I am trying to install pyzmq to get ipython wotking in qtconsole mode.
I have installed zeromq in the default location (/usr/local). Both the dynamic lib and the header are at the correct position.
The I cloned the git repo for pyzmq and run the configuration command :
[root#XXXXX pyzmq]# python setup.py configure --zmq=/usr/local
running configure
************************************************
Configure: Autodetecting ZMQ settings...
Custom ZMQ dir: /usr/local
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/local/include -Izmq/utils -Izmq/core -Izmq/devices -c detect/vers.c -o detect/vers.o
gcc -pthread detect/vers.o -L/usr/local/lib -Wl,-R/usr/local/lib -lzmq -o detect/vers
ZMQ version detected: 2.2.0
************************************************
So far so good. Then I run the installation command :
[root#XXXXXX pyzmq]# python setup.py install
running install
running build
running build_py
running build_ext
************************************************
Configure: Autodetecting ZMQ settings...
Custom ZMQ dir: /usr/local
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/local/include -Izmq/utils -Izmq/core -Izmq/devices -c detect/vers.c -o detect/vers.o
gcc -pthread detect/vers.o -L/usr/local/lib -Wl,-R/usr/local/lib -lzmq -o detect/vers
ZMQ version detected: 2.2.0
************************************************
skipping 'zmq/core/_poll.c' Cython extension (up-to-date)
skipping 'zmq/core/_version.c' Cython extension (up-to-date)
skipping 'zmq/core/constants.c' Cython extension (up-to-date)
skipping 'zmq/core/context.c' Cython extension (up-to-date)
skipping 'zmq/core/device.c' Cython extension (up-to-date)
skipping 'zmq/core/error.c' Cython extension (up-to-date)
skipping 'zmq/core/message.c' Cython extension (up-to-date)
skipping 'zmq/core/socket.c' Cython extension (up-to-date)
skipping 'zmq/core/stopwatch.c' Cython extension (up-to-date)
skipping 'zmq/utils/initthreads.c' Cython extension (up-to-date)
skipping 'zmq/utils/rebuffer.c' Cython extension (up-to-date)
skipping 'zmq/devices/monitoredqueue.c' Cython extension (up-to-date)
running install_lib
running install_egg_info
Writing /usr/lib64/python2.7/site-packages/pyzmq-2.2dev-py2.7.egg-info
Then I try to load the module in python :
>>> import zmq
This works (after having added the --inplace in the setup.py command)
But when I start ipython qtconsole I get this error (after several other lines):
import zmq
File "/usr/lib64/python2.7/site-packages/zmq/__init__.py", line 29, in <module>
from zmq import core, devices
File "/usr/lib64/python2.7/site-packages/zmq/core/__init__.py", line 26, in <module>
from zmq.core import (constants, error, message, context,
File "message.pxd", line 39, in init zmq.core.poll (zmq/core/poll.c:2950)
ValueError: zmq.core.message.Message has the wrong size, try recompiling
Any idea where this could come from ?
#akira - It could be that you checkout the tag (v2.2.0) from their github repository. I saw the same issue by doing so. Then I downloaded the tar.gz for v2.2.0 from pypi and it worked fine.
Related
I am trying to install mitproxy on my EC2 linux instance using pip:
sudo pip install mitmproxy
I have python2.7 installed, and now 2 instances of libffi
$ rpm -qa | grep libff
libffi-3.0.13-11.4.amzn1.x86_64
libffi-devel-3.0.13-11.4.amzn1.x86_64
but each time I try to run the install command I get the following error message:
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -c build/temp.linux-x86_64-2.7/_openssl.c -o build/temp.linux-x86_64-2.7/build/temp.linux-x86_64-2.7/_openssl.o
build/temp.linux-x86_64-2.7/_openssl.c:423:30: fatal error: openssl/opensslv.h: No such file or directory
#include <openssl/opensslv.h>
^
compilation terminated.
error: command 'gcc' failed with exit status 1
Any thoughts where I'm going wrong?
