I have installed R with Anaconda. Trying to execute
install.packages("isoband")
in Jupyter Notebook yields to error message
Warning message in install.packages("isoband"): “installation of
package ‘isoband’ had non-zero exit status”Updating HTML index of
packages in '.Library' Making 'packages.html' ... done
Does anyone have a guess what the problem might be? I am using a Macbook (M1). Thank you!
Here the whole error message:
trying URL 'https://cran.rstudio.com/src/contrib/isoband_0.2.5.tar.gz'
Content type 'application/x-gzip' length 1671911 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
* installing *source* package ‘isoband’ ...
** package ‘isoband’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/patrick/opt/anaconda3/envs/r_environment/lib/R/include" -DNDEBUG -Itestthat -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/patrick/opt/anaconda3/envs/r_environment=/usr/local/src/conda-prefix -c clip-lines.cpp -o clip-lines.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/patrick/opt/anaconda3/envs/r_environment/lib/R/include" -DNDEBUG -Itestthat -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/patrick/opt/anaconda3/envs/r_environment=/usr/local/src/conda-prefix -c init.cpp -o init.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/patrick/opt/anaconda3/envs/r_environment/lib/R/include" -DNDEBUG -Itestthat -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/patrick/opt/anaconda3/envs/r_environment=/usr/local/src/conda-prefix -c isoband.cpp -o isoband.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/patrick/opt/anaconda3/envs/r_environment/lib/R/include" -DNDEBUG -Itestthat -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/patrick/opt/anaconda3/envs/r_environment=/usr/local/src/conda-prefix -c polygon.cpp -o polygon.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/patrick/opt/anaconda3/envs/r_environment/lib/R/include" -DNDEBUG -Itestthat -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/patrick/opt/anaconda3/envs/r_environment=/usr/local/src/conda-prefix -c separate-polygons.cpp -o separate-polygons.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/patrick/opt/anaconda3/envs/r_environment/lib/R/include" -DNDEBUG -Itestthat -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/patrick/opt/anaconda3/envs/r_environment=/usr/local/src/conda-prefix -c test-clip-lines.cpp -o test-clip-lines.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/patrick/opt/anaconda3/envs/r_environment/lib/R/include" -DNDEBUG -Itestthat -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/patrick/opt/anaconda3/envs/r_environment=/usr/local/src/conda-prefix -c test-runner.cpp -o test-runner.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/patrick/opt/anaconda3/envs/r_environment/lib/R/include" -DNDEBUG -Itestthat -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/patrick/opt/anaconda3/envs/r_environment/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/patrick/opt/anaconda3/envs/r_environment=/usr/local/src/conda-prefix -c test-separate-polygons.cpp -o test-separate-polygons.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Users/patrick/opt/anaconda3/envs/r_environment/lib/R/lib -Wl,-dead_strip_dylibs -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/patrick/opt/anaconda3/envs/r_environment/lib -L/Users/patrick/opt/anaconda3/envs/r_environment/lib -o isoband.dylib clip-lines.o init.o isoband.o polygon.o separate-polygons.o test-clip-lines.o test-runner.o test-separate-polygons.o -L/Users/patrick/opt/anaconda3/envs/r_environment/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation
ld: warning: -pie being ignored. It is only used when linking a main executable
ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd' for architecture x86_64
clang-12: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [/Users/patrick/opt/anaconda3/envs/r_environment/lib/R/share/make/shlib.mk:6: isoband.dylib] Error 1
ERROR: compilation failed for package ‘isoband’
* removing ‘/Users/patrick/opt/anaconda3/envs/r_environment/lib/R/library/isoband’
Warning in install.packages :
installation of package ‘isoband’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/90/dbqm7c3s4rs4r_0fg249fgsm0000gn/T/RtmpVOx7tE/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Related
I enter git push heroku master into the command prompt and all goes well for a while then...
WARNING: The Python installation you are using does not appear to have
been installed with a shared library, or in the case of MacOS X, as a
framework. Where these are not present, the compilation of mod_wsgi may
fail, or if it does succeed, will result in extra memory being used by
all processes at run time as a result of the static library needing to
be loaded in its entirety to every process. It is highly recommended
that you reinstall the Python installation being used from source code,
supplying the '--enable-shared' option to the 'configure' script when
configuring the source code prior to building and installing it.
then...
