id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 506 pip install overrides LD_LIBRARY_PATH tic20@… Conrad Huang "If I define a little bash script, chimera-python, wrapping ChimeraX's Python: #!/bin/bash CHIMERA_HOME=/home/tic20/apps/chimerax export LD_LIBRARY_PATH=$CHIMERA_HOME/lib:/home/tic20/apps/gcc-4.9.2/lib64 $CHIMERA_HOME/bin/python3.5 $* ... then try: chimera-python -m pip install lxml ... I get the output pasted below. The short story is that LD_LIBRARY_PATH appears to have been overridden, and the gcc flags have the library path hard-coded to -L/var/tmp/chimerax_build/develop/chimerax/build/lib. Collecting lxml Using cached lxml-3.7.0.tar.gz Building wheels for collected packages: lxml Running setup.py bdist_wheel for lxml ... error Complete output from command /home/tic20/apps/chimerax/bin/python3.5 -u -c ""import setuptools, tokenize;__file__='/tmp/pip-build-ujjcqr36/lxml/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))"" bdist_wheel -d /tmp/tmpln9kgi9dpip-wheel- --python-tag cp35: Building lxml version 3.7.0. Building without Cython. Using build configuration of libxslt 1.1.28 Building against libxml2/libxslt in the following directory: /usr/lib64 running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.5 creating build/lib.linux-x86_64-3.5/lxml copying src/lxml/builder.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/cssselect.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/pyclasslookup.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/usedoctest.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/ElementInclude.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/sax.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/_elementpath.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/__init__.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/doctestcompare.py -> build/lib.linux-x86_64-3.5/lxml creating build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/__init__.py -> build/lib.linux-x86_64-3.5/lxml/includes creating build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/_html5builder.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/builder.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/html5parser.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/_diffcommand.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/clean.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/formfill.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/usedoctest.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/_setmixin.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/soupparser.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/ElementSoup.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/__init__.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/defs.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/diff.py -> build/lib.linux-x86_64-3.5/lxml/html creating build/lib.linux-x86_64-3.5/lxml/isoschematron copying src/lxml/isoschematron/__init__.py -> build/lib.linux-x86_64-3.5/lxml/isoschematron copying src/lxml/lxml.etree.h -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/lxml.etree_api.h -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/includes/relaxng.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/xmlerror.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/etreepublic.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/c14n.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/dtdvalid.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/config.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/schematron.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/xpath.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/xmlparser.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/tree.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/xslt.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/htmlparser.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/xmlschema.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/uri.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/xinclude.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/lxml-version.h -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/etree_defs.h -> build/lib.linux-x86_64-3.5/lxml/includes creating build/lib.linux-x86_64-3.5/lxml/isoschematron/resources creating build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/rng copying src/lxml/isoschematron/resources/rng/iso-schematron.rng -> build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/rng creating build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/xsl copying src/lxml/isoschematron/resources/xsl/XSD2Schtrn.xsl -> build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/xsl copying src/lxml/isoschematron/resources/xsl/RNG2Schtrn.xsl -> build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/xsl creating build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/xsl/iso-schematron-xslt1 copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_dsdl_include.xsl -> build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/xsl/iso-schematron-xslt1 copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_schematron_message.xsl -> build/lib.linux-x86_64-3.5/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_64-3.5/lxml/isoschematron/resources/xsl/iso-schematron-xslt1 copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_abstract_expand.xsl -> build/lib.linux-x86_64-3.5/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_64-3.5/lxml/isoschematron/resources/xsl/iso-schematron-xslt1 copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/readme.txt -> build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/xsl/iso-schematron-xslt1 running build_ext building 'lxml.etree' extension creating build/temp.linux-x86_64-3.5 creating build/temp.linux-x86_64-3.5/src creating build/temp.linux-x86_64-3.5/src/lxml gcc -pipe -fPIC -std=gnu99 -I/var/tmp/chimerax_build/develop/chimerax/build/include -L/var/tmp/chimerax_build/develop/chimerax/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -pthread -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/include/libxml2 -Isrc/lxml/includes -I/home/tic20/apps/chimerax/include/python3.5m -c src/lxml/lxml.etree.c -o build/temp.linux-x86_64-3.5/src/lxml/lxml.etree.o -w gcc -pipe -fPIC -std=gnu99 -I/var/tmp/chimerax_build/develop/chimerax/build/include -L/var/tmp/chimerax_build/develop/chimerax/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -pthread -shared -O3 -Wall -Wextra -Wl,-rpath,/var/tmp/chimerax_build/develop/chimerax/build/lib build/temp.linux-x86_64-3.5/src/lxml/lxml.etree.o -L/usr/lib64 -L/var/tmp/chimerax_build/develop/chimerax/build/lib -lxslt -lexslt -lxml2 -lrt -lz -lm -lpython3.5m -o build/lib.linux-x86_64-3.5/lxml/etree.cpython-35m-x86_64-linux-gnu.so /usr/bin/ld: cannot find -lpython3.5m collect2: error: ld returned 1 exit status error: command 'gcc' failed with exit status 1 ---------------------------------------- Failed building wheel for lxml Running setup.py clean for lxml Failed to build lxml Installing collected packages: lxml Running setup.py install for lxml ... error Complete output from command /home/tic20/apps/chimerax/bin/python3.5 -u -c ""import setuptools, tokenize;__file__='/tmp/pip-build-ujjcqr36/lxml/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))"" install --record /tmp/pip-yq0vr531-record/install-record.txt --single-version-externally-managed --compile: Building lxml version 3.7.0. Building without Cython. Using build configuration of libxslt 1.1.28 Building against libxml2/libxslt in the following directory: /usr/lib64 running install running build running build_py creating build creating build/lib.linux-x86_64-3.5 creating build/lib.linux-x86_64-3.5/lxml copying src/lxml/builder.