cryoem / eman2 Goto Github PK
View Code? Open in Web Editor NEWA scientific image processing software suite with a focus on CryoEM and CryoET
A scientific image processing software suite with a focus on CryoEM and CryoET
Steps to reproduce:
python -m eman2_gui.emimagemx
Traceback (most recent call last):
File "/miniconda/lib/python2.7/site-packages/eman2_gui/emimagemx.py", line 1968, in mouseReleaseEvent
self.__app_mode_mouse_up(event)
File "/miniconda/lib/python2.7/site-packages/eman2_gui/emimagemx.py", line 1729, in __app_mode_mouse_up
self.mx_mouseup.emit(event, lc)
TypeError: EMImageMXWidget.mx_mouseup[QMouseEvent, tuple].emit(): argument 2 has unexpected type 'NoneType'
diff --git libpyEM/libpyTypeConverter2.cpp libpyEM/libpyTypeConverter2.cpp
index c9c4461fa..5aa4ff983 100644
--- libpyEM/libpyTypeConverter2.cpp
+++ libpyEM/libpyTypeConverter2.cpp
@@ -112,6 +112,7 @@ BOOST_PYTHON_MODULE(libpyTypeConverter2)
EMAN::EMObject_to_python();
EMAN::Dict_to_python();
EMAN::String_to_python();
EMAN::String_from_python();
EMAN::Dict_from_python();
EMAN::tuple3_to_pythonEMAN::IntPoint();
diff --git libpyEM/typeconverter.h libpyEM/typeconverter.h
index ace5ab315..34b474b55 100644
--- libpyEM/typeconverter.h
+++ libpyEM/typeconverter.h
@@ -915,6 +916,51 @@ namespace EMAN {
};
struct String_from_python {
String_from_python() {
boost::python::converter::registry::push_back(
&convertible,
&construct,
boost::python::type_id<std::string>());
}
// Determine if obj_ptr can be converted in a std::string
static void* convertible(PyObject* obj_ptr) {
if (!PyUnicode_Check(obj_ptr) && !PyBytes_Check(obj_ptr)) {
return 0;
}
return obj_ptr;
}
// Convert obj_ptr into a std::string
static void construct(
PyObject* obj_ptr,
boost::python::converter::rvalue_from_python_stage1_data* data) {
const char* value(nullptr);
boost::python::object temp_bytes_obj;
if (PyUnicode_Check(obj_ptr)) {
PyObject * temp_bytes(PyUnicode_AsEncodedString(obj_ptr, "UTF-8", "strict")); // Owned reference
if (temp_bytes != nullptr) {
// Take over lifetime management of temp_bytes
temp_bytes_obj = boost::python::object(boost::python::handle<>(temp_bytes));
value = PyBytes_AS_STRING(temp_bytes);
} else {
boost::python::throw_error_already_set();
}
} else if (PyBytes_Check(obj_ptr)) {
value = PyBytes_AS_STRING(obj_ptr);
} else {
boost::python::throw_error_already_set();
}
if (value == nullptr) boost::python::throw_error_already_set();
void* storage = (
(boost::python::converter::rvalue_from_python_storage<std::string>*)
data)->storage.bytes;
new (storage) std::string(value);
data->convertible = storage;
}
};
}
This is libEM/emdata_transform.cpp:1242-1245:
float k2 = (float)(kx*kx+ky*ky);
if (k2==0) { continue;}
float phiK =0;
if (k2>0) phiK= jxjyatan2[ (ky+Mid-1)*End + kx+Mid-1]; phiK= atan2((float)ky,(float)kx);
I observe first that unless the computation of k2
overflows, it never produces a negative value, and that if it produces exactly zero then the last two lines are not reached.
In that case, it is not necessary to check explicitly at line 1245 whether k2
exceeds 0. More significantly, however, the value copied into phiK
from jxjyatan2
is always immediately overwritten by the result of calling atan2()
. This probably constitutes only a trivial performance problem as long as the computed index into jxjyatan2
is a valid one, but it begs the question of whether something else was intended here.
An analogous computation of phiQ
appears deeper in the same loop nest, at lines 1255-1258. Comments analogous to the above apply to it.
Disabled openmpi test in PR #218, but, probably, needs to be fixed before the release. Tracking in this issue.
1 2 3
2 3 4
5 4 3
3 3 4
Plot 3D
Option + LeftClick
Traceback (most recent call last):
File "/miniconda/lib/python2.7/site-packages/eman2_gui/emplot3d.py", line 891, in mouseMoveEvent
self.add_shape("lcross",EMShape(("scrlabel",0,0,0,self.scrlim[2]-220,self.scrlim[3]-10,"%1.5g (%s), %1.5g"%(lc[0],recip,lc[1]),120.0,-1)))
NameError: global name 'lc' is not defined
This is libEM/processor.cpp:13695-13697:
EMData* selem = params["selem"];
float *sd = selem->get_data();
kernel = vector<float>(sd, sd + sizeof sd / sizeof sd[0]);
The intent appears to be to construct a vector<float>
representation of the data referenced by selem->get_data()
, but it does not actually do that. The problem is that sizeof sd
evaluates to the size of a pointer, probably 8 bytes on most current machines, whereas what is needed for computing the number of elements that way is the size of the whole array to which sd
points.
It looks like changing the last of those lines to
kernel = vector<float>(sd, sd + selem->get_size());
might produce the wanted result.
Hey guys,
I compiled your software (with the help of miniconda) and it compiled all right but when I ran make tests-verbose I got the following error:
` test 4
Start 4: progs
4: Test command: /bin/bash "/usr/local/eman2/tests/run_prog_tests.sh"
4: Test timeout computed to be: 9.99988e+06
4: basename: missing operand
4: Try 'basename --help' for more information.
4/5 Test #4: progs ............................***Failed 0.01 sec
test 5
Start 5: py-compile
5: Test command: /home/mbelouso/miniconda2/bin/python "-m" "compileall" "-q" "/usr/local/eman2"
5: Test timeout computed to be: 9.99988e+06
5/5 Test #5: py-compile ....................... Passed 0.04 sec
80% tests passed, 1 tests failed out of 5
Total Test time (real) = 12.47 sec
The following tests FAILED:
4 - progs (Failed)
Errors while running CTest
CMakeFiles/test-verbose.dir/build.make:57: recipe for target 'CMakeFiles/test-verbose' failed
make[3]: *** [CMakeFiles/test-verbose] Error 8
CMakeFiles/Makefile2:163: recipe for target 'CMakeFiles/test-verbose.dir/all' failed
make[2]: *** [CMakeFiles/test-verbose.dir/all] Error 2
CMakeFiles/Makefile2:170: recipe for target 'CMakeFiles/test-verbose.dir/rule' failed
make[1]: *** [CMakeFiles/test-verbose.dir/rule] Error 2
Makefile:214: recipe for target 'test-verbose' failed
make: *** [test-verbose] Error 2 `
And when I try and run something basic like e2display.py
File "/home/mbelouso/miniconda2/bin/e2display.py", line 2 from __future__ import print_function SyntaxError: future feature print_function is not defined
cmake didn't give any glaring errors, although when it compiled there we lots and lots of warnings about unused variables...
Thanks for your time and efforts with this project!
Steps to reproduce:
python -m eman2_gui.emimage2d
Shift
+ scroll mouse wheelTraceback (most recent call last):
File "/miniconda/lib/python2.7/site-packages/eman2_gui/emimage2d.py", line 1748, in wheelEvent
self.mousewheel.emit(event)
TypeError: EMImage2DWidget.mousewheel[QMouseEvent].emit(): argument 1 has unexpected type 'QWheelEvent'
The definition in libEM/sparx/util_sparx.h says
static vector<float> multiref_polar_ali_2d_delta(EMData* image, const vector< EMData* >& crefim,
vector<float> xrng, vector<float> yrng, float step, string mode,
vector< int >numr, float cnx, float cny, float delta_start, float delta);
while the one in libpyUtils2.cpp says
.def("multiref_polar_ali_2d_delta", &EMAN::Util::multiref_polar_ali_2d_delta, args("image", "crefim", "xrng", "yrng", "step", "mode", "numr", "cnx", "cny"), "formerly known as apmq\nDetermine shift and rotation between image and many referenceimages (crefim, weights have to be applied) quadratic\ninterpolation")
Note the missing two arguments in the libpyUtils2 definition.
I have been trying to install EMAN 2.22 and 2.3 on linux and get the same errors about not being able to import: from past.utils import old_div
As far as I can tell, this is backwards-compat shim, but the python installed by the eman2 installer is not python 3... so this is not needed?
Dear developer:
I am trying to build from source according to the webpage.
However when I execute the cmake line I encounter the following error:
(eman-env) user@ubuntu16:~/EMANSRC/eman2-src$ sudo cmake ../eman2
CMake Deprecation Warning at CMakeLists.txt:9 (cmake_policy):
The OLD behavior for policy CMP0002 will be removed from a future version
of CMake.
The cmake-policies(7) manual explains that the OLD behaviors of all
policies are deprecated and that a policy should be set to OLD only under
specific short-term circumstances. Projects should be ported to the NEW
behavior and not rely on setting a policy to OLD.
# conda environments:
#
/home/user/EMAN2
base * /usr/local/anaconda2
eman-env /usr/local/anaconda2/envs/eman-env
py36 /usr/local/anaconda2/envs/py36
CMAKE_PREFIX_PATH: /usr/local/anaconda2/envs/eman-env;/usr/local/anaconda2/envs/eman-env/..
PYTHON_EXECUTABLE: /usr/local/anaconda2/envs/eman-env/bin/python
PYTHON_LIBRARIES: /usr/local/anaconda2/envs/eman-env/lib/libpython2.7.so
PYTHON_INCLUDE_DIRS: /usr/local/anaconda2/envs/eman-env/include/python2.7
PYTHON_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include/python2.7
PYTHON_INCLUDE_DIR: /usr/local/anaconda2/envs/eman-env/include/python2.7
NUMPY_INCLUDE_DIR: /usr/local/anaconda2/envs/eman-env/lib/python2.7/site-packages/numpy/core/include
Python site-packages: /usr/local/anaconda2/envs/eman-env/lib/python2.7/site-packages
### BEGIN ### CHECK_REQUIRED_LIB FFTW3F fftw3f fftw3.h libfftw3f-3
FFTW3F_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include
FFTW3F_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libfftw3f.so
Searching in /usr/local/anaconda2/envs/eman-env/include for fftw3.h and ...
FIND_LIBRARY: FFTW3F_LIBRARY NAMES fftw3f libfftw3f-3 PATHS /lib /usr/local/anaconda2/envs/eman-env/lib
### END ### CHECK_REQUIRED_LIB FFTW3F fftw3f fftw3.h libfftw3f-3
FFTW3F_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include
FFTW3F_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libfftw3f.so
### BEGIN ### CHECK_REQUIRED_LIB FFTW3D fftw3 fftw3.h libfftw3-3
FFTW3D_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include
FFTW3D_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libfftw3.so
Searching in /usr/local/anaconda2/envs/eman-env/include for fftw3.h and ...
FIND_LIBRARY: FFTW3D_LIBRARY NAMES fftw3 libfftw3-3 PATHS /lib /usr/local/anaconda2/envs/eman-env/lib
### END ### CHECK_REQUIRED_LIB FFTW3D fftw3 fftw3.h libfftw3-3
FFTW3D_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include
FFTW3D_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libfftw3.so
TIFF_LIBRARIES: /usr/local/anaconda2/envs/eman-env/lib/libtiff.so
JPEG_LIBRARIES: /usr/local/anaconda2/envs/eman-env/lib/libjpeg.so
### BEGIN ### CHECK_REQUIRED_LIB HDF5 hdf5 hdf5.h
HDF5_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include
HDF5_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libhdf5.so
Searching in /usr/local/anaconda2/envs/eman-env/include for hdf5.h and ...
FIND_LIBRARY: HDF5_LIBRARY NAMES hdf5 PATHS /lib /usr/local/anaconda2/envs/eman-env/lib
### END ### CHECK_REQUIRED_LIB HDF5 hdf5 hdf5.h
HDF5_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include
HDF5_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libhdf5.so
HDF5_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libhdf5.so
PNG_LIBRARIES: /usr/local/anaconda2/envs/eman-env/lib/libpng.so;/usr/local/anaconda2/envs/eman-env/lib/libz.so
CMake Error at /usr/local/anaconda2/share/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find OpenGL (missing: OPENGL_gl_LIBRARY)
Call Stack (most recent call first):
/usr/local/anaconda2/share/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:377 (_FPHSA_FAILURE_MESSAGE)
/usr/local/anaconda2/share/cmake-3.9/Modules/FindOpenGL.cmake:170 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
cmake/OpenGL.cmake:1 (find_package)
libEM/CMakeLists.txt:175 (include)
-- Configuring incomplete, errors occurred!