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/mod_wsgi.c -o build/temp.linux-x86_64-3.7/src/server/mod_wsgi.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
src/server/mod_wsgi.c: In function ‘wsgi_socket_sendv’:
src/server/mod_wsgi.c:10966:44: warning: signed and unsigned type in conditional expression [-Wsign-compare]
(nvec < iov_max ? nvec : (int)iov_max));
^
src/server/mod_wsgi.c: In function ‘wsgi_scan_headers’:
src/server/mod_wsgi.c:11125:30: warning: signed and unsigned type in conditional expression [-Wsign-compare]
buflen = buffer ? buflen : sizeof(x);
^
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_memory.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_memory.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_daemon.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_daemon.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_server.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_server.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_metrics.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_metrics.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_stream.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_stream.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_convert.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_convert.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_restrict.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_restrict.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_apache.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_apache.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_buckets.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_buckets.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_logger.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_logger.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_validate.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_validate.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_thread.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_thread.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I/app/.heroku/python/include/python3.7m -c src/server/wsgi_interp.c -o build/temp.linux-x86_64-3.7/src/server/wsgi_interp.o -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apache/include -I. -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr/include/apr-1 -I/tmp/pip-build-oxraezk2/mod-wsgi/src/packages/apr-util/include/apr-1 -DLINUX -D_REENTRANT -D_GNU_SOURCE -g -O2 -pthread
gcc -pthread -shared build/temp.linux-x86_64-3.7/src/server/mod_wsgi.o build/temp.linux-x86_64-3.7/src/server/wsgi_memory.o build/temp.linux-x86_64-3.7/src/server/wsgi_daemon.o build/temp.linux-x86_64-3.7/src/server/wsgi_server.o build/temp.linux-x86_64-3.7/src/server/wsgi_metrics.o build/temp.linux-x86_64-3.7/src/server/wsgi_stream.o build/temp.linux-x86_64-3.7/src/server/wsgi_convert.o build/temp.linux-x86_64-3.7/src/server/wsgi_restrict.o build/temp.linux-x86_64-3.7/src/server/wsgi_apache.o build/temp.linux-x86_64-3.7/src/server/wsgi_buckets.o build/temp.linux-x86_64-3.7/src/server/wsgi_logger.o build/temp.linux-x86_64-3.7/src/server/wsgi_validate.o build/temp.linux-x86_64-3.7/src/server/wsgi_thread.o build/temp.linux-x86_64-3.7/src/server/wsgi_interp.o -o build/lib.linux-x86_64-3.7/mod_wsgi/server/mod_wsgi-py37.cpython-37m-x86_64-linux-gnu.so -L/app/.heroku/python/lib -L/app/.heroku/python/lib/python3.7/config-3.7m-linux -lpython3.7m
/usr/bin/ld: /app/.heroku/python/lib/libpython3.7m.a(ceval.o): relocation R_X86_64_PC32 against symbol `_PyRuntime' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Bad value
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/app/.heroku/python/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-oxraezk2/mod-wsgi/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-yla81xqj-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-oxraezk2/mod-wsgi/
! Push rejected, failed to compile Python app.
! Push failed
I have tried pip install gcc to no avail and I don't even know if gcc is the real issue. I am trying to learn how to use Heroku and Python with hopes of later deploying a django app (which I have already created) via Heroku.
I installed Cython 0.24.1 on my Raspberry Pi by doing this:
Pasted below is the command and terminal output.
pi#raspberrypi:~ $ sudo pip3 install --upgrade cython==0.24.1
Downloading/unpacking cython==0.24.1
Downloading Cython-0.24.1.tar.gz (1.7MB): 1.7MB downloaded
Running setup.py (path:/tmp/pip-build-hprgsgiw/cython/setup.py) egg_info for package cython
Unable to find pgen, not compiling formal grammar.
warning: no files found matching '*.pyx' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.pxd' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.h' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.pxd' under directory 'Cython/Utility'
Installing collected packages: cython
Running setup.py install for cython
Unable to find pgen, not compiling formal grammar.