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/cssselect.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/pyclasslookup.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/usedoctest.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/ElementInclude.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/sax.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/_elementpath.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/__init__.py -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/doctestcompare.py -> build/lib.linux-x86_64-3.5/lxml creating build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/__init__.py -> build/lib.linux-x86_64-3.5/lxml/includes creating build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/_html5builder.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/builder.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/html5parser.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/_diffcommand.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/clean.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/formfill.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/usedoctest.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/_setmixin.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/soupparser.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/ElementSoup.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/__init__.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/defs.py -> build/lib.linux-x86_64-3.5/lxml/html copying src/lxml/html/diff.py -> build/lib.linux-x86_64-3.5/lxml/html creating build/lib.linux-x86_64-3.5/lxml/isoschematron copying src/lxml/isoschematron/__init__.py -> build/lib.linux-x86_64-3.5/lxml/isoschematron copying src/lxml/lxml.etree.h -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/lxml.etree_api.h -> build/lib.linux-x86_64-3.5/lxml copying src/lxml/includes/relaxng.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/xmlerror.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/etreepublic.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/c14n.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/dtdvalid.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/config.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/schematron.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/xpath.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/xmlparser.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/tree.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/xslt.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/htmlparser.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/xmlschema.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/uri.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/xinclude.pxd -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/lxml-version.h -> build/lib.linux-x86_64-3.5/lxml/includes copying src/lxml/includes/etree_defs.h -> build/lib.linux-x86_64-3.5/lxml/includes creating build/lib.linux-x86_64-3.5/lxml/isoschematron/resources creating build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/rng copying src/lxml/isoschematron/resources/rng/iso-schematron.rng -> build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/rng creating build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/xsl copying src/lxml/isoschematron/resources/xsl/XSD2Schtrn.xsl -> build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/xsl copying src/lxml/isoschematron/resources/xsl/RNG2Schtrn.xsl -> build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/xsl creating build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/xsl/iso-schematron-xslt1 copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_dsdl_include.xsl -> build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/xsl/iso-schematron-xslt1 copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_schematron_message.xsl -> build/lib.linux-x86_64-3.5/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_64-3.5/lxml/isoschematron/resources/xsl/iso-schematron-xslt1 copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/iso_abstract_expand.xsl -> build/lib.linux-x86_64-3.5/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_64-3.5/lxml/isoschematron/resources/xsl/iso-schematron-xslt1 copying src/lxml/isoschematron/resources/xsl/iso-schematron-xslt1/readme.txt -> build/lib.linux-x86_64-3.5/lxml/isoschematron/resources/xsl/iso-schematron-xslt1 running build_ext building 'lxml.etree' extension creating build/temp.linux-x86_64-3.5 creating build/temp.linux-x86_64-3.5/src creating build/temp.linux-x86_64-3.5/src/lxml gcc -pipe -fPIC -std=gnu99 -I/var/tmp/chimerax_build/develop/chimerax/build/include -L/var/tmp/chimerax_build/develop/chimerax/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -pthread -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/include/libxml2 -Isrc/lxml/includes -I/home/tic20/apps/chimerax/include/python3.5m -c src/lxml/lxml.etree.c -o build/temp.linux-x86_64-3.5/src/lxml/lxml.etree.o -w gcc -pipe -fPIC -std=gnu99 -I/var/tmp/chimerax_build/develop/chimerax/build/include -L/var/tmp/chimerax_build/develop/chimerax/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -pthread -shared -O3 -Wall -Wextra -Wl,-rpath,/var/tmp/chimerax_build/develop/chimerax/build/lib build/temp.linux-x86_64-3.5/src/lxml/lxml.etree.o -L/usr/lib64 -L/var/tmp/chimerax_build/develop/chimerax/build/lib -lxslt -lexslt -lxml2 -lrt -lz -lm -lpython3.5m -o build/lib.linux-x86_64-3.5/lxml/etree.cpython-35m-x86_64-linux-gnu.so /usr/bin/ld: cannot find -lpython3.5m collect2: error: ld returned 1 exit status error: command 'gcc' failed with exit status 1 ---------------------------------------- Command ""/home/tic20/apps/chimerax/bin/python3.5 -u -c ""import setuptools, tokenize;__file__='/tmp/pip-build-ujjcqr36/lxml/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))"" install --record /tmp/pip-yq0vr531-record/install-record.txt --single-version-externally-managed --compile"" failed with error code 1 in /tmp/pip-build-ujjcqr36/lxml/" defect closed blocker Tool Shed fixed chimera-programmers@… all ChimeraX