See also "/home/user/EMANSRC/eman2-src/CMakeFiles/CMakeOutput.log".
See also "/home/user/EMANSRC/eman2-src/CMakeFiles/CMakeError.log".
But I think I have already installed opengl
(eman-env) user@ubuntu16:~/EMANSRC/eman2-src$ locate libGL.so
/home/users/user/MATLAB/R2017b/sys/opengl/lib/glnxa64/libGL.so.1
/home/users/user/MATLAB/R2017b/sys/opengl/lib/glnxa64/libGL.so.1.6.0
/usr/lib/i386-linux-gnu/mesa/libGL.so.1
/usr/lib/i386-linux-gnu/mesa/libGL.so.1.2.0
/usr/lib/nvidia-387/libGL.so
/usr/lib/nvidia-387/libGL.so.1
/usr/lib/nvidia-387/libGL.so.1.0.0
/usr/lib/x86_64-linux-gnu/libGL.so
/usr/lib/x86_64-linux-gnu/mesa/libGL.so
/usr/lib/x86_64-linux-gnu/mesa/libGL.so.1
/usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0
/usr/lib32/nvidia-387/libGL.so
/usr/lib32/nvidia-387/libGL.so.1
/usr/lib32/nvidia-387/libGL.so.1.0.0
Any suggestions will be appreciated!
Thanks!
When using e2projectmanager.py, python has an issue with its tk support. I am using EMAN2.2alpha binary installation in CentOS 7.
The error is the following:
import _tkinter # If this fails your Python may not be configured for Tk
ImportError: No module named _tkinter
Other version I have for python do not have this issue.
Cheers,
test_write_jpeg
started failing on Mac Jenkins, but not on TravisCI, and has been disabled in 29ee455, until it is sorted out.
I am using the latest version of EMAN2.2 and I am trying to segment a tomogram using the CNN protocol in EMAN. Annotation works quite fine for most of the features however, in some cases microtubules are being picked as single membrane feature, even after extensive training. In the online instruction it has been suggested to train the neuronal network separately on the features that cause ambiguity and then run annotations against each other using mergetomoseg.py <annotation #1> <annotation #2> <...> --output . However, when I run mergetomoseg.py, I get the error message that the command not found. I am wondering if you have any suggestion for this issue? Is there any replacement for this command in EMAN2.2?
Thanks very much for your help in advance.
Upon installing Eman2 on Ubuntu16.04, when I tried running e2projectmanager.py, this came up:
(eman-env) root@thlab:~/.conda/envs/eman-env/bin# e2projectmanager.py Traceback (most recent call last): File "/home/thlab/.conda/envs/eman-env/bin/e2projectmanager.py", line 35, in <module> from past.utils import old_div ImportError: No module named past.utils
Future is already installed using pip.
Hi,
Sorry for bothering you with that many questions.
I could now resolve almost all issues and can consistently build EMAN 2.3 from source, both, using dependencies built with CONDA and using dependencies built without CONDA.
The last missing piece is to make EMAN 2.3 using our centrally provided OpenMPI as it was compiled with support for our batch system (LSF).
Why do you have a requirement to have OpenMPI built with --disable-dlopen ? Unfortunately, our MPI is compiled with --enable-dlopen. This parameter determines, if the OpenMPI plugins are built as separate libraries (DSO) or if they are added to the main MPI library.
I don't understand how this can affect a software using OpenMPI. Shouldn't a software work independent of how OpenMPI is compiled with regards to DSO ?
Best regards and that you for the help you provided so far.
Sam
I was following the instructions on the EMAN wiki to build from source, but I'm stuck at the cmake step. Here is the error output:
HDF5_INCLUDE_PATH: /home/xguan/anaconda2/envs/eman-env/include
HDF5_LIBRARY: /home/xguan/anaconda2/envs/eman-env/lib/libhdf5.so
Searching in /home/xguan/anaconda2/envs/eman-env/include for hdf5.h and ...
FIND_LIBRARY: HDF5_LIBRARY NAMES hdf5 PATHS /lib /home/xguan/anaconda2/envs/eman-env/lib
HDF5_INCLUDE_PATH: /home/xguan/anaconda2/envs/eman-env/include
HDF5_LIBRARY: /home/xguan/anaconda2/envs/eman-env/lib/libhdf5.so
HDF5_LIBRARY: /home/xguan/anaconda2/envs/eman-env/lib/libhdf5.so
PNG_LIBRARIES: /home/xguan/anaconda2/envs/eman-env/lib/libpng.so;/home/xguan/anaconda2/envs/eman-env/lib/libz.so
CMake Error at /home/xguan/anaconda2/envs/eman-env/share/cmake-3.8/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find OpenGL (missing: OPENGL_gl_LIBRARY OPENGL_INCLUDE_DIR)
Call Stack (most recent call first):
/home/xguan/anaconda2/envs/eman-env/share/cmake-3.8/Modules/FindPackageHandleStandardArgs.cmake:377 (_FPHSA_FAILURE_MESSAGE)
/home/xguan/anaconda2/envs/eman-env/share/cmake-3.8/Modules/FindOpenGL.cmake:170 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
cmake/OpenGL.cmake:1 (find_package)
libEM/CMakeLists.txt:175 (include)
Thanks for your help!
Some code in e2ctf and e2eulerxplor is called from some places in libpyEM
. This prevents those modules to be run as programs which is useful for testing.
To be addressed after the release.
Traceback (most recent call last):
File "/Users/shadow_walker/eman2/bin/e2pdbviewer.py", line 34, in <module>
from emdataitem3d import EMStructureItem3D
ImportError: cannot import name EMStructureItem3D
@lucalusn , the commits on branch add_tests_sphire1_3 seem to be always failing. If the tests are not important for you, can you skip tests by including "[ci skip]" in your commit messages or move your branch from cryoem/eman2 to your own fork.
Hi specialists,
I'm trying to install eman2.31 on my ubuntu 16.04 system but met some problems.
I use cmake3.9 and can't find FFTW3. However, I have install fftw3.3.8 and make them in bashrc.
Here is the log file, please help me.
(base) linzhaohan@linzhaohan-MS-7B89:~/Downloads/eman2/build$ cmake ..
-- CMAKE_PREFIX_PATH="/home/linzhaohan/anaconda2;/home/linzhaohan/anaconda2/.."
PYTHON_EXECUTABLE: /home/linzhaohan/anaconda2/bin/python
PYTHON_LIBRARIES: /home/linzhaohan/anaconda2/lib/libpython2.7.so
PYTHON_INCLUDE_DIRS: /home/linzhaohan/anaconda2/include/python2.7
PYTHON_INCLUDE_PATH: /home/linzhaohan/anaconda2/include/python2.7
PYTHON_INCLUDE_DIR: /home/linzhaohan/anaconda2/include/python2.7
Python site-packages: /home/linzhaohan/anaconda2/lib/python2.7/site-packages
-- NUMPY_INCLUDE_DIR="/home/linzhaohan/anaconda2/lib/python2.7/site-packages/numpy/core/include"
-- Boost version: 1.58.0
-- Found the following Boost libraries:
-- python
Boost_LIBRARIES: /usr/lib/x86_64-linux-gnu/libboost_python.so
Boost_INCLUDE_DIR: /usr/local/include
-- HDF5_LIBRARY="/home/linzhaohan/anaconda2/lib/libhdf5.so"
CMake Error at cmake/functions.cmake:51 (MESSAGE):
ERROR: FFTW3F not found. please install FFTW3F first!
Call Stack (most recent call first):
cmake/FindFFTW3.cmake:1 (CHECK_REQUIRED_LIB)
libEM/CMakeLists.txt:95 (find_package)
CMake Error at cmake/functions.cmake:51 (MESSAGE):
ERROR: FFTW3D not found. please install FFTW3D first!
Call Stack (most recent call first):
cmake/FindFFTW3.cmake:2 (CHECK_REQUIRED_LIB)
libEM/CMakeLists.txt:95 (find_package)
CMake Error at cmake/functions.cmake:51 (MESSAGE):
ERROR: FFTW3F_THREADS not found. please install FFTW3F_THREADS first!
Call Stack (most recent call first):
cmake/FindFFTW3.cmake:4 (CHECK_REQUIRED_LIB)
libEM/CMakeLists.txt:95 (find_package)
CMake Error at cmake/functions.cmake:51 (MESSAGE):
ERROR: FFTW3D_THREADS not found. please install FFTW3D_THREADS first!
Call Stack (most recent call first):
cmake/FindFFTW3.cmake:5 (CHECK_REQUIRED_LIB)
libEM/CMakeLists.txt:95 (find_package)
CMake Error at /usr/local/share/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find FFTW3 (missing: FFTW3F_INCLUDE_PATH FFTW3F_LIBRARY
FFTW3D_INCLUDE_PATH FFTW3D_LIBRARY FFTW3F_THREADS_INCLUDE_PATH
FFTW3F_THREADS_LIBRARY FFTW3D_THREADS_INCLUDE_PATH FFTW3D_THREADS_LIBRARY)
Call Stack (most recent call first):
/usr/local/share/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:377 (_FPHSA_FAILURE_MESSAGE)
cmake/FindFFTW3.cmake:11 (find_package_handle_standard_args)
libEM/CMakeLists.txt:95 (find_package)
-- Configuring incomplete, errors occurred!
See also "/home/linzhaohan/Downloads/eman2/build/CMakeFiles/CMakeOutput.log".
See also "/home/linzhaohan/Downloads/eman2/build/CMakeFiles/CMakeError.log".
Thanks a lot!
Best,
Zhaohan Lin
It seems to be standard practice in this codebase to insert cast operators into the declarations of Boost.Python method wrappers, such as in this example from line 612 of libpyEM/libpyAligner2.cpp:
.def("compute_1d_fromimage", (std::vector<float,std::allocator<float> > (EMAN::EMAN2Ctf::*)(int, float, EMAN::EMData*) )&EMAN::EMAN2Ctf::compute_1d, (std::vector<float,std::allocator<float> > (EMAN_EMAN2Ctf_Wrapper::*)(int, float, EMAN::EMData*))&EMAN_EMAN2Ctf_Wrapper::default_compute_1d_fromimage)
I guess this is to match overloads. Such casts should be fine, provided that the target type of the cast is compatible with the type of the function. If it isn't compatible, however, as in the case of the above example, then undefined behavior ensues when the function is called via the wrapper. In practice, it looks like the mismatches of this type appearing in the codebase are likely to produce genuine misbehavior.
The issue with the above example is that EMAN2Ctf::compute_1d
takes four arguments (one with a default value), not three, and the type of the third is EMAN::Ctf::CtfType
, not EMAN::EMData *
.
Several other occurrences of such issues appear in libpyEM/libpyTransform2.cpp:
Vec4f.set_value
)Vec3f.set_value
)Vec3i.set_value
)Vec2f.set_value
)Transform.translate_newbasis
overload)The problem in all the vector cases is that the relevant set_value()
methods in the vector templates declare their arguments to be const
references, whereas the casts specify that they are ordinary passed-by-value built-in types. The problem in the Transform case appears to be that the wrong method is being wrapped -- from the signature and a comparison to the order of method declarations in libEM/transform.h, it appears that the intention was to wrap the fourth form of Transform.translate()
, not a second form of Transform.translate_newBasis()
(which does not exist).
Hi specialists,
I am trying install EMAN2.2 (centos6 or centos7 version). But when I ran e2display.py and failed with a error as following.
$ e2display.py
Traceback (most recent call last):
File "/home/jianhaoc/s/EMAN22centos6/bin/e2display.py", line 34, in
from EMAN2 import EMANVERSION, E2init, E2end, EMData, base_name, file_exists, EMArgumentParser
ImportError: cannot import name EMANVERSION
I tried other programmes. e2proc3d.py is ok for both versions, but e2proc2d.py or e2reliontoeman.py didn't work for neither versions.
$ e2reliontoeman.py --help
Traceback (most recent call last):
File "/home/jianhaoc/s/EMAN22centos7/bin/e2reliontoeman.py", line 157, in
main()
File "/home/jianhaoc/s/EMAN22centos7/bin/e2reliontoeman.py", line 56, in main
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
NameError: global name 'EMANVERSION' is not defined
$ e2proc2d.py --help
Traceback (most recent call last):
File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 1171, in
main()
File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 174, in main
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
NameError: global name 'EMANVERSION' is not defined
Am I missing something? Thank you!