Just solved the problem with following solution:
wget source code gzip package from https://www.openssl.org/source/
config&&make&&make install
Good luck!
This is in continuation with my earlier question Geospatial Analytics in Python
I started a new question to keep the 2 issues logically separate.
I have trying to install geopandas on python 2.6
surprisingly, geopandas is already installed by GeoSeries doesn't work and it needs a package "Fiona". I followed the instruction provided here
I installed the libraries required by searching and following the suggestions (including dev libraries thinking I'll get the .h files), I am however stuck with these two issues:
https://github.com/Toblerity/Fiona
after cloning from git and python setup.py install on Fiona, I get the error:
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.6 -c fiona/_geometry.c -o build/temp.linux-x86_64-2.6/fiona/_geometry.o
gcc: fiona/_geometry.c: No such file or directory
pip install geopandas gives
fiona/_transform.cpp:269:18: error: gdal.h: No such file or directory
fiona/_transform.cpp:270:26: error: gdal_version.h: No such file or directory
fiona/_transform.cpp:271:22: error: cpl_conv.h: No such file or directory
fiona/_transform.cpp:272:24: error: cpl_string.h: No such file or directory
fiona/_transform.cpp:273:21: error: cpl_vsi.h: No such file or directory
fiona/_transform.cpp:274:22: error: ogr_core.h: No such file or directory
Any help with sorting the issues and getting geopandas installed will be greatly appreciated
On Linux Mint, Python 2.7.10 (Anaconda):
sudo apt-get install libgeos-dev
sudo apt-get install libgdal-dev
pip install geopandas
Successfully installed descartes-1.0.1 fiona-1.6.2 geopandas-0.1.1 pyproj-1.9.4
I would recommend moving to 2.7.10. The two development libraries were all that I needed on my system. It seems that you are likely missing libgdal-dev.
I'm struggling to install the mysql-python pip either systemwide or in a venv on Ubuntu 14.04 with MariaDB 10 installed. Also tried with MariaDB 5.5 and getting the same error. I don't have this issue with vanilla mysql-server installed.
I have the following installed via apt-get:
build-essential
python-dev
libmariadbclient-dev (thats the MariaDB replacement for libmysqlclient-dev)
python-mysqldb
Originally I thought this was an issue installing this into a venv but I've subsequently noticed mysql-python won't install systemwide either. Below are the cmds I used to install in a venv.
virtualenv venv
. venv/bin/activate
pip install mysql-python==1.2.5
In file included from _mysql.c:44:0:
/usr/include/mysql/my_config.h:439:0: warning: "HAVE_WCSCOLL" redefined [enabled by default]
#define HAVE_WCSCOLL
^
In file included from /usr/include/python2.7/pyconfig.h:3:0,
from /usr/include/python2.7/Python.h:8,
from _mysql.c:29:
/usr/include/x86_64-linux-gnu/python2.7/pyconfig.h:911:0: note: this is the location of the previous definition
#define HAVE_WCSCOLL 1
^x86_64-linux-gnu-gcc -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 --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/_mysql.o -L/usr/lib/x86_64-linux-gnu -lmariadbclient_r -lpthread -lz -lm -lssl -lcrypto -ldl -o build/lib.linux-x86_64-2.7/_mysql.so
/usr/bin/ld: cannot find -lssl
/usr/bin/ld: cannot find -lcrypto
collect2: error: ld returned 1 exit status
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
Cleaning up...
Command /root/env/bin/python -c "import setuptools, tokenize;__file__='/root/env/build/mysql- python/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-EyhO2v-record/install-record.txt --single-version-externally-managed --compile --install-headers /root/env/include/site/python2.7 failed with error code 1 in /root/env/build/mysql-python
Storing debug log for failure in /root/.pip/pip.log
You need to have installed the development libraries of OpenSSL. It can be a libssl-dev, libssl-devel if your distribution provides separated packages for the dev libraries. Or install the complete openssl package if they don't.
