I am getting an error while installing pyminizip package inside docker container ( docker version 17.03.1-ce). I am doing it inside virtual environment with python 2.7.13.
I ended up with below message while trying to install it.
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc -Izlib123 -I/usr/local/include/python2.7 -c src/py_minizip.c -o build/temp.linux-x86_64-2.7/src/py_minizip.o
src/py_minizip.c: In function ‘_compress’:
src/py_minizip.c:251: warning: ‘filepathnameinzip’ may be used uninitialized in this function
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc -Izlib123 -I/usr/local/include/python2.7 -c src/zip.c -o build/temp.linux-x86_64-2.7/src/zip.o
In file included from src/zip.c:66:
src/crypt.h:34: error: redefinition of typedef ‘z_crc_t’
src/zip.h:83: note: previous declaration of ‘z_crc_t’ was here
src/zip.c:201: warning: function declaration isn’t a prototype
src/zip.c:203: warning: function declaration isn’t a prototype
error: command 'gcc' failed with exit status 1
Is there any alternate of pyminizip package ?
I want to create a password protected zip. So, even if there is any alternate solution to it, please let me know.
Would be useful know what docker image you use... but Try to Install python developer version:
sudo apt-get install python-dev
and libevent libraries
sudo apt-get install libevent-dev
This issue has been resolved. It is working fine with pyminizip version 0.2.1. I had faced this issue on 0.2.2 and
0.2.3 but version 0.2.1 is working fine for me.
Related
I am trying to install aspell-python package for spell correction.
Facing problem while installing the package.
Error :
python setup.py install
running install
running build
running build_ext
building 'aspell' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c aspell.c -o build/temp.linux-i686-2.7/aspell.o
aspell.c:53:20: fatal error: aspell.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1
GCC is already install version gcc (Ubuntu/Linaro 4.7.2-2ubuntu1) 4.7.2
libaspell15 is already install
Need to install sudo apt-get install libaspell-dev
I am working with ubuntu 14. I have downloaded the dpkg package for sklearn and unpacked it. i try to run sudo python setup.py installBut it seems to be stuck in a loop
compiling C++ sources
C compiler: c++ -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC
creating build/temp.linux-x86_64-2.7/sklearn/utils/src
compile options: '-Isklearn/utils/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
c++: sklearn/utils/src/MurmurHash3.cpp
c++ -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/sklearn/utils/murmurhash.o build/temp.linux-x86_64-2.7/sklearn/utils/src/MurmurHash3.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/sklearn/utils/murmurhash.so
building 'sklearn.utils.lgamma' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC
compile options: '-Isklearn/utils/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
x86_64-linux-gnu-gcc: sklearn/utils/lgamma.c
x86_64-linux-gnu-gcc: sklearn/utils/src/gamma.c
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/sklearn/utils/lgamma.o build/temp.linux-x86_64-2.7/sklearn/utils/src/gamma.o -Lbuild/temp.linux-x86_64-2.7 -lm -o build/lib.linux-x86_64-2.7/sklearn/utils/lgamma.so
building 'sklearn.utils.graph_shortest_path' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC
compile options: '-I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
x86_64-linux-gnu-gcc: sklearn/utils/graph_shortest_path.c
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from sklearn/utils/graph_shortest_path.c:256:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ufuncobject.h:327:0,
from sklearn/utils/graph_shortest_path.c:257:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
_import_umath(void)
^
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/sklearn/utils/graph_shortest_path.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/sklearn/utils/graph_shortest_path.so
building 'sklearn.utils.fast_dict' extension
compiling C++ sources
C compiler: c++ -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC
compile options: '-I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
c++: sklearn/utils/fast_dict.cpp
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from sklearn/utils/fast_dict.cpp:320:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
sklearn/utils/fast_dict.cpp: In function ‘PyObject* __pyx_pw_7sklearn_5utils_9fast_dict_1argmin(PyObject*, PyObject*)’:
sklearn/utils/fast_dict.cpp:18786:44: warning: ‘__pyx_v_min_key’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return PyInt_FromLong((long)val);
^
sklearn/utils/fast_dict.cpp:3316:46: note: ‘__pyx_v_min_key’ was declared here
__pyx_t_7sklearn_5utils_9fast_dict_ITYPE_t __pyx_v_min_key;
^
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ufuncobject.h:327:0,
from sklearn/utils/fast_dict.cpp:321:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/__ufunc_api.h: At global scope:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘int _import_umath()’ defined but not used [-Wunused-function]
_import_umath(void)
^
.. and continues on like that.