Regards,
Jianhao
When I run this code on my local HPC cluster, I receive this error when running the refine.py script for multi-reference refinement:
Traceback (most recent call last):
File "/opt/qb3/eman2-2.05/contrib/nogales/refine.py", line 35, in <module>
import global_def
ImportError: No module named global_def
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
Hello. I have installed the binary version of EMAN2 on a rather old linux workstation and when we tried to run e2tomoseg_convnet.py we got the error of:
tensorflow.python.framework.errors_impl.InternalError: Failed to create session
i suspect that it is because the GPU is too old, because it works fine on newer workstations. And I am thinking about trying to compile EMAN2 against our GPU. However, I got stuck in the middle of compiling (even though I followed EMAN2 instructions) as I cannot let cmake recognize my conda path even though I ran cmake within conda environment.
Now at this stage, I have 3 questions:
Thanks a lot for any inputs!
Commit 817961d contains old-style QtCore.QObject.connect()
.
I have installed EMAN2 following this page: https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda/2.22
I'm working on my PC, the system is Ubuntu 16.04.
When I'm trying to test, the python e2version.py
works fine. Here's the output:
EMAN 2.22 final (GITHUB: 2018-08-20 20:32 - commit: f4f3952 )
Your EMAN2 is running on: Linux-4.8.0-36-generic-x86_64-with-debian-stretch-sid 4.8.0-36-generic
Your Python version is: 2.7.15
And when running e2speedtest.py
, the above error occurred:
ImportError: No module named past.utils
Could you give me some advice?
Thank you so much!!!
e2pdb2em.py:212-216
Also, can you provide a reference for constants (Table 1)?
I'm having difficulty installing EMAN2 2.3 on an Ubuntu 18.04 machine.
Following instructions, I run
bash eman2.3.linux64.sh
Installation proceeds for a while, but eventually this error is printed
wcwidth-0.1.7 | 25 KB | ########## | 100%
blas-1.0 | 6 KB | ########## | 100%
openmpi-2.0.2 | 2.6 MB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... ERROR conda.core.link:_execute_post_link_actions(658): An error occurred while installing package 'conda-forge::pyopengl-3.1.0-py27_0'.
LinkError: post-link script failed for package conda-forge::pyopengl-3.1.0-py27_0
running your command again with `-v` will provide additional information
location of failed script: /home/ubuntu/EMAN2/bin/.pyopengl-post-link.sh
==> script messages <==
<None>
Attempting to roll back.
failed
ERROR conda.core.link:_execute(568): An error occurred while installing package 'conda-forge::pyopengl-3.1.0-py27_0'.
LinkError: post-link script failed for package conda-forge::pyopengl-3.1.0-py27_0
running your command again with `-v` will provide additional information
location of failed script: /home/ubuntu/EMAN2/bin/.pyopengl-post-link.sh
==> script messages <==
<None>
Attempting to roll back.
Rolling back transaction: ...working... done
CondaMultiError: LinkError: post-link script failed for package conda-forge::pyopengl-3.1.0-py27_0
running your command again with `-v` will provide additional information
location of failed script: /home/ubuntu/EMAN2/bin/.pyopengl-post-link.sh
==> script messages <==
<None>
+ cat
INSTALLATION IS NOW COMPLETE
Afterwards, I cannot get EMAN2 binaries to work, with the following error:
ubuntu@ip-172-31-12-165:~$ e2proc3d.py
Traceback (most recent call last):
File "/home/ubuntu/EMAN2/bin/e2proc3d.py", line 37, in <module>
from past.utils import old_div
ImportError: No module named past.utils
Any help is appreciated! A similar error occurred when I tried to install the previous version 2.22
The machine is a relatively fresh EC2 instance - I did have an existing Anaconda3 install, but I removed it from .bashrc
and my environment prior to installing EMAN2.
Also, e2version.py
appears to work:
ubuntu@ip-172-31-12-165:~$ e2version.py
EMAN 2.3 final (GITHUB: 2019-04-25 14:05 - commit: 6aaac88 )
Your EMAN2 is running on: Linux-4.15.0-1045-aws-x86_64-with-debian-buster-sid 4.15.0-1045-aws
Your Python version is: 2.7.16
This is the main issue to track fixing individual programs.
It was created by ZenHub, https://app.zenhub.com/workspace/o/cryoem/eman2/boards?repos=48064767, as an Epic issue
, but doesn't show the sub-issues, maybe, because ZenHub is not used organization-wide.
This error comes up when compiled with py3
.
eman2/examples/e2ddd_external.py
Lines 87 to 88 in 98bea25
*** Error compiling './examples/e2ddd_external.py'...
File "./examples/e2ddd_external.py", line 89
parser.add_argument("--dark", default = None, type=str, help="Use this dark reference.", guitype='filebox', browser="EMMovieDataTable(withmodal=True,multiselect=True)", row=2, col=0, rowspan=1, colspan=2, mode="align", mode="movie")
^
SyntaxError: keyword argument repeated
Hi,
I am using CMake 3.12.4 to build eman2 from source (I also tested with CMake 3.14.4 and got the same error) and got the following error:
CMake Error at /cluster/apps/gcc-4.8.5/cmake-3.14.4-2yckzriatk5ei7cuqncwz5il26gb63oz/share/cmake-3.14/Modules/FindFreetype.cmake:178
(set_property):
set_property can not be used on an ALIAS target.
Call Stack (most recent call first):
cmake/Freetype.cmake:1 (find_package)
cmake/FindFTGL.cmake:27 (include)
libEM/CMakeLists.txt:180 (find_package)
Is this a known problem ?
What version of CMake do you recommend to build eman2 ?
Any help is appreciated.
Hi, I'm a graduate student for biophysics.
I'm studying Single Particle Analysis recently, and I find EMAN2.
It's a wonderful software and helps me a lot. Thanks for your work!
Though I know it's a matter to solve dependencies problem of old codes. I still want to ask that do you have a plan or schedule to update EMAN2 from python2 to python3?
Anyway, best wishes! :)
$ e2refinetorelion2d.py -h
Running e2refinetorelion2d.py
Traceback (most recent call last):
File "/Users/shadow_walker/eman2/bin/e2refinetorelion2d.py", line 79, in <module>
(options, args) = parser.parse_args()
File "/Users/shadow_walker/EMAN2/lib/EMAN2.py", line 506, in parse_args
parsedargs = argparse.ArgumentParser.parse_args(self)
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 1701, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 1733, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 1939, in _parse_known_args
start_index = consume_optional(start_index)
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 1879, in consume_optional
take_action(action, args, option_string)
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 1807, in take_action
action(self, namespace, argument_values, option_string)
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 996, in __call__
parser.print_help()
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 2340, in print_help
self._print_message(self.format_help(), file)
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 2314, in format_help
return formatter.format_help()
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 281, in format_help
help = self._root_section.format_help()
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 211, in format_help
func(*args)
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 211, in format_help
func(*args)
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 517, in _format_action
help_text = self._expand_help(action)
File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 603, in _expand_help
return self._get_help_string(action) % params
ValueError: unsupported format character '=' (0x3d) at index 41
We have several researchers clamoring for this new and improved version of EMAN2, but I am having a heck of a time getting it to run. To troubleshoot, I have started my install attempts in a docker container. The install feels like it could use some work. I can try to run parts of EMAN2 after an install and figure out which things are missing here and there, but that feels inefficient if there are folks who have this running for them.
I'm hopeful that someone more familiar with what is needed could give it a once-over and update things so all needed packages are properly installed (preferably once?). It would also be really nice if the site that the installer points to for documentation (https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda) had some. If there is some way in which I can contribute I am open to suggestions.
Here is the dockerfile:
FROM ubuntu:18.04
RUN apt-get update && \
apt-get -y install build-essential \
libgl1-mesa-dev \
libglu1-mesa \
libglu1-mesa-dev \
libsm-dev \
libxrender-dev \
mesa-common-dev \
mesa-utils \
wget
RUN cd /tmp && \
wget --quiet https://cryoem.bcm.edu/cryoem/static/software/release-2.3/eman2.3.linux64.sh && \
bash ./eman2.3.linux64.sh -b -t -p /opt/EMAN2
ENV PATH="/opt/EMAN2/bin:$PATH"
And the log from a build attempt:
$ docker build -t eman2:2.3-testing .
Sending build context to Docker daemon 2.56kB
Step 1/4 : FROM ubuntu:18.04
---> d131e0fa2585
Step 2/4 : RUN apt-get update && apt-get -y install build-essential libgl1-mesa-dev libglu1-mesa libglu1-mesa-dev libsm-dev libxrender-dev mesa-common-dev mesa-utils wget
---> Running in b96d2a72e160
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
binutils binutils-common binutils-x86-64-linux-gnu ca-certificates cpp cpp-7
dirmngr dpkg-dev fakeroot g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base gnupg
gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf
gpgsm libalgorithm-diff-perl libalgorithm-diff-xs-perl
libalgorithm-merge-perl libasan4 libasn1-8-heimdal libassuan0 libatomic1
libbinutils libbsd0 libc-dev-bin libc6-dev libcc1-0 libcilkrts5 libdpkg-perl
libdrm-amdgpu1 libdrm-common libdrm-dev libdrm-intel1 libdrm-nouveau2
libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1 libexpat1
libfakeroot libfile-fcntllock-perl libgbm1 libgcc-7-dev libgcc1
libgdbm-compat4 libgdbm5 libgl1 libgl1-mesa-dri libglapi-mesa libgles1
libgles2 libglvnd-core-dev libglvnd-dev libglvnd0 libglx-mesa0 libglx0
libgomp1 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
libheimntlm0-heimdal libhx509-5-heimdal libice-dev libice6 libisl19 libitm1
libkrb5-26-heimdal libksba8 libldap-2.4-2 libldap-common libllvm7
liblocale-gettext-perl liblsan0 libmpc3 libmpfr6 libmpx2 libnpth0 libopengl0
libpciaccess0 libperl5.26 libpsl5 libpthread-stubs0-dev libquadmath0
libreadline7 libroken18-heimdal libsasl2-2 libsasl2-modules
libsasl2-modules-db libsensors4 libsm6 libsqlite3-0 libssl1.1
libstdc++-7-dev libstdc++6 libtsan0 libubsan0 libwayland-client0
libwayland-server0 libwind0-heimdal libx11-6 libx11-data libx11-dev
libx11-doc libx11-xcb-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0
libxcb-dri2-0-dev libxcb-dri3-0 libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev
libxcb-present-dev libxcb-present0 libxcb-randr0 libxcb-randr0-dev
libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev
libxcb-sync-dev libxcb-sync1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb1
libxcb1-dev libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev
libxext6 libxfixes-dev libxfixes3 libxrender1 libxshmfence-dev libxshmfence1
libxxf86vm-dev libxxf86vm1 linux-libc-dev make manpages manpages-dev
multiarch-support netbase openssl patch perl perl-modules-5.26
pinentry-curses publicsuffix readline-common x11-common x11proto-core-dev
x11proto-damage-dev x11proto-dev x11proto-fixes-dev x11proto-xext-dev
x11proto-xf86vidmode-dev xorg-sgml-doctools xtrans-dev xz-utils
Suggested packages:
binutils-doc cpp-doc gcc-7-locales dbus-user-session libpam-systemd
pinentry-gnome3 tor debian-keyring g++-multilib g++-7-multilib gcc-7-doc
libstdc++6-7-dbg gcc-multilib autoconf automake libtool flex bison gdb
gcc-doc gcc-7-multilib libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
libasan4-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg
libmpx2-dbg libquadmath0-dbg parcimonie xloadimage scdaemon glibc-doc git
bzr gdbm-l10n libice-doc pciutils libsasl2-modules-gssapi-mit
| libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp
libsasl2-modules-sql lm-sensors libsm-doc libstdc++-7-doc libxcb-doc
libxext-doc make-doc man-browser ed diffutils-doc perl-doc
libterm-readline-gnu-perl | libterm-readline-perl-perl pinentry-doc
readline-doc
The following NEW packages will be installed:
binutils binutils-common binutils-x86-64-linux-gnu build-essential
ca-certificates cpp cpp-7 dirmngr dpkg-dev fakeroot g++ g++-7 gcc gcc-7
gcc-7-base gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client
gpg-wks-server gpgconf gpgsm libalgorithm-diff-perl
libalgorithm-diff-xs-perl libalgorithm-merge-perl libasan4 libasn1-8-heimdal
libassuan0 libatomic1 libbinutils libbsd0 libc-dev-bin libc6-dev libcc1-0
libcilkrts5 libdpkg-perl libdrm-amdgpu1 libdrm-common libdrm-dev
libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0
libegl1 libelf1 libexpat1 libfakeroot libfile-fcntllock-perl libgbm1
libgcc-7-dev libgdbm-compat4 libgdbm5 libgl1 libgl1-mesa-dev libgl1-mesa-dri
libglapi-mesa libgles1 libgles2 libglu1-mesa libglu1-mesa-dev
libglvnd-core-dev libglvnd-dev libglvnd0 libglx-mesa0 libglx0 libgomp1
libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
libheimntlm0-heimdal libhx509-5-heimdal libice-dev libice6 libisl19 libitm1
libkrb5-26-heimdal libksba8 libldap-2.4-2 libldap-common libllvm7
liblocale-gettext-perl liblsan0 libmpc3 libmpfr6 libmpx2 libnpth0 libopengl0
libpciaccess0 libperl5.26 libpsl5 libpthread-stubs0-dev libquadmath0
libreadline7 libroken18-heimdal libsasl2-2 libsasl2-modules
libsasl2-modules-db libsensors4 libsm-dev libsm6 libsqlite3-0 libssl1.1
libstdc++-7-dev libtsan0 libubsan0 libwayland-client0 libwayland-server0
libwind0-heimdal libx11-6 libx11-data libx11-dev libx11-doc libx11-xcb-dev
libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri2-0-dev libxcb-dri3-0
libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev libxcb-present-dev
libxcb-present0 libxcb-randr0 libxcb-randr0-dev libxcb-render0
libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev libxcb-sync-dev
libxcb-sync1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb1 libxcb1-dev
libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6
libxfixes-dev libxfixes3 libxrender-dev libxrender1 libxshmfence-dev
libxshmfence1 libxxf86vm-dev libxxf86vm1 linux-libc-dev make manpages
manpages-dev mesa-common-dev mesa-utils multiarch-support netbase openssl
patch perl perl-modules-5.26 pinentry-curses publicsuffix readline-common
wget x11-common x11proto-core-dev x11proto-damage-dev x11proto-dev
x11proto-fixes-dev x11proto-xext-dev x11proto-xf86vidmode-dev
xorg-sgml-doctools xtrans-dev xz-utils
The following packages will be upgraded:
gcc-8-base libgcc1 libstdc++6
3 upgraded, 180 newly installed, 0 to remove and 2 not upgraded.