cythoning /tmp/pip-build-hprgsgiw/cython/Cython/Plex/Scanners.py to /tmp/pip-build-hprgsgiw/cython/Cython/Plex/Scanners.c
building 'Cython.Plex.Scanners' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c /tmp/pip-build-hprgsgiw/cython/Cython/Plex/Scanners.c -o build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Plex/Scanners.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Plex/Scanners.o -o build/lib.linux-armv7l-3.4/Cython/Plex/Scanners.cpython-34m.so
cythoning /tmp/pip-build-hprgsgiw/cython/Cython/Plex/Actions.py to /tmp/pip-build-hprgsgiw/cython/Cython/Plex/Actions.c
building 'Cython.Plex.Actions' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c /tmp/pip-build-hprgsgiw/cython/Cython/Plex/Actions.c -o build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Plex/Actions.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Plex/Actions.o -o build/lib.linux-armv7l-3.4/Cython/Plex/Actions.cpython-34m.so
cythoning /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Lexicon.py to /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Lexicon.c
building 'Cython.Compiler.Lexicon' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Lexicon.c -o build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Lexicon.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Lexicon.o -o build/lib.linux-armv7l-3.4/Cython/Compiler/Lexicon.cpython-34m.so
cythoning /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Scanning.py to /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Scanning.c
building 'Cython.Compiler.Scanning' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Scanning.c -o build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Scanning.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Scanning.o -o build/lib.linux-armv7l-3.4/Cython/Compiler/Scanning.cpython-34m.so
cythoning /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Parsing.py to /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Parsing.c
building 'Cython.Compiler.Parsing' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Parsing.c -o build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Parsing.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Parsing.o -o build/lib.linux-armv7l-3.4/Cython/Compiler/Parsing.cpython-34m.so
cythoning /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Visitor.py to /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Visitor.c
building 'Cython.Compiler.Visitor' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Visitor.c -o build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Visitor.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Visitor.o -o build/lib.linux-armv7l-3.4/Cython/Compiler/Visitor.cpython-34m.so
cythoning /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/FlowControl.py to /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/FlowControl.c
building 'Cython.Compiler.FlowControl' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/FlowControl.c -o build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Compiler/FlowControl.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Compiler/FlowControl.o -o build/lib.linux-armv7l-3.4/Cython/Compiler/FlowControl.cpython-34m.so
cythoning /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Code.py to /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Code.c
building 'Cython.Compiler.Code' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c /tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Code.c -o build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Code.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Compiler/Code.o -o build/lib.linux-armv7l-3.4/Cython/Compiler/Code.cpython-34m.so
cythoning /tmp/pip-build-hprgsgiw/cython/Cython/Runtime/refnanny.pyx to /tmp/pip-build-hprgsgiw/cython/Cython/Runtime/refnanny.c
building 'Cython.Runtime.refnanny' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c /tmp/pip-build-hprgsgiw/cython/Cython/Runtime/refnanny.c -o build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Runtime/refnanny.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Runtime/refnanny.o -o build/lib.linux-armv7l-3.4/Cython/Runtime/refnanny.cpython-34m.so
cythoning /tmp/pip-build-hprgsgiw/cython/Cython/Tempita/_tempita.py to /tmp/pip-build-hprgsgiw/cython/Cython/Tempita/_tempita.c
building 'Cython.Tempita._tempita' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c /tmp/pip-build-hprgsgiw/cython/Cython/Tempita/_tempita.c -o build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Tempita/_tempita.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/tmp/pip-build-hprgsgiw/cython/Cython/Tempita/_tempita.o -o build/lib.linux-armv7l-3.4/Cython/Tempita/_tempita.cpython-34m.so
warning: no files found matching '*.pyx' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.pxd' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.h' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.pxd' under directory 'Cython/Utility'
Installing cygdb script to /usr/local/bin
Installing cython script to /usr/local/bin
Installing cythonize script to /usr/local/bin
Successfully installed cython
Cleaning up...
Looks like the installation has completed fine. But after this, if I do the following, it still return the old version. What am I missing?
pi#raspberrypi:~ $ python3 -c "import cython;print(cython.__version__)"
0.21.1
From the log, I can read Installing cython script to /usr/local/bin. I extrapolate that the library has installed in /usr/local/python3something. Two alternatives:
re-install using pip3 install --user --upgrade cython==0.24.1 and make sure that ~/.local/bin is in your PATH environment variable.
add /usr/local/bin to your PATH environment variable and /usr/local/python3something/site-packages to your LD_LIBRARY_PATH environment variable.
Indeed, the python3something part must be changed to reflect the exact path on your system. Option "1" above should work even if my extrapolation is wrong.
