Stuck on an issue?
Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.
And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.
singularity container for brainiak
See original GitHub issueHello,
I’m new to neurodocker and I’m trying to use it to write a recipe for building a singularity container, for the purpose of using Brainiak package on cluster. I know that brainiak is hard to install (it was a hassle to just set it up on my laptop), and I’m encountering some error while building the container with the recipe. And I’m wondering if it is solvable. I would super appreciate any insights, thank you all in advance!
here is the command i used for generating the recipe:
neurodocker generate singularity --base=debian:stretch \
--pkg-manager=apt --install gcc g++ libopenmpi-dev \
--miniconda create_env=neuro \
conda_install='python=3.7 numpy pandas traits scipy' \
pip_install='nipype mpi4py psutil brainiak nibabel nilearn matplotlib networkx seaborn' \
--miniconda use_env=neuro conda_install='jupyter' \
--install python3.7-dev
While building the container use the recipe, here is the error I got
Building wheel for brainiak (PEP 517) ... error
ERROR: Command errored out with exit status 1:
command: /opt/miniconda-latest/envs/neuro/bin/python3.7 /opt/miniconda-latest/envs/neuro/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /tmp/tmp0at4q9vt
cwd: /tmp/pip-install-wimld_zc/brainiak
Complete output (250 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/brainiak
copying brainiak/__init__.py -> build/lib.linux-x86_64-3.7/brainiak
copying brainiak/isc.py -> build/lib.linux-x86_64-3.7/brainiak
copying brainiak/image.py -> build/lib.linux-x86_64-3.7/brainiak
copying brainiak/io.py -> build/lib.linux-x86_64-3.7/brainiak
creating build/lib.linux-x86_64-3.7/brainiak/reprsimil
copying brainiak/reprsimil/__init__.py -> build/lib.linux-x86_64-3.7/brainiak/reprsimil
copying brainiak/reprsimil/brsa.py -> build/lib.linux-x86_64-3.7/brainiak/reprsimil
creating build/lib.linux-x86_64-3.7/brainiak/fcma
copying brainiak/fcma/voxelselector.py -> build/lib.linux-x86_64-3.7/brainiak/fcma
copying brainiak/fcma/classifier.py -> build/lib.linux-x86_64-3.7/brainiak/fcma
copying brainiak/fcma/mvpa_voxelselector.py -> build/lib.linux-x86_64-3.7/brainiak/fcma
copying brainiak/fcma/__init__.py -> build/lib.linux-x86_64-3.7/brainiak/fcma
copying brainiak/fcma/preprocessing.py -> build/lib.linux-x86_64-3.7/brainiak/fcma
copying brainiak/fcma/util.py -> build/lib.linux-x86_64-3.7/brainiak/fcma
creating build/lib.linux-x86_64-3.7/brainiak/reconstruct
copying brainiak/reconstruct/__init__.py -> build/lib.linux-x86_64-3.7/brainiak/reconstruct
copying brainiak/reconstruct/iem.py -> build/lib.linux-x86_64-3.7/brainiak/reconstruct
creating build/lib.linux-x86_64-3.7/brainiak/utils
copying brainiak/utils/__init__.py -> build/lib.linux-x86_64-3.7/brainiak/utils
copying brainiak/utils/fmrisim.py -> build/lib.linux-x86_64-3.7/brainiak/utils
copying brainiak/utils/utils.py -> build/lib.linux-x86_64-3.7/brainiak/utils
creating build/lib.linux-x86_64-3.7/brainiak/eventseg
copying brainiak/eventseg/__init__.py -> build/lib.linux-x86_64-3.7/brainiak/eventseg
copying brainiak/eventseg/event.py -> build/lib.linux-x86_64-3.7/brainiak/eventseg
creating build/lib.linux-x86_64-3.7/brainiak/funcalign
copying brainiak/funcalign/__init__.py -> build/lib.linux-x86_64-3.7/brainiak/funcalign
copying brainiak/funcalign/sssrm.py -> build/lib.linux-x86_64-3.7/brainiak/funcalign
copying brainiak/funcalign/fastsrm.py -> build/lib.linux-x86_64-3.7/brainiak/funcalign
copying brainiak/funcalign/srm.py -> build/lib.linux-x86_64-3.7/brainiak/funcalign
copying brainiak/funcalign/rsrm.py -> build/lib.linux-x86_64-3.7/brainiak/funcalign
creating build/lib.linux-x86_64-3.7/brainiak/factoranalysis
copying brainiak/factoranalysis/__init__.py -> build/lib.linux-x86_64-3.7/brainiak/factoranalysis
copying brainiak/factoranalysis/htfa.py -> build/lib.linux-x86_64-3.7/brainiak/factoranalysis
copying brainiak/factoranalysis/tfa.py -> build/lib.linux-x86_64-3.7/brainiak/factoranalysis
creating build/lib.linux-x86_64-3.7/brainiak/searchlight
copying brainiak/searchlight/searchlight.py -> build/lib.linux-x86_64-3.7/brainiak/searchlight
copying brainiak/searchlight/__init__.py -> build/lib.linux-x86_64-3.7/brainiak/searchlight