I have installed numpy, but I did it through ubuntu's software center. When I try to import sklearn within python I get
from sklearn.ensemble import RandomForestClassifier Traceback (most
recent call last): File "", line 1, in File
"sklearn/init.py", line 37, in
from . import check_build File "sklearn/__check_build/__init.py", line 46, in
raise_build_error(e) File "sklearn/check_build/__init.py", line 41, in raise_build_error
%s""" % (e, local_dir, ''.join(dir_content).strip(), msg)) ImportError: No module named _check_build
_______________________________________________________________________ Contents of sklearn/check_build: setup.py
__init.py _check_build.pyx
_check_build.c setup.pyc init.pyc
_______________________________________________________________________ It seems that scikit-learn has not been built correctly.
If you have installed scikit-learn from source, please do not forget
to build the package before using it: run python setup.py install or
make in the source directory.
If you have used an installer, please check that it is suited for your
Python version, your operating system and your platform.
I have no idea where sklearn/check_build is located.
My folder in /usr/lib/python2.7/dist-packages is empty, but I can import numpy within python. Like I said, I used the ubuntu software center to install numpy, but not for sklearn which I regret doing now.
I recommend installing sklearn and all dependencies with Anaconda package: https://www.continuum.io/downloads#_unix
It will be installed together with numpy and other packages, full list is available here: http://docs.continuum.io/anaconda/pkg-docs
If you want your package manager to handle everything, that usually works although you won't necessarily be on the most recent version
Otherwise do something along the lines of
sudo apt-get install build-essential gcc g++ python-dev python3-dev python-scipy python3-scipy
and try to install/compile again. compiling python extension modules relies on having a working compilation environment, plus the extended or development headers for python. I'm not sure if those dependencies are 100% exactly right for Ubuntu b/c I've been using more openSUSE lately, but apt-cache search will turn you up the correct naming if I've made a typo
One of new ways to handle issues due to environment is to handle it using docker images. This allows any developer to recreate the environment in any server within a single minute. You can pull the image from here.
This can also be performed very easily using the datmo CLI tool. We faced these problems ourselves and decided to build it.
Edit: You could install as follows,
apt-get update; \
apt-get install -y python python-pip \
python-numpy \
python-scipy \
build-essential \
python-dev \
python-setuptools \
libatlas-dev \
libatlas3gf-base
update-alternatives --set libblas.so.3 /usr/lib/atlas-base/atlas/libblas.so.3; update-alternatives --set liblapack.so.3 /usr/lib/atlas-base/atlas/liblapack.so.3
pip install -U scikit-learn
Disclaimer: I work at Datmo
Tried installing scipy on Mountain Lion, and couldn't get anything to work except:
sudo pip install -e git+https://github.com/scipy/scipy#egg=scipy-dev
which I believe installs the development version of scipy. For some reason it leaves an src directory inside my current folder, which contains a pip-delete-this-directory.txt and scipy directory containing all scipy files. I can import scipy from anywhere, but removing this folder removes scipy entirely. What's going on?
If I try installing with simply sudo pip install scipy, I get the following
/System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:22:4: error: "<vecLib/vecLib.h> is deprecated. Please #include <Accelerate/Accelerate.h> and link to Accelerate.framework."
#error "<vecLib/vecLib.h> is deprecated. Please #include <Accelerate/Accelerate.h> and link to Accelerate.framework."