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Get:36 http://archive.ubuntu.com/ubuntu bionic/main amd64 manpages all 4.15-1 [1234 kB]
Get:37 http://archive.ubuntu.com/ubuntu bionic/main amd64 publicsuffix all 20180223.1310-1 [97.6 kB]
Get:38 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 wget amd64 1.19.4-1ubuntu2.2 [316 kB]
Get:39 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 binutils-common amd64 2.30-21ubuntu1~18.04.1 [193 kB]
Get:40 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libbinutils amd64 2.30-21ubuntu1~18.04.1 [501 kB]
Get:41 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 binutils-x86-64-linux-gnu amd64 2.30-21ubuntu1~18.04.1 [1854 kB]
Get:42 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 binutils amd64 2.30-21ubuntu1~18.04.1 [3396 B]
Get:43 http://archive.ubuntu.com/ubuntu bionic/main amd64 libc-dev-bin amd64 2.27-3ubuntu1 [71.8 kB]
Get:44 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 linux-libc-dev amd64 4.15.0-48.51 [1006 kB]
Get:45 http://archive.ubuntu.com/ubuntu bionic/main amd64 libc6-dev amd64 2.27-3ubuntu1 [2587 kB]
Get:46 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gcc-7-base amd64 7.4.0-1ubuntu1~18.04 [19.0 kB]
Get:47 http://archive.ubuntu.com/ubuntu bionic/main amd64 libisl19 amd64 0.19-1 [551 kB]
Get:48 http://archive.ubuntu.com/ubuntu bionic/main amd64 libmpfr6 amd64 4.0.1-1 [243 kB]
Get:49 http://archive.ubuntu.com/ubuntu bionic/main amd64 libmpc3 amd64 1.1.0-1 [40.8 kB]
Get:50 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 cpp-7 amd64 7.4.0-1ubuntu1~18.04 [6740 kB]
Get:51 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 cpp amd64 4:7.4.0-1ubuntu2.2 [27.6 kB]
Get:52 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libcc1-0 amd64 8.3.0-6ubuntu1~18.04 [47.4 kB]
Get:53 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgomp1 amd64 8.3.0-6ubuntu1~18.04 [76.4 kB]
Get:54 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libitm1 amd64 8.3.0-6ubuntu1~18.04 [27.9 kB]
Get:55 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libatomic1 amd64 8.3.0-6ubuntu1~18.04 [9180 B]
Get:56 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libasan4 amd64 7.4.0-1ubuntu1~18.04 [359 kB]
Get:57 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 liblsan0 amd64 8.3.0-6ubuntu1~18.04 [133 kB]
Get:58 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libtsan0 amd64 8.3.0-6ubuntu1~18.04 [288 kB]
Get:59 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libubsan0 amd64 7.4.0-1ubuntu1~18.04 [126 kB]
Get:60 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libcilkrts5 amd64 7.4.0-1ubuntu1~18.04 [42.5 kB]
Get:61 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libmpx2 amd64 8.3.0-6ubuntu1~18.04 [11.6 kB]
Get:62 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libquadmath0 amd64 8.3.0-6ubuntu1~18.04 [134 kB]
Get:63 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgcc-7-dev amd64 7.4.0-1ubuntu1~18.04 [2381 kB]
Get:64 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gcc-7 amd64 7.4.0-1ubuntu1~18.04 [7462 kB]
Get:65 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gcc amd64 4:7.4.0-1ubuntu2.2 [5184 B]
Get:66 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libstdc++-7-dev amd64 7.4.0-1ubuntu1~18.04 [1467 kB]
Get:67 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 g++-7 amd64 7.4.0-1ubuntu1~18.04 [7575 kB]
Get:68 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 g++ amd64 4:7.4.0-1ubuntu2.2 [1568 B]
Get:69 http://archive.ubuntu.com/ubuntu bionic/main amd64 make amd64 4.1-9.1ubuntu1 [154 kB]
Get:70 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdpkg-perl all 1.19.0.5ubuntu2.1 [211 kB]
Get:71 http://archive.ubuntu.com/ubuntu bionic/main amd64 patch amd64 2.7.6-2ubuntu1 [102 kB]
Get:72 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 dpkg-dev all 1.19.0.5ubuntu2.1 [608 kB]
Get:73 http://archive.ubuntu.com/ubuntu bionic/main amd64 build-essential amd64 12.4ubuntu1 [4758 B]
Get:74 http://archive.ubuntu.com/ubuntu bionic/main amd64 libassuan0 amd64 2.5.1-2 [35.0 kB]
Get:75 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpgconf amd64 2.2.4-1ubuntu1.2 [123 kB]
Get:76 http://archive.ubuntu.com/ubuntu bionic/main amd64 libksba8 amd64 1.3.5-2 [92.6 kB]
Get:77 http://archive.ubuntu.com/ubuntu bionic/main amd64 libroken18-heimdal amd64 7.5.0+dfsg-1 [41.3 kB]
Get:78 http://archive.ubuntu.com/ubuntu bionic/main amd64 libasn1-8-heimdal amd64 7.5.0+dfsg-1 [175 kB]
Get:79 http://archive.ubuntu.com/ubuntu bionic/main amd64 libheimbase1-heimdal amd64 7.5.0+dfsg-1 [29.3 kB]
Get:80 http://archive.ubuntu.com/ubuntu bionic/main amd64 libhcrypto4-heimdal amd64 7.5.0+dfsg-1 [85.9 kB]
Get:81 http://archive.ubuntu.com/ubuntu bionic/main amd64 libwind0-heimdal amd64 7.5.0+dfsg-1 [47.8 kB]
Get:82 http://archive.ubuntu.com/ubuntu bionic/main amd64 libhx509-5-heimdal amd64 7.5.0+dfsg-1 [107 kB]
Get:83 http://archive.ubuntu.com/ubuntu bionic/main amd64 libkrb5-26-heimdal amd64 7.5.0+dfsg-1 [206 kB]
Get:84 http://archive.ubuntu.com/ubuntu bionic/main amd64 libheimntlm0-heimdal amd64 7.5.0+dfsg-1 [14.8 kB]
Get:85 http://archive.ubuntu.com/ubuntu bionic/main amd64 libgssapi3-heimdal amd64 7.5.0+dfsg-1 [96.5 kB]
Get:86 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [14.8 kB]
Get:87 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [49.2 kB]
Get:88 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libldap-common all 2.4.45+dfsg-1ubuntu1.2 [16.7 kB]
Get:89 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libldap-2.4-2 amd64 2.4.45+dfsg-1ubuntu1.2 [155 kB]
Get:90 http://archive.ubuntu.com/ubuntu bionic/main amd64 libnpth0 amd64 1.5-3 [7668 B]
Get:91 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 dirmngr amd64 2.2.4-1ubuntu1.2 [316 kB]
Get:92 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfakeroot amd64 1.22-2ubuntu1 [25.9 kB]
Get:93 http://archive.ubuntu.com/ubuntu bionic/main amd64 fakeroot amd64 1.22-2ubuntu1 [62.3 kB]
Get:94 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gnupg-l10n all 2.2.4-1ubuntu1.2 [49.6 kB]
Get:95 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gnupg-utils amd64 2.2.4-1ubuntu1.2 [127 kB]
Get:96 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpg amd64 2.2.4-1ubuntu1.2 [467 kB]
Get:97 http://archive.ubuntu.com/ubuntu bionic/main amd64 pinentry-curses amd64 1.1.0-1 [35.8 kB]
Get:98 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpg-agent amd64 2.2.4-1ubuntu1.2 [227 kB]
Get:99 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpg-wks-client amd64 2.2.4-1ubuntu1.2 [91.9 kB]
Get:100 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpg-wks-server amd64 2.2.4-1ubuntu1.2 [84.9 kB]
Get:101 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpgsm amd64 2.2.4-1ubuntu1.2 [215 kB]
Get:102 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gnupg amd64 2.2.4-1ubuntu1.2 [249 kB]
Get:103 http://archive.ubuntu.com/ubuntu bionic/main amd64 libalgorithm-diff-perl all 1.19.03-1 [47.6 kB]
Get:104 http://archive.ubuntu.com/ubuntu bionic/main amd64 libalgorithm-diff-xs-perl amd64 0.04-5 [11.1 kB]
Get:105 http://archive.ubuntu.com/ubuntu bionic/main amd64 libalgorithm-merge-perl all 0.08-3 [12.0 kB]
Get:106 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-amdgpu1 amd64 2.4.95-1~18.04.1 [17.4 kB]
Get:107 http://archive.ubuntu.com/ubuntu bionic/main amd64 libpciaccess0 amd64 0.14-1 [17.9 kB]
Get:108 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-intel1 amd64 2.4.95-1~18.04.1 [59.9 kB]
Get:109 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-radeon1 amd64 2.4.95-1~18.04.1 [21.7 kB]
Get:110 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-nouveau2 amd64 2.4.95-1~18.04.1 [16.5 kB]
Get:111 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-dev amd64 2.4.95-1~18.04.1 [121 kB]
Get:112 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libwayland-server0 amd64 1.16.0-1ubuntu1.1~18.04.1 [29.8 kB]
Get:113 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgbm1 amd64 18.2.8-0ubuntu0~18.04.2 [24.2 kB]
Get:114 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglapi-mesa amd64 18.2.8-0ubuntu0~18.04.2 [23.4 kB]
Get:115 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libwayland-client0 amd64 1.16.0-1ubuntu1.1~18.04.1 [23.8 kB]
Get:116 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-xcb1 amd64 2:1.6.4-3ubuntu0.2 [9376 B]
Get:117 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-dri2-0 amd64 1.13-2~ubuntu18.04 [6920 B]
Get:118 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-dri3-0 amd64 1.13-2~ubuntu18.04 [6568 B]
Get:119 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-present0 amd64 1.13-2~ubuntu18.04 [5552 B]
Get:120 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-sync1 amd64 1.13-2~ubuntu18.04 [8808 B]
Get:121 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-xfixes0 amd64 1.13-2~ubuntu18.04 [9352 B]
Get:122 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxshmfence1 amd64 1.3-1 [5028 B]
Get:123 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libegl-mesa0 amd64 18.2.8-0ubuntu0~18.04.2 [87.5 kB]
Get:124 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfile-fcntllock-perl amd64 0.22-3build2 [33.2 kB]
Get:125 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libllvm7 amd64 1:7-3~ubuntu0.18.04.1 [15.9 MB]
Get:126 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsensors4 amd64 1:3.4.0-4 [28.8 kB]
Get:127 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgl1-mesa-dri amd64 18.2.8-0ubuntu0~18.04.2 [6587 kB]
Get:128 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglvnd0 amd64 1.0.0-2ubuntu2.2 [46.6 kB]
Get:129 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgles1 amd64 1.0.0-2ubuntu2.2 [11.2 kB]
Get:130 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-glx0 amd64 1.13-2~ubuntu18.04 [22.1 kB]
Get:131 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxdamage1 amd64 1:1.1.4-3 [6934 B]
Get:132 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxfixes3 amd64 1:5.0.3-1 [10.8 kB]
Get:133 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglx-mesa0 amd64 18.2.8-0ubuntu0~18.04.2 [135 kB]
Get:134 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglx0 amd64 1.0.0-2ubuntu2.2 [28.1 kB]
Get:135 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgl1 amd64 1.0.0-2ubuntu2.2 [84.8 kB]
Get:136 http://archive.ubuntu.com/ubuntu bionic/main amd64 libglu1-mesa amd64 9.0.0-2.1build1 [168 kB]
Get:137 http://archive.ubuntu.com/ubuntu bionic/main amd64 xorg-sgml-doctools all 1:1.11-1 [12.9 kB]
Get:138 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-dev all 2018.4-4 [251 kB]
Get:139 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-core-dev all 2018.4-4 [2620 B]
Get:140 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxau-dev amd64 1:1.0.8-1 [11.1 kB]
Get:141 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [25.1 kB]
Get:142 http://archive.ubuntu.com/ubuntu bionic/main amd64 xtrans-dev all 1.3.5-1 [70.5 kB]
Get:143 http://archive.ubuntu.com/ubuntu bionic/main amd64 libpthread-stubs0-dev amd64 0.3-4 [4068 B]
Get:144 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb1-dev amd64 1.13-2~ubuntu18.04 [80.0 kB]
Get:145 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-dev amd64 2:1.6.4-3ubuntu0.2 [640 kB]
Get:146 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 mesa-common-dev amd64 18.2.8-0ubuntu0~18.04.2 [559 kB]