creating build/lib.linux-x86_64-3.7/brainiak/hyperparamopt
copying brainiak/hyperparamopt/__init__.py -> build/lib.linux-x86_64-3.7/brainiak/hyperparamopt
copying brainiak/hyperparamopt/hpo.py -> build/lib.linux-x86_64-3.7/brainiak/hyperparamopt
copying brainiak/utils/grey_matter_mask.npy -> build/lib.linux-x86_64-3.7/brainiak/utils
running build_ext
creating tmp
gcc -pthread -B /opt/miniconda-latest/envs/neuro/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/miniconda-latest/envs/neuro/include/python3.7m -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/numpy/core/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -c /tmp/tmpuh8fl78n.cpp -o tmp/tmpuh8fl78n.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /opt/miniconda-latest/envs/neuro/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/miniconda-latest/envs/neuro/include/python3.7m -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/numpy/core/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -c /tmp/tmpcibmfakg.cpp -o tmp/tmpcibmfakg.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /opt/miniconda-latest/envs/neuro/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/miniconda-latest/envs/neuro/include/python3.7m -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/numpy/core/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -c /tmp/tmp_eefqft1.cpp -o tmp/tmp_eefqft1.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /opt/miniconda-latest/envs/neuro/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/miniconda-latest/envs/neuro/include/python3.7m -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/numpy/core/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -c /tmp/tmpensq11bd.cpp -o tmp/tmpensq11bd.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
cythoning brainiak/fcma/cython_blas.pyx to brainiak/fcma/cython_blas.c
cythoning brainiak/eventseg/_utils.pyx to brainiak/eventseg/_utils.c
building 'brainiak.factoranalysis.tfa_extension' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/brainiak
creating build/temp.linux-x86_64-3.7/brainiak/factoranalysis
gcc -pthread -B /opt/miniconda-latest/envs/neuro/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/miniconda-latest/envs/neuro/include/python3.7m -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/numpy/core/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -c brainiak/factoranalysis/tfa_extension.cpp -o build/temp.linux-x86_64-3.7/brainiak/factoranalysis/tfa_extension.o -g0 -fopenmp -DVERSION_INFO="0.10" -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/pytypes.h:12:0,
from /tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/cast.h:13,
from /tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/attr.h:13,
from /tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/pybind11.h:44,
from brainiak/factoranalysis/tfa_extension.cpp:24:
brainiak/factoranalysis/tfa_extension.cpp: In function ‘PyObject* PyInit_tfa_extension()’:
/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/detail/common.h:271:20: warning: ‘PyObject* pybind11_init()’ is deprecated: PYBIND11_PLUGIN is deprecated, use PYBIND11_MODULE [-Wdeprecated-declarations]
return pybind11_init(); \
^
brainiak/factoranalysis/tfa_extension.cpp:242:1: note: in expansion of macro ‘PYBIND11_PLUGIN’
PYBIND11_PLUGIN(tfa_extension) {
^~~~~~~~~~~~~~~
/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/detail/common.h:266:22: note: declared here
static PyObject *pybind11_init(); \
^
brainiak/factoranalysis/tfa_extension.cpp:242:1: note: in expansion of macro ‘PYBIND11_PLUGIN’
PYBIND11_PLUGIN(tfa_extension) {
^~~~~~~~~~~~~~~
/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/detail/common.h:271:34: warning: ‘PyObject* pybind11_init()’ is deprecated: PYBIND11_PLUGIN is deprecated, use PYBIND11_MODULE [-Wdeprecated-declarations]
return pybind11_init(); \
^
brainiak/factoranalysis/tfa_extension.cpp:242:1: note: in expansion of macro ‘PYBIND11_PLUGIN’
PYBIND11_PLUGIN(tfa_extension) {
^~~~~~~~~~~~~~~
/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/detail/common.h:266:22: note: declared here
static PyObject *pybind11_init(); \
^
brainiak/factoranalysis/tfa_extension.cpp:242:1: note: in expansion of macro ‘PYBIND11_PLUGIN’
PYBIND11_PLUGIN(tfa_extension) {
^~~~~~~~~~~~~~~