(venv)➜ src pip install mysql-python==1.2.5
Downloading/unpacking mysql-python==1.2.5
Downloading MySQL-python-1.2.5.zip (108kB): 108kB downloaded
Running setup.py (path:/home/braiam/src/venv/build/mysql-python/setup.py) egg_info for package mysql-python
Installing collected packages: mysql-python
Running setup.py install for mysql-python
building '_mysql' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Dversion_info=(1,2,5,'final',1) -D__version__=1.2.5 -I/usr/include/mysql -I/usr/include/python2.7 -c _mysql.c -o build/temp.linux-x86_64-2.7/_mysql.o -DBIG_JOINS=1 -fno-strict-aliasing -g -static-libgcc -fno-omit-frame-pointer -fno-strict-aliasing
In file included from _mysql.c:44:0:
/usr/include/mysql/my_config.h:439:0: warning: "HAVE_WCSCOLL" redefined
#define HAVE_WCSCOLL
^
In file included from /usr/include/python2.7/pyconfig.h:3:0,
from /usr/include/python2.7/Python.h:8,
from _mysql.c:29:
/usr/include/x86_64-linux-gnu/python2.7/pyconfig.h:911:0: note: this is the location of the previous definition
#define HAVE_WCSCOLL 1
^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -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,-z,relro -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/_mysql.o -L/usr/lib/x86_64-linux-gnu -lmariadbclient_r -lpthread -lz -lm -lssl -lcrypto -ldl -o build/lib.linux-x86_64-2.7/_mysql.so
Successfully installed mysql-python
Cleaning up...
But, there were two messages that you have that I didn't, namely:
/usr/bin/ld: cannot find -lssl
/usr/bin/ld: cannot find -lcrypto
Which if you did ld -lcrypto --verbose or ld -lssl --verbose wouldn't produce this results:
➜ src ld -lcrypto --verbose | grep succeeded
attempt to open //usr/lib/x86_64-linux-gnu/libcrypto.so succeeded
ld: warning: cannot find entry symbol _start; not setting start address
➜ src ld -lssl --verbose | grep succeeded
attempt to open //usr/lib/x86_64-linux-gnu/libssl.so succeeded
ld: warning: cannot find entry symbol _start; not setting start address
So, to fix this just make sure you have installed the libssl-dev package which provides both libraries.
I meet the similar error on MacOS but there is no "/usr/bin/ld: cannot find -lssl" for me.
Solved with the following steps:
Step 1. Make sure you have installed openssl with homebrew.
brew install openssl
Step 2. In a terminal:
export LIBRARY_PATH=$LIBRARY_PATH:/usr/local/opt/openssl/lib/
For Linux you can also try yum install your missing library and add them to LIBRARY_PATH.
For Debian 9.x:
apt install libssl-dev
For CentOS:
sudo yum install openssl-devel
I recently upgraded to Mac OS X 10.7 from 10.6.
I decided to use Python 2.7.
But when I'm trying to install the MySQLdb module to run Django, it fails:
$ sudo pip install MySQL-python
Downloading/unpacking MySQL-python
[…]
Running setup.py install for MySQL-python
building '_mysql' extension
llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -pipe -Dversion_info=(1,2,3,'final',0) -D__version__=1.2.3 -I/usr/local/mysql/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _mysql.c -o build/temp.macosx-10.7-intel-2.7/_mysql.o -Os -g -fno-common -fno-strict-aliasing -arch x86_64
unable to execute llvm-gcc-4.2: No such file or directory
error: command 'llvm-gcc-4.2' failed with exit status 1
Complete output from command /usr/bin/python -c "import setuptools;__file__='~/Sites/gugsm/build/MySQL-python/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --single-version-externally-managed --record /tmp/pip-AwMuqj-record/install-record.txt:
running install
running build
[…]
building '_mysql' extension
creating build/temp.macosx-10.7-intel-2.7
llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -pipe -Dversion_info=(1,2,3,'final',0) -D__version__=1.2.3 -I/usr/local/mysql/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _mysql.c -o build/temp.macosx-10.7-intel-2.7/_mysql.o -Os -g -fno-common -fno-strict-aliasing -arch x86_64
unable to execute llvm-gcc-4.2: No such file or directory
error: command 'llvm-gcc-4.2' failed with exit status 1
----------------------------------------
The reason is that I no longer have llvm-gcc nor gcc binaries.