Get:147 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglvnd-core-dev amd64 1.0.0-2ubuntu2.2 [12.9 kB]
Get:148 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libegl1 amd64 1.0.0-2ubuntu2.2 [31.9 kB]
Get:149 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgles2 amd64 1.0.0-2ubuntu2.2 [17.4 kB]
Get:150 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libopengl0 amd64 1.0.0-2ubuntu2.2 [31.3 kB]
Get:151 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglvnd-dev amd64 1.0.0-2ubuntu2.2 [3408 B]
Get:152 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-xcb-dev amd64 2:1.6.4-3ubuntu0.2 [9756 B]
Get:153 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-dri3-dev amd64 1.13-2~ubuntu18.04 [7384 B]
Get:154 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-randr0 amd64 1.13-2~ubuntu18.04 [16.4 kB]
Get:155 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-render0 amd64 1.13-2~ubuntu18.04 [14.7 kB]
Get:156 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-render0-dev amd64 1.13-2~ubuntu18.04 [18.4 kB]
Get:157 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-randr0-dev amd64 1.13-2~ubuntu18.04 [20.4 kB]
Get:158 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-shape0 amd64 1.13-2~ubuntu18.04 [5972 B]
Get:159 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-shape0-dev amd64 1.13-2~ubuntu18.04 [7144 B]
Get:160 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-xfixes0-dev amd64 1.13-2~ubuntu18.04 [11.7 kB]
Get:161 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-sync-dev amd64 1.13-2~ubuntu18.04 [10.6 kB]
Get:162 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-present-dev amd64 1.13-2~ubuntu18.04 [6972 B]
Get:163 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxshmfence-dev amd64 1.3-1 [3692 B]
Get:164 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-dri2-0-dev amd64 1.13-2~ubuntu18.04 [8472 B]
Get:165 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-glx0-dev amd64 1.13-2~ubuntu18.04 [27.9 kB]
Get:166 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-fixes-dev all 1:2018.4-4 [2620 B]
Get:167 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxfixes-dev amd64 1:5.0.3-1 [11.0 kB]
Get:168 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-damage-dev all 1:2018.4-4 [2620 B]
Get:169 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxdamage-dev amd64 1:1.1.4-3 [5028 B]
Get:170 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-xext-dev all 2018.4-4 [2620 B]
Get:171 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxext-dev amd64 2:1.3.3-1 [82.1 kB]
Get:172 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-xf86vidmode-dev all 2018.4-4 [2632 B]
Get:173 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxxf86vm-dev amd64 1:1.1.4-1 [13.3 kB]
Get:174 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgl1-mesa-dev amd64 18.2.8-0ubuntu0~18.04.2 [4428 B]
Get:175 http://archive.ubuntu.com/ubuntu bionic/main amd64 libglu1-mesa-dev amd64 9.0.0-2.1build1 [206 kB]
Get:176 http://archive.ubuntu.com/ubuntu bionic/main amd64 libice-dev amd64 2:1.0.9-2 [46.8 kB]
Get:177 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsasl2-modules amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [48.7 kB]
Get:178 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsm-dev amd64 2:1.2.2-1 [16.2 kB]
Get:179 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-doc all 2:1.6.4-3ubuntu0.2 [2065 kB]
Get:180 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxrender1 amd64 1:0.9.10-1 [18.7 kB]
Get:181 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxrender-dev amd64 1:0.9.10-1 [24.9 kB]
Get:182 http://archive.ubuntu.com/ubuntu bionic/main amd64 manpages-dev all 4.15-1 [2217 kB]
Get:183 http://archive.ubuntu.com/ubuntu bionic/universe amd64 mesa-utils amd64 8.4.0-1 [34.3 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking multiarch-support (2.27-3ubuntu1) ...
Setting up multiarch-support (2.27-3ubuntu1) ...
Selecting previously unselected package libxau6:amd64.
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Unpacking libxau6:amd64 (1:1.0.8-1) ...
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Unpacking libbsd0:amd64 (0.8.7-1) ...
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Unpacking libxdmcp6:amd64 (1:1.1.2-3) ...
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Unpacking libxcb1:amd64 (1.13-2~ubuntu18.04) ...
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Unpacking libx11-data (2:1.6.4-3ubuntu0.2) ...
Selecting previously unselected package libx11-6:amd64.
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Unpacking libx11-6:amd64 (2:1.6.4-3ubuntu0.2) ...
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Unpacking libxext6:amd64 (2:1.3.3-1) ...
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dpkg-query: no packages found matching nux-tools
Unpacking x11-common (1:7.7+19ubuntu7.1) ...
Selecting previously unselected package libice6:amd64.
Preparing to unpack .../08-libice6_2%3a1.0.9-2_amd64.deb ...
Unpacking libice6:amd64 (2:1.0.9-2) ...
Selecting previously unselected package libsm6:amd64.
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Unpacking libsm6:amd64 (2:1.2.2-1) ...
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Unpacking libxxf86vm1:amd64 (1:1.1.4-1) ...
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update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode
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debconf: unable to initialize frontend: Dialog
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133 added, 0 removed; done.
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Setting up fakeroot (1.22-2ubuntu1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
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update-alternatives: warning: skip creation of /usr/share/man/man1/faked.1.gz because associated file /usr/share/man/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/es/man1/fakeroot.1.gz because associated file /usr/share/man/es/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/es/man1/faked.1.gz because associated file /usr/share/man/es/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/fr/man1/fakeroot.1.gz because associated file /usr/share/man/fr/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/fr/man1/faked.1.gz because associated file /usr/share/man/fr/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/sv/man1/fakeroot.1.gz because associated file /usr/share/man/sv/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/sv/man1/faked.1.gz because associated file /usr/share/man/sv/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist
Setting up libhx509-5-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libgcc-7-dev:amd64 (7.4.0-1ubuntu1~18.04) ...
Setting up cpp-7 (7.4.0-1ubuntu1~18.04) ...
Setting up libdrm2:amd64 (2.4.95-1~18.04.1) ...
Setting up libstdc++-7-dev:amd64 (7.4.0-1ubuntu1~18.04) ...
Setting up libdrm-intel1:amd64 (2.4.95-1~18.04.1) ...
Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ...
Setting up libperl5.26:amd64 (5.26.1-6ubuntu0.3) ...
Setting up gpgsm (2.2.4-1ubuntu1.2) ...
Setting up gnupg-utils (2.2.4-1ubuntu1.2) ...
Setting up libice6:amd64 (2:1.0.9-2) ...
Setting up pinentry-curses (1.1.0-1) ...
Setting up libdrm-radeon1:amd64 (2.4.95-1~18.04.1) ...
Setting up libkrb5-26-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libdrm-nouveau2:amd64 (2.4.95-1~18.04.1) ...
Setting up libxcb1:amd64 (1.13-2~ubuntu18.04) ...
Setting up libheimntlm0-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up gpg (2.2.4-1ubuntu1.2) ...
Setting up binutils-x86-64-linux-gnu (2.30-21ubuntu1~18.04.1) ...
Setting up cpp (4:7.4.0-1ubuntu2.2) ...
Setting up libxcb-present0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-dri2-0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libsm6:amd64 (2:1.2.2-1) ...
Setting up libxcb-dri3-0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-glx0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-randr0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-xfixes0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-render0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libdrm-amdgpu1:amd64 (2.4.95-1~18.04.1) ...
Setting up libdrm-dev:amd64 (2.4.95-1~18.04.1) ...
Setting up libgbm1:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up libx11-6:amd64 (2:1.6.4-3ubuntu0.2) ...
Setting up libgl1-mesa-dri:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up gpg-agent (2.2.4-1ubuntu1.2) ...
Setting up gpg-wks-server (2.2.4-1ubuntu1.2) ...
Setting up libxcb-sync1:amd64 (1.13-2~ubuntu18.04) ...
Setting up perl (5.26.1-6ubuntu0.3) ...
Setting up libfile-fcntllock-perl (0.22-3build2) ...
Setting up libice-dev:amd64 (2:1.0.9-2) ...
Setting up libalgorithm-diff-perl (1.19.03-1) ...
Setting up libxcb-shape0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxrender1:amd64 (1:0.9.10-1) ...
Setting up libxcb1-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-glx0-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libegl-mesa0:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up binutils (2.30-21ubuntu1~18.04.1) ...
Setting up libx11-dev:amd64 (2:1.6.4-3ubuntu0.2) ...
Setting up libgssapi3-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libxcb-sync-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libx11-xcb-dev:amd64 (2:1.6.4-3ubuntu0.2) ...
Setting up libsm-dev:amd64 (2:1.2.2-1) ...
Setting up libxdamage1:amd64 (1:1.1.4-3) ...
Setting up mesa-common-dev:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up libxext6:amd64 (2:1.3.3-1) ...
Setting up libxfixes3:amd64 (1:5.0.3-1) ...
Setting up gcc-7 (7.4.0-1ubuntu1~18.04) ...
Setting up g++-7 (7.4.0-1ubuntu1~18.04) ...
Setting up libdpkg-perl (1.19.0.5ubuntu2.1) ...
Setting up libxrender-dev:amd64 (1:0.9.10-1) ...
Setting up gcc (4:7.4.0-1ubuntu2.2) ...
Setting up libxcb-dri2-0-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-render0-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libegl1:amd64 (1.0.0-2ubuntu2.2) ...
Setting up libalgorithm-merge-perl (0.08-3) ...
Setting up libxcb-dri3-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up dpkg-dev (1.19.0.5ubuntu2.1) ...
Setting up libalgorithm-diff-xs-perl (0.04-5) ...
Setting up libldap-2.4-2:amd64 (2.4.45+dfsg-1ubuntu1.2) ...
Setting up libxext-dev:amd64 (2:1.3.3-1) ...
Setting up libxcb-shape0-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up g++ (4:7.4.0-1ubuntu2.2) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/c++.1.gz because associated file /usr/share/man/man1/g++.1.gz (of link group c++) doesn't exist
Setting up libxxf86vm1:amd64 (1:1.1.4-1) ...
Setting up libxxf86vm-dev:amd64 (1:1.1.4-1) ...
Setting up libxfixes-dev:amd64 (1:5.0.3-1) ...
Setting up dirmngr (2.2.4-1ubuntu1.2) ...
Setting up libglx-mesa0:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up libxcb-randr0-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up build-essential (12.4ubuntu1) ...
Setting up libxcb-xfixes0-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxdamage-dev:amd64 (1:1.1.4-3) ...
Setting up gpg-wks-client (2.2.4-1ubuntu1.2) ...
Setting up libxcb-present-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libglx0:amd64 (1.0.0-2ubuntu2.2) ...
Setting up gnupg (2.2.4-1ubuntu1.2) ...
Setting up libgl1:amd64 (1.0.0-2ubuntu2.2) ...