g++ -pthread -shared -B /opt/miniconda-latest/envs/neuro/compiler_compat -L/opt/miniconda-latest/envs/neuro/lib -Wl,-rpath=/opt/miniconda-latest/envs/neuro/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/brainiak/factoranalysis/tfa_extension.o -o build/lib.linux-x86_64-3.7/brainiak/factoranalysis/tfa_extension.cpython-37m-x86_64-linux-gnu.so -g0 -fopenmp -DVERSION_INFO="0.10" -std=c++14
building 'brainiak.fcma.fcma_extension' extension
creating build/temp.linux-x86_64-3.7/brainiak/fcma
creating build/temp.linux-x86_64-3.7/brainiak/fcma/src
gcc -pthread -B /opt/miniconda-latest/envs/neuro/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/miniconda-latest/envs/neuro/include/python3.7m -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/numpy/core/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -c brainiak/fcma/src/fcma_extension.cc -o build/temp.linux-x86_64-3.7/brainiak/fcma/src/fcma_extension.o -g0 -fopenmp -DVERSION_INFO="0.10" -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
brainiak/fcma/src/fcma_extension.cc:60:0: warning: ignoring #pragma simd [-Wunknown-pragmas]
#pragma simd
brainiak/fcma/src/fcma_extension.cc: In function ‘void within_subject_norm_native(pybind11::array_t<float, 17>, int)’:
brainiak/fcma/src/fcma_extension.cc:54:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int v = 0 ; v < nSelectedVoxels*nSubjs ; v++)
~~^~~~~~~~~~~~~~~~~~~~~~~~
brainiak/fcma/src/fcma_extension.cc:61:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j = 0 ; j < nVoxels ; j++)
~~^~~~~~~~~
In file included from /tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/pytypes.h:12:0,
from /tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/cast.h:13,
from /tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/attr.h:13,
from /tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/pybind11.h:44,
from brainiak/fcma/src/fcma_extension.cc:23:
brainiak/fcma/src/fcma_extension.cc: In function ‘PyObject* PyInit_fcma_extension()’:
/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/detail/common.h:271:20: warning: ‘PyObject* pybind11_init()’ is deprecated: PYBIND11_PLUGIN is deprecated, use PYBIND11_MODULE [-Wdeprecated-declarations]
return pybind11_init(); \
^
brainiak/fcma/src/fcma_extension.cc:87:1: note: in expansion of macro ‘PYBIND11_PLUGIN’
PYBIND11_PLUGIN(fcma_extension) {
^~~~~~~~~~~~~~~
/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/detail/common.h:266:22: note: declared here
static PyObject *pybind11_init(); \
^
brainiak/fcma/src/fcma_extension.cc:87:1: note: in expansion of macro ‘PYBIND11_PLUGIN’
PYBIND11_PLUGIN(fcma_extension) {
^~~~~~~~~~~~~~~
/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/detail/common.h:271:34: warning: ‘PyObject* pybind11_init()’ is deprecated: PYBIND11_PLUGIN is deprecated, use PYBIND11_MODULE [-Wdeprecated-declarations]
return pybind11_init(); \
^
brainiak/fcma/src/fcma_extension.cc:87:1: note: in expansion of macro ‘PYBIND11_PLUGIN’
PYBIND11_PLUGIN(fcma_extension) {
^~~~~~~~~~~~~~~
/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include/pybind11/detail/common.h:266:22: note: declared here
static PyObject *pybind11_init(); \
^
brainiak/fcma/src/fcma_extension.cc:87:1: note: in expansion of macro ‘PYBIND11_PLUGIN’
PYBIND11_PLUGIN(fcma_extension) {
^~~~~~~~~~~~~~~
g++ -pthread -shared -B /opt/miniconda-latest/envs/neuro/compiler_compat -L/opt/miniconda-latest/envs/neuro/lib -Wl,-rpath=/opt/miniconda-latest/envs/neuro/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/brainiak/fcma/src/fcma_extension.o -o build/lib.linux-x86_64-3.7/brainiak/fcma/fcma_extension.cpython-37m-x86_64-linux-gnu.so -g0 -fopenmp -DVERSION_INFO="0.10" -std=c++14
building 'brainiak.fcma.cython_blas' extension
gcc -pthread -B /opt/miniconda-latest/envs/neuro/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/miniconda-latest/envs/neuro/include/python3.7m -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/numpy/core/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -I/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/pybind11/include -c brainiak/fcma/cython_blas.c -o build/temp.linux-x86_64-3.7/brainiak/fcma/cython_blas.o -g0 -fopenmp -DVERSION_INFO="0.10"
brainiak/fcma/cython_blas.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
#error Do not use this file, it is the result of a failed Cython compilation.