^
1 error generated.
error: Command "clang -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 -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -Iscipy/sparse/linalg/eigen/arpack/ARPACK/SRC -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -c scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c -o build/temp.macosx-10.8-intel-2.7/scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.o" failed with exit status 1
From the pip documentation page:
Edit mode
Packages normally install under site-packages, but when you’re making changes, it makes more sense to run the package straight from the checked-out source tree. “Editable” installs create a .pth file in site-packages that extends Python’s import path to find the package:
$ pip install -e path/to/SomePackage
So this means you can simply solve your problems by running:
$ sudo mv src/scipy/scipy /Library/Python/2.7/site-packages/
And then if you want to be clean, you can edit the file to remove the line that was added by pip:
$ sudo vim /Library/Python/2.7/site-packages/easy-install.pth
I followed the installation instructions for installing oursql on Mac OS X. Since
sudo pip install oursql
told me, that it couldn't find mysql_config I (located it with locate mysql_config and) told it where to find it by
sudo MYSQL_CONFIG=/usr/local/mysql-5.5.14-osx10.6-x86_64/bin/mysql_config pip install oursql
I added the terminal output at the bottom for readability reasons. After that I fired up python in terminal (On Mac OS Lion it is python 2.7 now,...) and did
>>> import oursql
but python keeps telling me:
>>> import oursql
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: dlopen(/Library/Python/2.7/site-packages/oursql.so, 2): Library not loaded: libmysqlclient.18.dylib
Referenced from: /Library/Python/2.7/site-packages/oursql.so
Reason: image not found
What do I miss? Any suggestions?
Terminal Output, of pip installation:
Downloading/unpacking oursql
Downloading oursql-0.9.2.tar.bz2 (113Kb): 113Kb downloaded
Running setup.py egg_info for package oursql
Installing collected packages: oursql
Running setup.py install for oursql
skipping 'oursqlx/oursql.c' Cython extension (up-to-date)
building 'oursql' extension
/usr/local/mysql-5.5.14-osx10.6-x86_64/bin/mysql_config --cflags
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 -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c oursqlx/oursql.c -o build/temp.macosx-10.7-intel-2.7/oursqlx/oursql.o -I/usr/local/mysql-5.5.14-osx10.6-x86_64/include -Os -g -fno-common -fno-strict-aliasing -arch x86_64
oursqlx/oursql.c: In function ‘__pyx_pf_6oursql_10Connection___cinit__’:
oursqlx/oursql.c:4630: warning: implicit conversion shortens 64-bit value into a 32-bit value
oursqlx/oursql.c: In function ‘__pyx_pf_6oursql_10_Statement_execute’:
oursqlx/oursql.c:10219: warning: implicit conversion shortens 64-bit value into a 32-bit value
oursqlx/oursql.c: In function ‘__pyx_pf_6oursql_16_DBAPITypeObject___richcmp__’:
oursqlx/oursql.c:17597: warning: implicit conversion shortens 64-bit value into a 32-bit value
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 -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c oursqlx/compat.c -o build/temp.macosx-10.7-intel-2.7/oursqlx/compat.o -I/usr/local/mysql-5.5.14-osx10.6-x86_64/include -Os -g -fno-common -fno-strict-aliasing -arch x86_64
/usr/local/mysql-5.5.14-osx10.6-x86_64/bin/mysql_config --libs
llvm-gcc-4.2 -Wl,-F. -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 -arch x86_64 build/temp.macosx-10.7-intel-2.7/oursqlx/oursql.o build/temp.macosx-10.7-intel-2.7/oursqlx/compat.o -o build/lib.macosx-10.7-intel-2.7/oursql.so -L/usr/local/mysql-5.5.14-osx10.6-x86_64/lib -lmysqlclient -lpthread
ld: warning: ignoring file build/temp.macosx-10.7-intel-2.7/oursqlx/oursql.o, file was built for unsupported file format which is not the architecture being linked (i386)
ld: warning: ignoring file build/temp.macosx-10.7-intel-2.7/oursqlx/compat.o, file was built for unsupported file format which is not the architecture being linked (i386)
ld: warning: ignoring file /usr/local/mysql-5.5.14-osx10.6-x86_64/lib/libmysqlclient.dylib, file was built for unsupported file format which is not the architecture being linked (i386)
Successfully installed oursql
Cleaning up...