I tried to upgrade XCode from 3.something to 4.3.2, but it din't help. It comes as a simple app and it doesn't populate /usr/bin with llvm-gcc.
What am I doing wrong?
In Xcode 4.3's Preferences menu, select Downloads and then install Command Line Tools.
making a symlink worked for me:
sudo ln -s /usr/bin/gcc /usr/bin/gcc-4.2
As a requirement for chef-client, I am trying to install yajl-ruby on OpenSUSE 12.1. So far, it is returning the following message:
linux:~ # gem install yajl-ruby
Building native extensions. This could take a while...
ERROR: Error installing yajl-ruby:
ERROR: Failed to build gem native extension.
/usr/bin/ruby extconf.rb
creating Makefile
make
gcc -I. -I/usr/lib64/ruby/1.8/x86_64-linux -I/usr/lib64/ruby/1.8/x86_64-linux -I. -fPIC -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -g -fno-strict-aliasing -fPIC -Wall -funroll-loops -c yajl.c
gcc -I. -I/usr/lib64/ruby/1.8/x86_64-linux -I/usr/lib64/ruby/1.8/x86_64-linux -I. -fPIC -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -g -fno-strict-aliasing -fPIC -Wall -funroll-loops -c yajl_alloc.c
gcc -I. -I/usr/lib64/ruby/1.8/x86_64-linux -I/usr/lib64/ruby/1.8/x86_64-linux -I. -fPIC -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -g -fno-strict-aliasing -fPIC -Wall -funroll-loops -c yajl_buf.c
gcc -I. -I/usr/lib64/ruby/1.8/x86_64-linux -I/usr/lib64/ruby/1.8/x86_64-linux -I. -fPIC -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -g -fno-strict-aliasing -fPIC -Wall -funroll-loops -c yajl_encode.c
yajl_encode.c: In function ‘hexToDigit’:
yajl_encode.c:201:1: internal compiler error: Aborted
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugs.opensuse.org/> for instructions.
make: *** [yajl_encode.o] Error 1
Gem files will remain installed in /usr/lib64/ruby/gems/1.8/gems/yajl-ruby-1.1.0 for inspection.
Results logged to /usr/lib64/ruby/gems/1.8/gems/yajl-ruby-1.1.0/ext/yajl/gem_make.out
The appropriate packages are installed:
zypper install ruby ruby-devel ruby-ri ruby-rdoc ruby-shadow gcc gcc-c++ automake autoconf make curl dmidecode
It may be an issue with the compiler or there may be an issue specific on OpenSUSE. So far, I am not sure which path to take.
gcc clearly recommends you to send bug report to OpenSuse with full preprocessed source (-E option instead of "-c" and add a redirect to file). This may be because opensuse gcc might have some modifications. You should check instructions on bugs.opensuse.org and send a bug report to OpenSuse. If the bug is in basic gcc too, opensuse bugzilla people will forward it upstream or will ask you to do this
To avoid an "internal compiler error" without sending bugs you can try to change build options. Usually "internal compiler error" means that something goes wrong in complex process of optimizations, so you can just change this process (order of optimization stages and which are enabled). Easiest is to change level of optimization (e.g. replace -O2 with -O1 or -O0) or add something like -Osize.