^~~~~
/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-install-wimld_zc/brainiak/brainiak/fcma/cython_blas.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Error compiling Cython file:
------------------------------------------------------------
...
# limitations under the License.
# Authors: Yida Wang
# (Intel Labs), 2016
cimport scipy.linalg.cython_blas as blas
^
------------------------------------------------------------
brainiak/fcma/cython_blas.pyx:18:8: 'scipy/linalg/cython_blas.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
A = py_a
cdef float[:, ::1] B
B = py_b
cdef float[:, :, ::1] C
C = py_c
blas.sgemm(trans_a, trans_b, &M, &N, &K, &alpha, &A[0, 0], &lda,
^
------------------------------------------------------------
brainiak/fcma/cython_blas.pyx:115:8: cimported module has no attribute 'sgemm'
Error compiling Cython file:
------------------------------------------------------------
...
beta = py_beta
cdef float[:, :, ::1] A
A = py_a
cdef float[:, ::1] C
C = py_c
blas.ssyrk(uplo, trans, &N, &K, &alpha, &A[py_start_voxel, 0, 0], &lda,
^
------------------------------------------------------------
brainiak/fcma/cython_blas.pyx:197:8: cimported module has no attribute 'ssyrk'
Error compiling Cython file:
------------------------------------------------------------
...
beta = py_beta
cdef float[:, ::1] A
A = py_a
cdef float[:, :, ::1] C
C = py_c
blas.ssyrk(uplo, trans, &N, &K, &alpha, &A[0, 0], &lda,
^
------------------------------------------------------------
brainiak/fcma/cython_blas.pyx:286:8: cimported module has no attribute 'ssyrk'
Error compiling Cython file:
------------------------------------------------------------
...
beta = py_beta
cdef float[:, ::1] A
A = py_a
cdef float[:, :, ::1] C
C = py_c
blas.sgemm(trans_a, trans_b, &M, &N, &K, &alpha, &A[0, 0], &lda,
^
------------------------------------------------------------
brainiak/fcma/cython_blas.pyx:385:8: cimported module has no attribute 'sgemm'
Error compiling Cython file:
------------------------------------------------------------
...
A = py_a
cdef float[:, ::1] B
B = py_b
cdef float[:, :, ::1] C
C = py_c
blas.sgemm(trans_a, trans_b, &M, &N, &K, &alpha, &A[0, 0], &lda,
^
------------------------------------------------------------
brainiak/fcma/cython_blas.pyx:477:8: cimported module has no attribute 'sgemm'
Error compiling Cython file:
------------------------------------------------------------
...