Setting up libglu1-mesa:amd64 (9.0.0-2.1build1) ...
Setting up mesa-utils (8.4.0-1) ...
Setting up libglvnd-dev:amd64 (1.0.0-2ubuntu2.2) ...
Setting up libgl1-mesa-dev:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up libglu1-mesa-dev:amd64 (9.0.0-2.1build1) ...
Processing triggers for libc-bin (2.27-3ubuntu1) ...
Processing triggers for ca-certificates (20180409) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Removing intermediate container b96d2a72e160
---> 34c96cbdfc45
Step 3/4 : RUN cd /tmp && wget https://cryoem.bcm.edu/cryoem/static/software/release-2.3/eman2.3.linux64.sh && bash ./eman2.3.linux64.sh -b -t -p /opt/EMAN2
---> Running in 31eb568c7942
PREFIX=/opt/EMAN2
installing: python-2.7.16-h9bab390_0 ...
Python 2.7.16 :: Anaconda, Inc.
installing: asn1crypto-0.24.0-py27_0 ...
installing: backports-1.0-py27_1 ...
installing: backports.functools_lru_cache-1.5-py27_1 ...
installing: beautifulsoup4-4.7.1-py27_1 ...
installing: bzip2-1.0.6-h14c3975_5 ...
installing: ca-certificates-2019.1.23-0 ...
installing: certifi-2019.3.9-py27_0 ...
installing: cffi-1.12.3-py27h2e261b9_0 ...
installing: chardet-3.0.4-py27_1 ...
installing: conda-4.6.14-py27_0 ...
installing: conda-build-3.17.8-py27_0 ...
installing: contextlib2-0.5.5-py27hbf4c468_0 ...
installing: cryptography-2.6.1-py27h1ba5d50_0 ...
installing: enum34-1.1.6-py27_1 ...
installing: filelock-3.0.10-py27_0 ...
installing: futures-3.2.0-py27_0 ...
installing: glob2-0.6-py27_1 ...
installing: gsl-2.4-h14c3975_4 ...
installing: icu-58.2-h9c2bf20_1 ...
installing: idna-2.8-py27_0 ...
installing: ipaddress-1.0.22-py27_0 ...
installing: jinja2-2.10.1-py27_0 ...
installing: libarchive-3.3.3-h5d8350f_5 ...
installing: libedit-3.1.20181209-hc058e9b_0 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: libgcc-ng-8.2.0-hdf63c60_1 ...
installing: libgfortran-ng-7.3.0-hdf63c60_0 ...
installing: liblief-0.9.0-h7725739_2 ...
installing: libstdcxx-ng-8.2.0-hdf63c60_1 ...
installing: libxml2-2.9.9-he19cac6_0 ...
installing: lz4-c-1.8.1.2-h14c3975_0 ...
installing: lzo-2.10-h49e0be7_2 ...
installing: markupsafe-1.1.1-py27h7b6447c_0 ...
installing: ncurses-6.1-he6710b0_1 ...
installing: openssl-1.1.1b-h7b6447c_1 ...
installing: patchelf-0.9-he6710b0_3 ...
installing: pip-19.0.3-py27_0 ...
installing: pkginfo-1.5.0.1-py27_0 ...
installing: psutil-5.6.1-py27h7b6447c_0 ...
installing: py-lief-0.9.0-py27h7725739_2 ...
installing: pycosat-0.6.3-py27h14c3975_0 ...
installing: pycparser-2.19-py27_0 ...
installing: pyopenssl-19.0.0-py27_0 ...
installing: pysocks-1.6.8-py27_0 ...
installing: python-libarchive-c-2.8-py27_6 ...
installing: pytz-2019.1-py_0 ...
installing: pyyaml-5.1-py27h7b6447c_0 ...
installing: readline-7.0-h7b6447c_5 ...
installing: requests-2.21.0-py27_0 ...
installing: ruamel_yaml-0.15.46-py27h14c3975_0 ...
installing: scandir-1.10.0-py27h7b6447c_0 ...
installing: setuptools-41.0.0-py27_0 ...
installing: six-1.12.0-py27_0 ...
installing: soupsieve-1.8-py27_0 ...
installing: sqlite-3.28.0-h7b6447c_0 ...
installing: tk-8.6.8-hbc83047_0 ...
installing: tqdm-4.31.1-py27_1 ...
installing: urllib3-1.24.1-py27_0 ...
installing: wheel-0.33.1-py27_0 ...
installing: xz-5.2.4-h14c3975_4 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-h7b6447c_3 ...
installing: zstd-1.3.7-h0b5b093_0 ...
installing: eman2-2.3-h6bb024c_0 ...
+ source /opt/EMAN2/bin/activate
++ _CONDA_ROOT=/opt/EMAN2
++ . /opt/EMAN2/etc/profile.d/conda.sh
+++ export CONDA_EXE=/opt/EMAN2/bin/conda
+++ CONDA_EXE=/opt/EMAN2/bin/conda
+++ export _CE_M=
+++ _CE_M=
+++ export _CE_CONDA=
+++ _CE_CONDA=
+++ export CONDA_PYTHON_EXE=/opt/EMAN2/bin/python
+++ CONDA_PYTHON_EXE=/opt/EMAN2/bin/python
+++ '[' -z '' ']'
+++ export CONDA_SHLVL=0
+++ CONDA_SHLVL=0
+++ '[' -n x ']'
+++ '[' -n '' ']'
+++++ dirname /opt/EMAN2/bin/conda
++++ dirname /opt/EMAN2/bin
+++ PATH=/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ export PATH
+++ '[' -z '' ']'
+++ PS1=
++ conda activate
++ '[' 1 -lt 1 ']'
++ local cmd=activate
++ shift
++ case "$cmd" in
++ __conda_activate activate
++ '[' -n '' ']'
++ local cmd=activate
++ shift
++ local ask_conda
++ OLDPATH=/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ __add_sys_prefix_to_path
++ '[' -n '' ']'
+++ dirname /opt/EMAN2/bin/conda
++ SYSP=/opt/EMAN2/bin
+++ dirname /opt/EMAN2/bin
++ SYSP=/opt/EMAN2
++ '[' -n '' ']'
++ PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ export PATH
+++ PS1=
+++ /opt/EMAN2/bin/conda shell.posix activate
++ ask_conda='PS1='\''(base) '\''
export PATH='\''/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/opt/EMAN2'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''base'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
export CONDA_EXE='\''/opt/EMAN2/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/EMAN2/bin/python'\'''
++ PATH=/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ eval 'PS1='\''(base) '\''
export PATH='\''/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/opt/EMAN2'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''base'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
export CONDA_EXE='\''/opt/EMAN2/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/EMAN2/bin/python'\'''
+++ PS1='(base) '
+++ export PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ export CONDA_PREFIX=/opt/EMAN2
+++ CONDA_PREFIX=/opt/EMAN2
+++ export CONDA_SHLVL=1
+++ CONDA_SHLVL=1
+++ export CONDA_DEFAULT_ENV=base
+++ CONDA_DEFAULT_ENV=base
+++ export 'CONDA_PROMPT_MODIFIER=(base) '
+++ CONDA_PROMPT_MODIFIER='(base) '
+++ export CONDA_EXE=/opt/EMAN2/bin/conda
+++ CONDA_EXE=/opt/EMAN2/bin/conda
+++ export _CE_M=
+++ _CE_M=
+++ export _CE_CONDA=
+++ _CE_CONDA=
+++ export CONDA_PYTHON_EXE=/opt/EMAN2/bin/python
+++ CONDA_PYTHON_EXE=/opt/EMAN2/bin/python
++ __conda_hashr
++ '[' -n '' ']'
++ '[' -n '' ']'
++ hash -r
+ mkdir /opt/EMAN2/install_logs
+ conda info -a
+ conda list
+ conda install eman-deps=14.1 -c cryoem -c defaults -c conda-forge -y
+ '[' 9 -lt 1 ']'
+ local cmd=install
+ tee /opt/EMAN2/install_logs/install_log.txt
+ shift
+ case "$cmd" in
+ OLDPATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ __add_sys_prefix_to_path
+ '[' -n '' ']'
++ dirname /opt/EMAN2/bin/conda
+ SYSP=/opt/EMAN2/bin
++ dirname /opt/EMAN2/bin
+ SYSP=/opt/EMAN2
+ '[' -n '' ']'
+ PATH=/opt/EMAN2/bin:/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
+ /opt/EMAN2/bin/conda install eman-deps=14.1 -c cryoem -c defaults -c conda-forge -y
Collecting package metadata: ...working... done
Solving environment: ...working...
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- file://home/eman2/anaconda2/conda-bld/linux-64::eman2==2.3=h6bb024c_0
done
## Package Plan ##
environment location: /opt/EMAN2
added / updated specs:
- eman-deps=14.1
The following packages will be downloaded:
package | build
---------------------------|-----------------
absl-py-0.7.1 | py27_0 154 KB
backports.shutil_get_terminal_size-1.0.0| py27_2 8 KB
backports.weakref-1.0.post1| py27_0 8 KB
backports_abc-0.5 | py27h7b3c97b_0 12 KB
blas-1.0 | mkl 6 KB
bleach-1.5.0 | py27_0 21 KB
boost-1.63.0 | py27_5 325 KB conda-forge
boost-cpp-1.63.0 | 2 17.6 MB conda-forge
bsddb-1.0 | py27_1 202 KB
configparser-3.7.4 | py27_0 41 KB
cryptography-2.3.1 | py27hc365091_0 576 KB
cudatoolkit-8.0 | 3 322.4 MB
cudnn-7.0.5 | cuda8.0_0 249.3 MB
cupti-8.0.61 | 0 1.4 MB
cycler-0.10.0 | py27_0 13 KB
db-5.3.28 | 1 2.4 MB
dbus-1.13.6 | h746ee38_0 587 KB
decorator-4.4.0 | py27_1 18 KB
eman-deps-14.1 | 1 3 KB cryoem
expat-2.2.6 | he6710b0_0 187 KB
fftw-mpi-3.3.6 | 2 3.9 MB cryoem
fontconfig-2.13.0 | h9420a91_0 291 KB
freetype-2.9.1 | h8a8886c_1 822 KB
ftgl-2.1.3 | 1 687 KB cryoem
funcsigs-1.0.2 | py27h83f16ab_0 20 KB
functools32-3.2.3.2 | py27_1 23 KB
future-0.17.1 | py27_0 710 KB
glib-2.56.2 | hd408876_0 5.0 MB
gst-plugins-base-1.14.0 | hbbd80ab_1 6.3 MB
gstreamer-1.14.0 | hb453b48_1 3.8 MB
hdf5-1.8.18 | h6792536_1 4.2 MB
html5lib-0.9999999 | py27_0 183 KB
intel-openmp-2019.3 | 199 886 KB
ipython-5.8.0 | py27_0 1.0 MB
ipython_genutils-0.2.0 | py27_0 38 KB
jpeg-9b | h024ee3a_2 248 KB
kiwisolver-1.1.0 | py27he6710b0_0 91 KB
libarchive-3.3.3 | h7d0bbab_0 1.5 MB
libgcc-7.2.0 | h69d50b8_2 304 KB
libpng-1.6.34 | hb9fc6fc_0 334 KB
libprotobuf-3.7.1 | hd408876_0 4.7 MB
libtiff-4.0.9 | he85c1e1_2 567 KB
libuuid-1.0.3 | h1bed415_2 16 KB
libxcb-1.13 | h1bed415_1 502 KB
markdown-3.1 | py27_0 111 KB
matplotlib-2.2.3 | py27hb69df0a_0 6.5 MB
mkl-2018.0.3 | 1 198.7 MB
mkl_fft-1.0.6 | py27h7dd41cf_0 148 KB
mkl_random-1.0.1 | py27h4414c95_1 361 KB
mock-2.0.0 | py27_0 100 KB
nose-1.3.7 | py27_2 213 KB
numpy-1.13.3 | py27hdbf6ddf_4 3.9 MB
openmpi-2.0.2 | 0 2.6 MB cryoem
openssl-1.0.2r | h7b6447c_0 3.2 MB
pathlib2-2.3.3 | py27_0 31 KB
pbr-5.1.3 | py_0 74 KB
pcre-8.43 | he6710b0_0 260 KB
pexpect-4.7.0 | py27_0 80 KB
pickleshare-0.7.5 | py27_0 12 KB
prompt_toolkit-1.0.15 | py27h1b593e1_0 333 KB
protobuf-3.7.1 | py27he6710b0_0 657 KB
ptyprocess-0.6.0 | py27_0 22 KB
pydusa-1.15 | np113_11 120 KB cryoem
pygments-2.3.1 | py27_0 1.4 MB
pyopengl-3.1.0 | py27_0 982 KB conda-forge
