lxml installation error ubuntu 14.04 (internal compiler error)

python installation pip lxml ubuntu-14.04
salmanwahed picture salmanwahed · Jun 27, 2014 · Viewed 28.3k times · Source

I am having problems with installing lxml. I have tried the solutions of the relative questions in this site and other sites but could not fix the problem. Need some suggestions/solution on this.

I am providing the full log after executing pip install lxml, 

Downloading/unpacking lxml
  Downloading lxml-3.3.5.tar.gz (3.5MB): 3.5MB downloaded
  Running setup.py (path:/tmp/pip_build_root/lxml/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 3.3.5.
    Building without Cython.
    Using build configuration of libxslt 1.1.28

    warning: no previously-included files found matching '*.py'
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 3.3.5.
    Building without Cython.
    Using build configuration of libxslt 1.1.28
    building 'lxml.etree' extension
    x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/libxml2 -I/tmp/pip_build_root/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 -w
    x86_64-linux-gnu-gcc: internal compiler error: Killed (program cc1)
    Please submit a full bug report,
    with preprocessed source if appropriate.
    See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 4
    Complete output from command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_root/lxml/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-KUq9VD-record/install-record.txt --single-version-externally-managed --compile:
    /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'bugtrack_url'

  warnings.warn(msg)

Building lxml version 3.3.5.

Building without Cython.

Using build configuration of libxslt 1.1.28

running install

running build

running build_py

creating build

creating build/lib.linux-x86_64-2.7

creating build/lib.linux-x86_64-2.7/lxml

copying src/lxml/pyclasslookup.py -> build/lib.linux-x86_64-2.7/lxml

copying src/lxml/doctestcompare.py -> build/lib.linux-x86_64-2.7/lxml

copying src/lxml/builder.py -> build/lib.linux-x86_64-2.7/lxml

copying src/lxml/cssselect.py -> build/lib.linux-x86_64-2.7/lxml

copying src/lxml/sax.py -> build/lib.linux-x86_64-2.7/lxml

copying src/lxml/_elementpath.py -> build/lib.linux-x86_64-2.7/lxml

copying src/lxml/ElementInclude.py -> build/lib.linux-x86_64-2.7/lxml

copying src/lxml/__init__.py -> build/lib.linux-x86_64-2.7/lxml

copying src/lxml/usedoctest.py -> build/lib.linux-x86_64-2.7/lxml

creating build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/__init__.py -> build/lib.linux-x86_64-2.7/lxml/includes

creating build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/html5parser.py -> build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/ElementSoup.py -> build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/builder.py -> build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/clean.py -> build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/_diffcommand.py -> build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/diff.py -> build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/_html5builder.py -> build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/_setmixin.py -> build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/defs.py -> build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/formfill.py -> build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/soupparser.py -> build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/__init__.py -> build/lib.linux-x86_64-2.7/lxml/html

copying src/lxml/html/usedoctest.py -> build/lib.linux-x86_64-2.7/lxml/html

creating build/lib.linux-x86_64-2.7/lxml/isoschematron

copying src/lxml/isoschematron/__init__.py -> build/lib.linux-x86_64-2.7/lxml/isoschematron

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

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

copying src/lxml/includes/config.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/xpath.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/tree.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/dtdvalid.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/xmlparser.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/etreepublic.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/xslt.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/schematron.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/uri.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/c14n.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/xinclude.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/xmlschema.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/xmlerror.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/relaxng.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

copying src/lxml/includes/htmlparser.pxd -> build/lib.linux-x86_64-2.7/lxml/includes

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

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

creating build/lib.linux-x86_64-2.7/lxml/isoschematron/resources

creating build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/rng

copying src/lxml/isoschematron/resources/rng/iso-schematron.rng -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/rng

creating build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl

copying src/lxml/isoschematron/resources/xsl/RNG2Schtrn.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl

copying src/lxml/isoschematron/resources/xsl/XSD2Schtrn.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl

creating build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1

copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_schematron_skeleton_for_xslt1.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1

copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_dsdl_include.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1

copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_schematron_message.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1

copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_svrl_for_xslt1.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1

copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_abstract_expand.xsl -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1

copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/readme.txt -> build/lib.linux-x86_64-2.7/lxml/isoschematron/resources/xsl/iso-schematron-xslt1

running build_ext

building 'lxml.etree' extension

creating build/temp.linux-x86_64-2.7

creating build/temp.linux-x86_64-2.7/src

creating build/temp.linux-x86_64-2.7/src/lxml

x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/libxml2 -I/tmp/pip_build_root/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 -w

x86_64-linux-gnu-gcc: internal compiler error: Killed (program cc1)

Please submit a full bug report,

with preprocessed source if appropriate.

See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.

error: command 'x86_64-linux-gnu-gcc' failed with exit status 4

----------------------------------------
Cleaning up...
Command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_root/lxml/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-KUq9VD-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_root/lxml
Storing debug log for failure in /root/.pip/pip.log

Also, the pip.log file looks like this,

status = self.run(options, args)
  File "/usr/lib/python2.7/dist-packages/pip/commands/install.py", line 283, in run
    requirement_set.install(install_options, global_options, root=options.root_path)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1435, in install
    requirement.install(install_options, global_options, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 706, in install
    cwd=self.source_dir, filter_stdout=self._filter_install, show_stdout=False)
  File "/usr/lib/python2.7/dist-packages/pip/util.py", line 697, in call_subprocess
    % (command_desc, proc.returncode, cwd))
InstallationError: Command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_root/lxml/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-KUq9VD-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_root/lxml

dmesg | tail command shows output like this,

[1744367.676147] Out of memory: Kill process 25518 (cc1) score 388 or sacrifice child
[1744367.676665] Killed process 25518 (cc1) total-vm:242352kB, anon-rss:200608kB, file-rss:0kB

It's seems like a memory issue. I am taking reference form this question

Answer

Michael Plakhov picture Michael Plakhov · Nov 5, 2014

Possible solution (if you have no ability to increase memory on that machine) is to add swap file.

sudo dd if=/dev/zero of=/swapfile bs=1024 count=524288
sudo chmod 600 /swapfile
sudo mkswap /swapfile
sudo swapon /swapfile

from https://github.com/pydata/pandas/issues/1880#issuecomment-9920484

This worked for me on smallest digital ocean machine

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