A = py_a
cdef float[:, ::1] B
B = py_b
cdef float[:, ::1] C
C = py_c
blas.sgemm(trans_a, trans_b, &M, &N, &K, &alpha, &A[0, 0], &lda,
^
------------------------------------------------------------
brainiak/fcma/cython_blas.pyx:559:8: cimported module has no attribute 'sgemm'
/tmp/pip-build-env-cc4bip_4/normal/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-install-wimld_zc/brainiak/brainiak/eventseg/_utils.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for brainiak
Building wheel for pydotplus (setup.py) ... done
Created wheel for pydotplus: filename=pydotplus-2.0.2-py3-none-any.whl size=24566 sha256=f88fbfc81d6ae36b550747eb2bae4bbc46fbae4597feb3dbaa64b83980af3e84
Stored in directory: /tmp/pip-ephem-wheel-cache-zvx3f8sk/wheels/1e/7b/04/7387cf6cc9e48b4a96e361b0be812f0708b394b821bf8c9c50
Building wheel for simplejson (setup.py) ... done
Created wheel for simplejson: filename=simplejson-3.17.0-cp37-cp37m-linux_x86_64.whl size=122414 sha256=521839bd4ca33aa60de095ad763c2132658474e266204e8b534b9fc2eb6f7491
Stored in directory: /tmp/pip-ephem-wheel-cache-zvx3f8sk/wheels/8a/2d/bb/65cfe3f590a9cbb199f2011a6e4ccecd858844fb04e0dee2e9
Building wheel for theano (setup.py) ... done
Created wheel for theano: filename=Theano-1.0.4-py3-none-any.whl size=2667177 sha256=3f5488666709066b5e3da5e0a2568deb21377fe5b0fb4dac585817b41d95f7ff
Stored in directory: /tmp/pip-ephem-wheel-cache-zvx3f8sk/wheels/33/e0/86/12647586a15bd29c062c9996231380908fb2dcf6a5df1c6f84
Building wheel for nitime (setup.py) ... done
Created wheel for nitime: filename=nitime-0.8.1-py3-none-any.whl size=3967490 sha256=caec50b6a27b45bfb5a218b1df0712f80e1a4f915b67d65bb7b8de6cdedf4dad
Stored in directory: /tmp/pip-ephem-wheel-cache-zvx3f8sk/wheels/fe/e9/5c/3626a4a5dae66799e04734001392429cfc747395278497bb90
Building wheel for sklearn (setup.py) ... done
Created wheel for sklearn: filename=sklearn-0.0-py2.py3-none-any.whl size=1315 sha256=398f060ec717f9321d976ee9f47de92f0ed2bc1657aa47617287ecdf42493b1d
Stored in directory: /tmp/pip-ephem-wheel-cache-zvx3f8sk/wheels/46/ef/c3/157e41f5ee1372d1be90b09f74f82b10e391eaacca8f22d33e
Successfully built mpi4py psutil pydotplus simplejson theano nitime sklearn
Failed to build brainiak
ERROR: Could not build wheels for brainiak which use PEP 517 and cannot be installed directly
FATAL: failed to execute %post proc: exit status 1
FATAL: While performing build: while running engine: while running /usr/local/libexec/singularity/bin/starter: exit status 255
Issue Analytics
- State:
- Created 3 years ago
- Comments:5
Top Results From Across the Web
bids/brainiak-srm - Singularity Hub Container Tools
This module is a singularity container wrapper for bids/brainiak-srm. Shared Response Model (SRM) from the Brain Imaging Analysis Kit (BrainIAK) ...
Read more >containers/README.md at master · ReproNim ... - GitHub
make Singularity images transparently usable on non-Linux (OSX) systems via Docker. ReproNim/containers as a YODA building block. All images are "registered" ...
Read more >Frequently Asked Questions - Brain Imaging Analysis Kit
How do I use BrainIAK? BrainIAK is a software package that can be installed by various standard ways for Python packages, such as...
Read more >brainiak/brainiak - Gitter
Hi, I encouter an issue when I was trying to use the container image to run brainiak. I did. singularity pull docker://brainiak/brainiak. singularity...
Read more >BrainIAK: The Brain Imaging Analysis Kit — - Aperture Neuro —
Here, we describe the Brain Imaging Analysis Kit (BrainIAK), ... variety of installation options for the tutorials with a Docker container, ...
Read more >
Top Related Medium Post
No results found
Top Related StackOverflow Question
No results found
Troubleshoot Live Code
Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free
Top Related Reddit Thread
No results found
Top Related Hackernoon Post
No results found
Top Related Tweet
No results found
Top Related Dev.to Post
No results found
Top Related Hashnode Post
No results found
You can use the
conda_optsoption in the--minicondastep to add--channel brainiak. I have outlined the steps below. Because you are only using one conda environment, I would suggest installing into the base environment instead of creating a separate environment.Let me know if you have any other questions!
Excellent! Closing this issue but please open a new one if you run into other problems.