This did the job:
export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:/usr/local/mysql/lib/"
If you don't want to install a full MySQL you can compile oursql with the mysql-connector-c.
Download mysql-connector-c, unzip and install:
wget http://dev.mysql.com/get/Downloads/Connector-C/mysql-connector-c-6.0.2-osx10.5-x86-64bit.tar.gz/from/http://cdn.mysql.com/
tar -xvf mysql-connector-c-6-1.0.2-osx10.5-x86-64bit.tar
cd mysql-connector-c-6.0.2-osx10.5-x86-64bit
sudo cp bin/* /usr/local/bin/
sudo cp lib/* /usr/local/lib/
sudo cp -r include/* /usr/local/include/
Download and unzip oursql:
wget --no-check-certificate https://launchpad.net/oursql/py3k/py3k-0.9.3/+download/oursql-0.9.3.zip
unzip oursql-0.9.3.zip
Compile oursql:
cd oursql-0.9.3
sudo python setup.py build_ext
This has been verified to work with OSX 10.8.2, Xcode 4.5.2 and Python 3.2.3
I came across this question looking for a solution to installing oursql on OSX 10.10.5. I had previously installed mysql using brew brew install mysql. For those looking to install oursql on yosemite, here is what works for me:
1) Download the package manually. See links here.
2) Open oursql/oursql-0.9.3.1/oursqlx/_exceptions.c in your favourite text editor
3) Comment the last “default”, should look something like this:
/*default:
if (err >= ER_ERROR_FIRST && err <= ER_ERROR_LAST)
return _oursqlx_ProgrammingError;
else if (err > CR_MIN_ERROR && err < CR_MAX_ERROR)
return _oursqlx_InterfaceError;*/
4) Now try running setup again:
[sudo] python setup.py install
The best way for installing mysql-server on mac os snow leopard is trying to install from source file in order to make sure you are compiling mysql for the correct architecture x86_64.
IF I use --no-site-packages option while creating a virtualenv and try to install MySQL-python afterwards I get :
error: command 'gcc' failed with exit status 1
Here are the steps I followed:
easy_install-2.7 --install-dir ~/src/lib/ virtualenv==dev
~/src/lib/virtualenv --no-site-packages ENV
.../ENV/bin/pip-2.7 install MySQL-python
I also tried downloading mySQL-python and install using
.../ENV/bin/python setup.py build
I get the same error wither way.
I assume I am missing the gcc from this virtualenv but how do I get it installed in this virtualenv while still using --no-site-packages option.
thanks
EDIT: as per below comments here is the whole error output.
running build
running build_py
copying MySQLdb/release.py -> build/lib.linux-x86_64-2.7/MySQLdb
running build_ext
building '_mysql' extension
gcc -m32 -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -Dversion_info=(1,2,3,'final',0) -D__version__=1.2.3 -I/usr/include/mysql -I/opt/lampp/include/python2.7 -c _mysql.c -o build/temp.linux-x86_64-2.7/_mysql.o -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fwrapv
In file included from /opt/lampp/include/python2.7/Python.h:58,
from pymemcompat.h:10,
from _mysql.c:29:
/opt/lampp/include/python2.7/pyport.h:849:2: error: #error "LONG_BIT definition appears wrong for platform (bad gcc/glibc config?)."
In file included from /usr/include/mysql/my_config.h:11,
from _mysql.c:36:
/usr/include/mysql/my_config_x86_64.h:1032:1: warning: "SIZEOF_LONG" redefined
In file included from /opt/lampp/include/python2.7/Python.h:8,
from pymemcompat.h:10,
from _mysql.c:29:
/opt/lampp/include/python2.7/pyconfig.h:989:1: warning: this is the location of the previous definition
error: command 'gcc' failed with exit status 1
you need the mysql-devel package. to install, you need to specify the actual package name -
sudo apt-get install libmysql++-dev
Have you tried using the sudo command. I am guessing you are having permission issues than issue with anything else here. Usually an install throws up this error as it is trying to access directories with root permission which you don't own.