(.newenv)[max#cyber life_besto]$ sudo pip install git+https://github.com/python-pillow/Pillow.git
Collecting git+https://github.com/python-pillow/Pillow.git
Cloning https://github.com/python-pillow/Pillow.git to /tmp/pip-zSgmXr-build
Installing collected packages: Pillow
Found existing installation: Pillow 3.0.0
Uninstalling Pillow-3.0.0:
Successfully uninstalled Pillow-3.0.0
Running setup.py install for Pillow ... error
Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-zSgmXr-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-BMRc40-record/install-record.txt --single-version-externally-managed --compile:
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/PIL
_____There are some codes_____
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c _imaging.c -o build/temp.linux-x86_64-2.7/_imaging.o
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c libImaging/Bands.c -o build/temp.linux-x86_64-2.7/libImaging/Bands.o
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c libImaging/ConvertYCbCr.c -o build/temp.linux-x86_64-2.7/libImaging/ConvertYCbCr.o
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c libImaging/Draw.c -o build/temp.linux-x86_64-2.7/libImaging/Draw.o
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c libImaging/GifEncode.c -o build/temp.linux-x86_64-2.7/libImaging/GifEncode.o
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c libImaging/Filter.c -o build/temp.linux-x86_64-2.7/libImaging/Filter.o
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c libImaging/LzwDecode.c -o build/temp.linux-x86_64-2.7/libImaging/LzwDecode.o
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c libImaging/Offset.c -o build/temp.linux-x86_64-2.7/libImaging/Offset.o
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c libImaging/Quant.c -o build/temp.linux-x86_64-2.7/libImaging/Quant.ogcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c libImaging/RawEncode.c -o build/temp.linux-x86_64-2.7/libImaging/RawEncode.o
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c libImaging/UnpackYCC.c -o build/temp.linux-x86_64-2.7/libImaging/UnpackYCC.o
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c libImaging/ZipEncode.c -o build/temp.linux-x86_64-2.7/libImaging/ZipEncode.o
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LIBJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -I/usr/include/freetype2 -I/tmp/pip-zSgmXr-build/libImaging -I/usr/include -I/usr/local/include -I/usr/include/python2.7 -c libImaging/BoxBlur.c -o build/temp.linux-x86_64-2.7/libImaging/BoxBlur.o
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory
gcc -pthread -shared -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld build/temp.linux-x86_64-2.7/_imaging.o build/temp.linux-x86_64-2.7/decode.o build/temp.linux-x86_64-2.7/encode.o build/temp.linux-x86_64-2.7/map.o build/temp.linux-x86_64-2.7/display.o build/temp.linux-x86_64-2.7/outline.o build/temp.linux-x86_64-2.7/path.o build/temp.linux-x86_64-2.7/libImaging/Access.o build/temp.linux-x86_64-2.7/libImaging/AlphaComposite.o build/temp.linux-x86_64-2.7/libImaging/Resample.o build/temp.linux-x86_64-2.7/libImaging/Bands.o build/temp.linux-x86_64-2.7/libImaging/BitDecode.o build/temp.linux-x86_64-2.7/libImaging/Blend.o build/temp.linux-x86_64-2.7/libImaging/Chops.o build/temp.linux-x86_64-2.7/libImaging/Convert.o build/temp.linux-x86_64-2.7/libImaging/ConvertYCbCr.o build/temp.linux-x86_64-2.7/libImaging/Copy.o build/temp.linux-x86_64-2.7/libImaging/Crc32.o build/temp.linux-x86_64-2.7/libImaging/Crop.o build/temp.linux-x86_64-2.7/libImaging/Dib.o build/temp.linux-x86_64-2.7/libImaging/Draw.o build/temp.linux-x86_64-2.7/libImaging/Effects.o build/temp.linux-x86_64-2.7/libImaging/EpsEncode.o build/temp.linux-x86_64-2.7/libImaging/File.o build/temp.linux-x86_64-2.7/libImaging/Fill.o build/temp.linux-x86_64-2.7/libImaging/Filter.o build/temp.linux-x86_64-2.7/libImaging/FliDecode.o build/temp.linux-x86_64-2.7/libImaging/Geometry.o build/temp.linux-x86_64-2.7/libImaging/GetBBox.o build/temp.linux-x86_64-2.7/libImaging/GifDecode.o build/temp.linux-x86_64-2.7/libImaging/GifEncode.o build/temp.linux-x86_64-2.7/libImaging/HexDecode.o build/temp.linux-x86_64-2.7/libImaging/Histo.o build/temp.linux-x86_64-2.7/libImaging/JpegDecode.o build/temp.linux-x86_64-2.7/libImaging/JpegEncode.o build/temp.linux-x86_64-2.7/libImaging/LzwDecode.o build/temp.linux-x86_64-2.7/libImaging/Matrix.o build/temp.linux-x86_64-2.7/libImaging/ModeFilter.o build/temp.linux-x86_64-2.7/libImaging/MspDecode.o build/temp.linux-x86_64-2.7/libImaging/Negative.o build/temp.linux-x86_64-2.7/libImaging/Offset.o build/temp.linux-x86_64-2.7/libImaging/Pack.o build/temp.linux-x86_64-2.7/libImaging/PackDecode.o build/temp.linux-x86_64-2.7/libImaging/Palette.o build/temp.linux-x86_64-2.7/libImaging/Paste.o build/temp.linux-x86_64-2.7/libImaging/Quant.o build/temp.linux-x86_64-2.7/libImaging/QuantOctree.o build/temp.linux-x86_64-2.7/libImaging/QuantHash.o build/temp.linux-x86_64-2.7/libImaging/QuantHeap.o build/temp.linux-x86_64-2.7/libImaging/PcdDecode.o build/temp.linux-x86_64-2.7/libImaging/PcxDecode.o build/temp.linux-x86_64-2.7/libImaging/PcxEncode.o build/temp.linux-x86_64-2.7/libImaging/Point.o build/temp.linux-x86_64-2.7/libImaging/RankFilter.o build/temp.linux-x86_64-2.7/libImaging/RawDecode.o build/temp.linux-x86_64-2.7/libImaging/RawEncode.o build/temp.linux-x86_64-2.7/libImaging/Storage.o build/temp.linux-x86_64-2.7/libImaging/SunRleDecode.o build/temp.linux-x86_64-2.7/libImaging/TgaRleDecode.o build/temp.linux-x86_64-2.7/libImaging/Unpack.o build/temp.linux-x86_64-2.7/libImaging/UnpackYCC.o build/temp.linux-x86_64-2.7/libImaging/UnsharpMask.o build/temp.linux-x86_64-2.7/libImaging/XbmDecode.o build/temp.linux-x86_64-2.7/libImaging/XbmEncode.o build/temp.linux-x86_64-2.7/libImaging/ZipDecode.o build/temp.linux-x86_64-2.7/libImaging/ZipEncode.o build/temp.linux-x86_64-2.7/libImaging/TiffDecode.o build/temp.linux-x86_64-2.7/libImaging/Incremental.o build/temp.linux-x86_64-2.7/libImaging/Jpeg2KDecode.o build/temp.linux-x86_64-2.7/libImaging/Jpeg2KEncode.o build/temp.linux-x86_64-2.7/libImaging/BoxBlur.o build/temp.linux-x86_64-2.7/libImaging/QuantPngQuant.o -L/usr/lib -L/usr/lib64 -L/usr/local/lib -L/usr/lib64 -ljpeg -lz -ltiff -lpython2.7 -o build/lib.linux-x86_64-2.7/PIL/_imaging.so