pyparsing-2.4.0 | py_0 58 KB
pyqt-5.9.2 | py27h05f1152_2 5.4 MB
python-2.7.14 | h1571d57_31 11.8 MB
python-dateutil-2.8.0 | py27_0 279 KB
qt-5.9.6 | h8703b6f_2 87.1 MB
scikit-learn-0.19.2 | py27h4989274_0 5.3 MB
scipy-1.1.0 | py27hd20e5f9_0 17.9 MB
simplegeneric-0.8.1 | py27_2 9 KB
singledispatch-3.4.0.3 | py27h9bcb476_0 15 KB
sip-4.19.8 | py27hf484d3e_0 291 KB
subprocess32-3.5.3 | py27h7b6447c_0 44 KB
tensorflow-gpu-1.5.0 | 0 3 KB
tensorflow-gpu-base-1.5.0 | py27had95abb_0 131.0 MB
tensorflow-tensorboard-1.5.1| py27hf484d3e_1 2.9 MB
tornado-5.1.1 | py27h7b6447c_0 643 KB
traitlets-4.3.2 | py27hd6ce930_0 126 KB
wcwidth-0.1.7 | py27h9e3e1ab_0 25 KB
werkzeug-0.15.2 | py_0 263 KB
------------------------------------------------------------
Total: 1.09 GB
The following NEW packages will be INSTALLED:
absl-py pkgs/main/linux-64::absl-py-0.7.1-py27_0
backports.shutil_~ pkgs/main/linux-64::backports.shutil_get_terminal_size-1.0.0-py27_2
backports.weakref pkgs/main/linux-64::backports.weakref-1.0.post1-py27_0
backports_abc pkgs/main/linux-64::backports_abc-0.5-py27h7b3c97b_0
blas pkgs/main/linux-64::blas-1.0-mkl
bleach pkgs/free/linux-64::bleach-1.5.0-py27_0
boost conda-forge/linux-64::boost-1.63.0-py27_5
boost-cpp conda-forge/linux-64::boost-cpp-1.63.0-2
bsddb pkgs/free/linux-64::bsddb-1.0-py27_1
configparser pkgs/main/linux-64::configparser-3.7.4-py27_0
cudatoolkit pkgs/free/linux-64::cudatoolkit-8.0-3
cudnn pkgs/main/linux-64::cudnn-7.0.5-cuda8.0_0
cupti pkgs/main/linux-64::cupti-8.0.61-0
cycler pkgs/main/linux-64::cycler-0.10.0-py27_0
db pkgs/free/linux-64::db-5.3.28-1
dbus pkgs/main/linux-64::dbus-1.13.6-h746ee38_0
decorator pkgs/main/linux-64::decorator-4.4.0-py27_1
eman-deps cryoem/linux-64::eman-deps-14.1-1
expat pkgs/main/linux-64::expat-2.2.6-he6710b0_0
fftw-mpi cryoem/linux-64::fftw-mpi-3.3.6-2
fontconfig pkgs/main/linux-64::fontconfig-2.13.0-h9420a91_0
freetype pkgs/main/linux-64::freetype-2.9.1-h8a8886c_1
ftgl cryoem/linux-64::ftgl-2.1.3-1
funcsigs pkgs/main/linux-64::funcsigs-1.0.2-py27h83f16ab_0
functools32 pkgs/main/linux-64::functools32-3.2.3.2-py27_1
future pkgs/main/linux-64::future-0.17.1-py27_0
glib pkgs/main/linux-64::glib-2.56.2-hd408876_0
gst-plugins-base pkgs/main/linux-64::gst-plugins-base-1.14.0-hbbd80ab_1
gstreamer pkgs/main/linux-64::gstreamer-1.14.0-hb453b48_1
hdf5 pkgs/main/linux-64::hdf5-1.8.18-h6792536_1
html5lib pkgs/free/linux-64::html5lib-0.9999999-py27_0
intel-openmp pkgs/main/linux-64::intel-openmp-2019.3-199
ipython pkgs/main/linux-64::ipython-5.8.0-py27_0
ipython_genutils pkgs/main/linux-64::ipython_genutils-0.2.0-py27_0
jpeg pkgs/main/linux-64::jpeg-9b-h024ee3a_2
kiwisolver pkgs/main/linux-64::kiwisolver-1.1.0-py27he6710b0_0
libgcc pkgs/main/linux-64::libgcc-7.2.0-h69d50b8_2
libpng pkgs/main/linux-64::libpng-1.6.34-hb9fc6fc_0
libprotobuf pkgs/main/linux-64::libprotobuf-3.7.1-hd408876_0
libtiff pkgs/main/linux-64::libtiff-4.0.9-he85c1e1_2
libuuid pkgs/main/linux-64::libuuid-1.0.3-h1bed415_2
libxcb pkgs/main/linux-64::libxcb-1.13-h1bed415_1
markdown pkgs/main/linux-64::markdown-3.1-py27_0
matplotlib pkgs/main/linux-64::matplotlib-2.2.3-py27hb69df0a_0
mkl pkgs/main/linux-64::mkl-2018.0.3-1
mkl_fft pkgs/main/linux-64::mkl_fft-1.0.6-py27h7dd41cf_0
mkl_random pkgs/main/linux-64::mkl_random-1.0.1-py27h4414c95_1
mock pkgs/main/linux-64::mock-2.0.0-py27_0
nose pkgs/main/linux-64::nose-1.3.7-py27_2
numpy pkgs/main/linux-64::numpy-1.13.3-py27hdbf6ddf_4
openmpi cryoem/linux-64::openmpi-2.0.2-0
pathlib2 pkgs/main/linux-64::pathlib2-2.3.3-py27_0
pbr pkgs/main/noarch::pbr-5.1.3-py_0
pcre pkgs/main/linux-64::pcre-8.43-he6710b0_0
pexpect pkgs/main/linux-64::pexpect-4.7.0-py27_0
pickleshare pkgs/main/linux-64::pickleshare-0.7.5-py27_0
prompt_toolkit pkgs/main/linux-64::prompt_toolkit-1.0.15-py27h1b593e1_0
protobuf pkgs/main/linux-64::protobuf-3.7.1-py27he6710b0_0
ptyprocess pkgs/main/linux-64::ptyprocess-0.6.0-py27_0
pydusa cryoem/linux-64::pydusa-1.15-np113_11
pygments pkgs/main/linux-64::pygments-2.3.1-py27_0
pyopengl conda-forge/linux-64::pyopengl-3.1.0-py27_0
pyparsing pkgs/main/noarch::pyparsing-2.4.0-py_0
pyqt pkgs/main/linux-64::pyqt-5.9.2-py27h05f1152_2
python-dateutil pkgs/main/linux-64::python-dateutil-2.8.0-py27_0
qt pkgs/main/linux-64::qt-5.9.6-h8703b6f_2
scikit-learn pkgs/main/linux-64::scikit-learn-0.19.2-py27h4989274_0
scipy pkgs/main/linux-64::scipy-1.1.0-py27hd20e5f9_0
simplegeneric pkgs/main/linux-64::simplegeneric-0.8.1-py27_2
singledispatch pkgs/main/linux-64::singledispatch-3.4.0.3-py27h9bcb476_0
sip pkgs/main/linux-64::sip-4.19.8-py27hf484d3e_0
subprocess32 pkgs/main/linux-64::subprocess32-3.5.3-py27h7b6447c_0
tensorflow-gpu pkgs/main/linux-64::tensorflow-gpu-1.5.0-0
tensorflow-gpu-ba~ pkgs/main/linux-64::tensorflow-gpu-base-1.5.0-py27had95abb_0
tensorflow-tensor~ pkgs/main/linux-64::tensorflow-tensorboard-1.5.1-py27hf484d3e_1
tornado pkgs/main/linux-64::tornado-5.1.1-py27h7b6447c_0
traitlets pkgs/main/linux-64::traitlets-4.3.2-py27hd6ce930_0
wcwidth pkgs/main/linux-64::wcwidth-0.1.7-py27h9e3e1ab_0
werkzeug pkgs/main/noarch::werkzeug-0.15.2-py_0
The following packages will be DOWNGRADED:
cryptography 2.6.1-py27h1ba5d50_0 --> 2.3.1-py27hc365091_0
libarchive 3.3.3-h5d8350f_5 --> 3.3.3-h7d0bbab_0
openssl 1.1.1b-h7b6447c_1 --> 1.0.2r-h7b6447c_0
python 2.7.16-h9bab390_0 --> 2.7.14-h1571d57_31
Downloading and Extracting Packages
mock-2.0.0 | 100 KB | ########## | 100%
fftw-mpi-3.3.6 | 3.9 MB | ########## | 100%
scipy-1.1.0 | 17.9 MB | ########## | 100%
tensorflow-gpu-base- | 131.0 MB | ########## | 100%
decorator-4.4.0 | 18 KB | ########## | 100%
pickleshare-0.7.5 | 12 KB | ########## | 100%
pexpect-4.7.0 | 80 KB | ########## | 100%
ipython-5.8.0 | 1.0 MB | ########## | 100%
pyparsing-2.4.0 | 58 KB | ########## | 100%
mkl_random-1.0.1 | 361 KB | ########## | 100%
dbus-1.13.6 | 587 KB | ########## | 100%
libuuid-1.0.3 | 16 KB | ########## | 100%
sip-4.19.8 | 291 KB | ########## | 100%
db-5.3.28 | 2.4 MB | ########## | 100%
libpng-1.6.34 | 334 KB | ########## | 100%
singledispatch-3.4.0 | 15 KB | ########## | 100%
ftgl-2.1.3 | 687 KB | ########## | 100%
pcre-8.43 | 260 KB | ########## | 100%
backports_abc-0.5 | 12 KB | ########## | 100%
funcsigs-1.0.2 | 20 KB | ########## | 100%
libarchive-3.3.3 | 1.5 MB | ########## | 100%
libtiff-4.0.9 | 567 KB | ########## | 100%
scikit-learn-0.19.2 | 5.3 MB | ########## | 100%
subprocess32-3.5.3 | 44 KB | ########## | 100%
jpeg-9b | 248 KB | ########## | 100%
bsddb-1.0 | 202 KB | ########## | 100%
cudatoolkit-8.0 | 322.4 MB | ########## | 100%
pygments-2.3.1 | 1.4 MB | ########## | 100%
gst-plugins-base-1.1 | 6.3 MB | ########## | 100%
eman-deps-14.1 | 3 KB | ########## | 100%
fontconfig-2.13.0 | 291 KB | ########## | 100%
functools32-3.2.3.2 | 23 KB | ########## | 100%
bleach-1.5.0 | 21 KB | ########## | 100%
backports.shutil_get | 8 KB | ########## | 100%
cupti-8.0.61 | 1.4 MB | ########## | 100%
numpy-1.13.3 | 3.9 MB | ########## | 100%
libxcb-1.13 | 502 KB | ########## | 100%
pydusa-1.15 | 120 KB | ########## | 100%
absl-py-0.7.1 | 154 KB | ########## | 100%
ipython_genutils-0.2 | 38 KB | ########## | 100%
mkl_fft-1.0.6 | 148 KB | ########## | 100%
tornado-5.1.1 | 643 KB | ########## | 100%
freetype-2.9.1 | 822 KB | ########## | 100%
backports.weakref-1. | 8 KB | ########## | 100%
ptyprocess-0.6.0 | 22 KB | ########## | 100%
intel-openmp-2019.3 | 886 KB | ########## | 100%
libprotobuf-3.7.1 | 4.7 MB | ########## | 100%
python-2.7.14 | 11.8 MB | ########## | 100%
glib-2.56.2 | 5.0 MB | ########## | 100%
gstreamer-1.14.0 | 3.8 MB | ########## | 100%
boost-cpp-1.63.0 | 17.6 MB | ########## | 100%
cryptography-2.3.1 | 576 KB | ########## | 100%
cycler-0.10.0 | 13 KB | ########## | 100%
wcwidth-0.1.7 | 25 KB | ########## | 100%
expat-2.2.6 | 187 KB | ########## | 100%
python-dateutil-2.8. | 279 KB | ########## | 100%
boost-1.63.0 | 325 KB | ########## | 100%
openssl-1.0.2r | 3.2 MB | ########## | 100%
matplotlib-2.2.3 | 6.5 MB | ########## | 100%
simplegeneric-0.8.1 | 9 KB | ########## | 100%
tensorflow-gpu-1.5.0 | 3 KB | ########## | 100%
libgcc-7.2.0 | 304 KB | ########## | 100%
hdf5-1.8.18 | 4.2 MB | ########## | 100%
werkzeug-0.15.2 | 263 KB | ########## | 100%
protobuf-3.7.1 | 657 KB | ########## | 100%
pbr-5.1.3 | 74 KB | ########## | 100%
cudnn-7.0.5 | 249.3 MB | ########## | 100%
mkl-2018.0.3 | 198.7 MB | ########## | 100%
pyqt-5.9.2 | 5.4 MB | ########## | 100%
prompt_toolkit-1.0.1 | 333 KB | ########## | 100%
configparser-3.7.4 | 41 KB | ########## | 100%
pathlib2-2.3.3 | 31 KB | ########## | 100%
qt-5.9.6 | 87.1 MB | ########## | 100%
nose-1.3.7 | 213 KB | ########## | 100%
kiwisolver-1.1.0 | 91 KB | ########## | 100%
markdown-3.1 | 111 KB | ########## | 100%
blas-1.0 | 6 KB | ########## | 100%
openmpi-2.0.2 | 2.6 MB | ########## | 100%
pyopengl-3.1.0 | 982 KB | ########## | 100%
traitlets-4.3.2 | 126 KB | ########## | 100%
html5lib-0.9999999 | 183 KB | ########## | 100%
tensorflow-tensorboa | 2.9 MB | ########## | 100%
future-0.17.1 | 710 KB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working...
