” again.It maybe work!

Answered By: xmduhan

For ubuntu 12.04 and virtual env:

sudo apt-get install libxml2-dev libxslt-dev
workon some-virt-env
pip install lxml
Answered By: Kostyantyn

Try to disable the C compiler optimizations by setting the FLAGS environment variable

CFLAGS="-O0"  pip install lxml

That solves for me without the need of more RAM

Answered By: Ignacio Vazquez
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