gcc: error: build/temp.linux-x86_64-2.7/_imaging.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/decode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/encode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/map.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/display.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/outline.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/path.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Access.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/AlphaComposite.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Resample.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Bands.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/BitDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Blend.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Chops.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Convert.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/ConvertYCbCr.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Copy.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Crc32.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Crop.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Dib.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Draw.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Effects.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/EpsEncode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/File.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Fill.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Filter.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/FliDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Geometry.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/GetBBox.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/GifDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/GifEncode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/HexDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Histo.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/JpegDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/JpegEncode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/LzwDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Matrix.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/ModeFilter.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/MspDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Negative.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Offset.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Pack.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/PackDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Palette.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Paste.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Quant.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/QuantOctree.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/QuantHash.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/QuantHeap.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/PcdDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/PcxDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/PcxEncode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Point.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/RankFilter.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/RawDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/RawEncode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Storage.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/SunRleDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/TgaRleDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Unpack.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/UnpackYCC.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/UnsharpMask.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/XbmDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/XbmEncode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/ZipDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/ZipEncode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/TiffDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Incremental.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Jpeg2KDecode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/Jpeg2KEncode.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/BoxBlur.o: No such file or directory
gcc: error: build/temp.linux-x86_64-2.7/libImaging/QuantPngQuant.o: No such file or directory
gcc: error: /usr/lib/rpm/redhat/redhat-hardened-ld: No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
Rolling back uninstall of Pillow
Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-zSgmXr-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-BMRc40-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-zSgmXr-build/
I also tried to install using pip install Pillow, but it didn't help too.
Try installing python-devel as well as redhat-rpm-config packages first (see how to do it here), then pip install Pillow.
