CWL: Linker error doing 'pip install cwlref-runner' on CentOS 6 system
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Entering edit mode
4.6 years ago

I get the following linker error trying to pip install cwel-runner on a CentOS 6 system, within a virtualenv using python27-python from the "centos-sclo-rh" repository:

$ virtualenv venv
$ source venv/bin/activate
(venv)$ pip install cwlref-runner
# >>> the usual 'pip' chatter, followed by a lot of compiler output <<<
gcc -pthread -shared -L/data/lab/opt/lib -L/data/lab/opt/lib64 -L/data/lab/local/lib -I/data/lab/opt/include -I/data/lab/local/include build/temp.linux-x86_64-2.7/ext/_ruamel_yaml.o build/temp.linux-x86_64-2.7/ext/api.o build/temp.linux-x86_64-2.7/ext/writer.o build/temp.linux-x86_64-2.7/ext/dumper.o build/temp.linux-x86_64-2.7/ext/loader.o build/temp.linux-x86_64-2.7/ext/reader.o build/temp.linux-x86_64-2.7/ext/scanner.o build/temp.linux-x86_64-2.7/ext/parser.o build/temp.linux-x86_64-2.7/ext/emitter.o -L/opt/rh/python27/root/usr/lib64 -lpython2.7 -o build/lib.linux-x86_64-2.7/_ruamel_yaml.so
    /usr/bin/ld: /data/lab/opt/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
    /data/lab/opt/lib/libpython2.7.a: could not read symbols: Bad value
    collect2: ld gab 1 als Ende-Status zurück
    error: command 'gcc' failed with exit status 1

    ----------------------------------------
Command "/users/myuserid/devel/cwl-workshop-20170614/venv/bin/python2 -c "import setuptools, tokenize;__file__='/tmp/pip-build-4J6vNA/ruamel.yaml/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-_0i2fv-record/install-record.txt --single-version-externally-managed --compile --install-headers /users/ern6xv/devel/cwl-workshop-20170614/venv/include/site/python2.7/ruamel.yaml" failed with error code 1 in /tmp/pip-build-4J6vNA/ruamel.yaml

The problem seems to be with some component of the ruamel.yaml package failing to compile ("a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order" according to its PyPI description). The German error message from collect2 means "ld returned 1 as exit code" or something along those lines.

Is there perhaps a quick resolution to this problem, without needing to hunt down where the linker error is, or worse, having to patch or recompile the offending module?

cwl common workflow language centos pip centos6 • 1.9k views
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1
Entering edit mode
4.6 years ago

It's entirely possible this situation arose in my case because I export CFLAGS and LDFLAGS, which contain another (older) Python's include and library files.

But if anyone finds themselves in this situation on CentOS 6, there is a relatively painless solution which just involves updating pip (within the virtualenv) and trying again:

(venv)$ pip install --upgrade pip
(venv)$ pip install ruamel.yaml  # succeeds this time, no errors
(venv)$ pip install cwlref-runner

Upgrade the virtualenv to use the latest version of pip (9.0.1 as of this writing), which can then fetch a precompiled "wheel" for ruamel.yaml appropriate for the current host's architecture, precluding the need to compile from source.

At that point, the pip install cwlref-runner runs through without further incident.

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