done
+ local t1=0
+ PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ '[' 0 = 0 ']'
+ __conda_reactivate
+ local ask_conda
+ OLDPATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ __add_sys_prefix_to_path
+ '[' -n '' ']'
++ dirname /opt/EMAN2/bin/conda
+ SYSP=/opt/EMAN2/bin
++ dirname /opt/EMAN2/bin
+ SYSP=/opt/EMAN2
+ '[' -n '' ']'
+ PATH=/opt/EMAN2/bin:/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
++ PS1='(base) '
++ /opt/EMAN2/bin/conda shell.posix reactivate
+ ask_conda='PS1='\''(base) '\''
export PATH='\''/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_SHLVL='\''1'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
. "/opt/EMAN2/etc/conda/activate.d/eman-deps_activate.sh"'
+ PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ eval 'PS1='\''(base) '\''
export PATH='\''/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_SHLVL='\''1'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
. "/opt/EMAN2/etc/conda/activate.d/eman-deps_activate.sh"'
++ PS1='(base) '
++ export PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ export CONDA_SHLVL=1
++ CONDA_SHLVL=1
++ export 'CONDA_PROMPT_MODIFIER=(base) '
++ CONDA_PROMPT_MODIFIER='(base) '
++ . /opt/EMAN2/etc/conda/activate.d/eman-deps_activate.sh
+++ echo
+++ echo 'INFO: eman-deps activation script is making the following environmental changes:'
+++ set -x
+++ LDFLAGS=
+++ LDFLAGS=
+++ CXXFLAGS=
+++ set +x
INFO: eman-deps activation script is making the following environmental changes:
+ cat
INSTALLATION IS NOW COMPLETE
Please, go to http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda
for detailed installation instructions, testing and troubleshooting information.
If this installation is on a Linux cluster,
you will require additional steps before installation is complete!
cat: /opt/EMAN2/.messages.txt: No such file or directory
installation finished.
INFO: Running package tests in a subshell
INFO: eman-deps activation script is making the following environmental changes:
++++ LDFLAGS=
++++ LDFLAGS=
++++ CXXFLAGS=
++++ set +x
Traceback (most recent call last):
File "/opt/EMAN2/bin/conda-index", line 7, in <module>
from conda_build.cli.main_index import main
File "/opt/EMAN2/lib/python2.7/site-packages/conda_build/cli/main_index.py", line 10, in <module>
from conda_build.index import DEFAULT_SUBDIRS, MAX_THREADS_DEFAULT
File "/opt/EMAN2/lib/python2.7/site-packages/conda_build/index.py", line 25, in <module>
import pytz
ImportError: No module named pytz
Traceback (most recent call last):
File "/opt/EMAN2/bin/conda-build", line 7, in <module>
from conda_build.cli.main_build import main
File "/opt/EMAN2/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 19, in <module>
import conda_build.build as build
File "/opt/EMAN2/lib/python2.7/site-packages/conda_build/build.py", line 63, in <module>
from conda_build import environ, source, tarcheck, utils
File "/opt/EMAN2/lib/python2.7/site-packages/conda_build/environ.py", line 29, in <module>
from conda_build.index import get_build_index
File "/opt/EMAN2/lib/python2.7/site-packages/conda_build/index.py", line 25, in <module>
import pytz
ImportError: No module named pytz
To re-run the tests for the above failed package, please enter:
. /opt/EMAN2/bin/activate
conda-build --override-channels --channel local --test <full-path-to-failed.tar.bz2>
ERROR: 1 test failed
The command '/bin/sh -c cd /tmp && wget https://cryoem.bcm.edu/cryoem/static/software/release-2.3/eman2.3.linux64.sh && bash ./eman2.3.linux64.sh -b -t -p /opt/EMAN2' returned a non-zero code: 1
Having recently engaged in the exercise of building the EMAN2 2.3 release from source, I had the opportunity to analyze compiler warnings to look for any that indicated genuine problems. There was a lot of noise, but a little signal, all of which appears still to apply to the current head. I'll be splitting that into four separate issues, of which this is the first.
libEM/mrcio.cpp:206-207 is this:
is_8_bit_packed = (mrch.mode == MRC_UHEX ||
(mrch.imod_flags & 16) == 1 || double_nx);
But the condition (mrch.imod_flags & 16) == 1
never evaluates to true, because anything & 16
always evaluates to either 0 or 16. From code analysis alone, I suspect that (mrch.imod_flags & 16) != 0
would be consistent with the intention, but I am not sufficiently familiar with the details of the MRC format to confirm that.
Hello.
We're having some issues with eman2 2.22 on a new system, CentOS 7.
As a user, trying to run e2projectmanager.py results in:
Traceback (most recent call last):
File "/opt/cryoem/EMAN2_2.22/bin/e2projectmanager.py", line 2134, in
pm = EMProjectManager()
File "/opt/cryoem/EMAN2_2.22/bin/e2projectmanager.py", line 67, in init
self.loadPMdb()
File "/opt/cryoem/EMAN2_2.22/bin/e2projectmanager.py", line 124, in loadPMdb
self.pm_projects_db = js_open_dict("info/project.json")
File "/opt/cryoem/EMAN2_2.22/lib/python2.7/site-packages/EMAN2jsondb.py", line 78, in js_open_dict
return JSDict.open_db(url)
File "/opt/cryoem/EMAN2_2.22/lib/python2.7/site-packages/EMAN2jsondb.py", line 577, in open_db
raise Exception("Unable to open "+path)
Exception: Unable to open info/project.json
However, I am able to run it normally as root. I have checked permissions, but can't seem to find an issue there. Any assistance is appreciated.
This was mentioned in #204. Tracking here as any other PRs will be failing until this is addressed.
Error:
Compiling ./examples/e2ddd_external.py ...
File "./examples/e2ddd_external.py", line 165
if options.patch != 1 1: cmd += " -Patch {} ".format(options.patch)
^
SyntaxError: invalid syntax
Suspect it is caused by this,
eman2/examples/e2ddd_external.py
Line 165 in 98bea25
First, follow the install instructions: https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda/2.22
Then, open terminal, and run open ~/.bash_profile
Add to that file export PATH="/Users/yourusername/EMAN2/bin:$PATH"
Save, and restart your terminal, then see if it works.
Hi,
Neither on https://blake.bcm.edu/emanwiki/EMAN2 nor on github the list of required dependencies for EMAN2 is available.
Install dependencies
conda install cmake=3.9 -c defaults
conda install eman-deps=14 -c cryoem -c defaults -c conda-forge
Not everybody uses conda. On many HPC clusters, conda is not available. On our HPC cluster, we do not support conda. Therefore could you please provide a list of dependencies required for EMAN2 ?
Best regards
Sam
Hi,
I would like to report an issue regarding using CMake to build eman2.
When trying to build eman 2.3 from source (using the v2.3 release tarball from github), then I receive a CMake Error caused by programs/CMakeLists.txt
CMake Error at programs/CMakeLists.txt:28 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.
According to
https://gitlab.kitware.com/cmake/cmake/issues/18737
this problem can be fixed by quoting the arguments of the function.
When changing programs/CMakeLists.txt:28 from
string(REGEX REPLACE
"^.*-.*-g" ""
EMAN_GITHASH ${EMAN_GITHASH}
)
to
string(REGEX REPLACE
"^.*-.*-g" ""
"EMAN_GITHASH" "${EMAN_GITHASH}"
)
then the error is no longer triggered
I've looked at the code and this seems to be a bug. I'm coping complete Traceback below. Please let me know if you have questions or need more information. Thank you.
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[3037,1],3]
Exit code: 1
1 2 3
2 3 4
5 4 3
3 3 4
Plot 2D
$ Traceback (most recent call last):
File "/minicondas/envs/eman-deps-11-gui/lib/python2.7/site-packages/eman2_gui/emplot2d.py", line 861, in mousePressEvent
self.update_selected((event.x(),event.y()),lc)
File "/miniconda/envs/eman-deps-11-gui/lib/python2.7/site-packages/eman2_gui/emplot2d.py", line 780, in update_selected
if r[srt[i]]<3 : self.selected.append(srt[i])
IndexError: index 4 is out of bounds for axis 0 with size 4
$ e2ctf.py --gui micrographs/BGal_000232.hdf &
[2] 95971
$ Using A/pix from header
Traceback (most recent call last):
File "/anaconda/bin/e2ctf.py", line 2912, in newSet
else : self.guirealim.set_data([EMData()])
File "/anaconda/lib/python2.7/site-packages/emimage2d.py", line 463, in set_data
self.auto_contrast(inspector_update=False,display_update=False)
File "/anaconda/lib/python2.7/site-packages/emimage2d.py", line 530, in auto_contrast
mean=self.data.get_attr("mean")
RuntimeError: NotExistingObjectException at /<some-path>/eman2/libEM/emdata_metadata.cpp:1148: error with 'mean': 'The requested key does not exist' caught
More recent runs:
$ e2ctf.py --gui micrographs/BGal_000232.hdf &
[1] 78530
$ Using A/pix from header
Traceback (most recent call last):
File "/minicondas/bin/e2ctf.py", line 2917, in newSet
else : self.guirealim.set_data([EMData()])
File "/minicondas/lib/python2.7/site-packages/eman2_gui/emimage2d.py", line 463, in set_data
self.auto_contrast(inspector_update=False,display_update=False)
File "/minicondas/lib/python2.7/site-packages/eman2_gui/emimage2d.py", line 530, in auto_contrast
mean=self.data.get_attr("mean")
RuntimeError
$ e2ctf.py --gui micrographs/BGal_000232.hdf
Using A/pix from header
Traceback (most recent call last):
File "/minicondas/bin/e2ctf.py", line 2917, in newSet
else : self.guirealim.set_data([EMData()])
File "/minicondas/lib/python2.7/site-packages/eman2_gui/emimage2d.py", line 463, in set_data
self.auto_contrast(inspector_update=False,display_update=False)
File "/minicondas/lib/python2.7/site-packages/eman2_gui/emimage2d.py", line 530, in auto_contrast
mean=self.data.get_attr("mean")
RuntimeError: NotExistingObjectException at /<some-path>/eman2/libEM/emdata_metadata.cpp:1148: error with 'mean': 'The requested key does not exist' caught
I see the following error when trying to build with gcc on CentOS 6.7,
libEM/sparx/util_sparx.cpp:26532: error: ‘fftwf_alloc_real’ was not declared in this scope
.... and the source file lists,
26529 #ifdef _WIN32
26530 float _cvv = (float *) malloc(2_size_sizeof(float));
26531 #else
26532 float *cvv = fftwf_alloc_real(2_size);
26533 #endif //_WIN32
26534
There is no other instance of "fftwf_alloc_real" in this file. I'm building with libfftw3f.so.3.3.2. I have not built the source in a few months, but this configuration used to work.
In e2projectmanager, we cannot run e2initialmodel.py jobs because the "symmetry number" field is too small to enter a valid number (it's only a few pixels wide). As a workaround, we have been running e2initialmodel.py in the shell.
This is on:
EMAN 2.22 final (GITHUB: 2018-08-20 20:33 - commit: f4f3952 )
Your EMAN2 is running on: Mac OS 10.14.1 x86_64
Your Python version is: 2.7.14
Traceback (most recent call last):
File "/Users/shadow_walker/eman2/bin/e2cmpxplor.py", line 36, in <module>
from e2eulerxplor import InputEventsManager
ImportError: cannot import name InputEventsManager
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.