More info on manual installation (as opposed to installing native OS packages like python-imaging) you'll find in official installation guide
I'm having troubles with an odd error. I use Cython to compile some c++ files. It works perfectly fine under OS X but under Linux i have the following error.
clang++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/test.o build/temp.linux-x86_64-2.7/ocv.o build/temp.linux-x86_64-2.7/fructueux.o build/temp.linux-x86_64-2.7/Face_keypoint_extractor_minimal.o build/temp.linux-x86_64-2.7/tools/mimic.o build/temp.linux-x86_64-2.7/Unrestricted_local_binary_pattern_modified.o build/temp.linux-x86_64-2.7/Over_sampling.o -L -o /home/AM/Documents/code_dw/Python_deep_dev/Cython_interface/First_import/test.so -L/usr/local/lib -lopencv_calib3d -lopencv_contrib -lopencv_core -lopencv_features2d -lopencv_flann -lopencv_gpu -lopencv_highgui -lopencv_imgproc -lopencv_legacy -lopencv_ml -lopencv_nonfree -lopencv_objdetect -lopencv_ocl -lopencv_photo -lopencv_stitching -lopencv_superres -lopencv_ts -lopencv_video -lopencv_videostab -ltbb -lrt -lpthread -lm -ldl -lboost_system -lboost_filesystem ./libFD.a
=> -L -o /home/AM/Documents/code_dw/Python_deep_dev/Cython_interface/First_import/test.so
clang: error: no such file or directory: '/home/AM/Documents/code_dw/Python_deep_dev/Cython_interface/First_import/test.so'
The -o is perfectly normal but i don't know the effect of the -L just before and i guess it is the reason it crashes.
Does someone has an idea of the reason why distutils and/or clang could produce such an output ?
PS : I have never written the string "test.so" in any of my file.
Stupid but it always happens
in the setup.py :
library_dirs=[""]
Create the -L in the compiler command and the -L ignore the -o and get the next path.
trying to install matplotlib (1.1.0 with python 2.7.3 on CentOS)
python setup.py build
looks good until:
running build_ext
building 'matplotlib.ft2font' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/numpy-1.5.1-release/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/include/python2.7 -c src/ft2font.cpp -o build/temp.linux-x86_64-2.7/src/ft2font.o
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/numpy-1.5.1-release/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/include/python2.7 -c src/mplutils.cpp -o build/temp.linux-x86_64-2.7/src/mplutils.o
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/numpy-1.5.1-release/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/include/python2.7 -c CXX/cxx_extensions.cxx -o build/temp.linux-x86_64-2.7/CXX/cxx_extensions.o
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/numpy-1.5.1-release/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/include/python2.7 -c CXX/IndirectPythonInterface.cxx -o build/temp.linux-x86_64-2.7/CXX/IndirectPythonInterface.o
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/numpy-1.5.1-release/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/include/python2.7 -c CXX/cxxsupport.cxx -o build/temp.linux-x86_64-2.7/CXX/cxxsupport.o
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/numpy-1.5.1-release/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/include/python2.7 -c CXX/cxxextensions.c -o build/temp.linux-x86_64-2.7/CXX/cxxextensions.o
g++ -pthread -shared build/temp.linux-x86_64-2.7/src/ft2font.o build/temp.linux-x86_64-2.7/src/mplutils.o build/temp.linux-x86_64-2.7/CXX/cxx_extensions.o build/temp.linux-x86_64-2.7/CXX/IndirectPythonInterface.o build/temp.linux-x86_64-2.7/CXX/cxxsupport.o build/temp.linux-x86_64-2.7/CXX/cxxextensions.o -L/usr/local/lib -L/usr/lib -L/usr/local/lib64 -L/usr/lib64 -L/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/lib -lfreetype -lz -lstdc++ -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/matplotlib/ft2font.so
**/usr/bin/ld: /usr/local/lib/libpython2.7.a(parsetok.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libpython2.7.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error: command 'g++' failed with exit status 1**
So I'm guessing I need to either edit the config file maybe to allow sharing? Any help appreciated, thanks.
matplotlib is one of the packages that can be really hard to install, there are plenty of others (ahem... lxml, pyside/pyqt4, etc).
Save yourself some trouble and checkout one of the pre-builts. Anaconda from continuum or canopy from enthought are good on cetos and will save you a log of headaches (free installs).
Just use pip and virtualenv, it should work fine (CentOS-6.5, x86_64, python-2.6) Installing Matplotlib on CentOS 6.5