pySCENIC
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20 hours ago •
aertslab
aertslab
Cannot execute pysenic: HDF5 library version mismatched error
Hi,
I am unable to run pySCENIC on ubuntu 16.04 LTS edition, 64 bit.
I have created a conda environment called pysenic using below command
conda create -n pysenic python=3.6
then, I activated the environment
conda activate pysenic
and then I followed the instructions mentioned at this link
Installation is successful; but when I run pysenic, I encounter below error:
(pysenic) bioinfo@bioinfo-pc:~/Downloads/pySCENIC$ /home/bioinfo/miniconda2/envs/pysenic/bin/pyscenic
/home/bioinfo/miniconda2/envs/pysenic/lib/python3.6/site-packages/dask/config.py:161: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
data = yaml.load(f.read()) or {}
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.10.4, library is 1.8.16
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.16
Configured on: Tue Aug 28 18:26:31 UTC 2018
Configured by: buildd@lgw01-amd64-024
Configure mode: production
Host system: x86_64-pc-linux-gnu
Uname information: Linux lgw01-amd64-024 4.4.0-128-generic #154-Ubuntu SMP Fri May 25 14:15:18 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries: static, shared
Installation point: /usr
Flavor name: serial
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/cc
CFLAGS: -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wc99-c11-compat -O3 -fstdarg-opt
AM_CFLAGS:
CPPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS: -Wl,-Bsymbolic-functions -Wl,-z,relro
H5_LDFLAGS: -Wl,--version-script,$(top_srcdir)/debian/map_serial.ver
AM_LDFLAGS:
Extra libraries: -lpthread -lsz -lz -ldl -lm
Archiver: ar
Ranlib: x86_64-linux-gnu-ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: yes
Fortran Compiler: /usr/bin/gfortran
Fortran 2003 Compiler: yes
Fortran Flags: -g -O2 -fstack-protector-strong
H5 Fortran Flags:
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes
C++: yes
C++ Compiler: /usr/bin/c++
C++ Flags: -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
H5 C++ Flags:
AM C++ Flags:
Shared C++ Library: yes
Static C++ Library: yes
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: yes
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
Strict File Format Checks: no
Optimization Instrumentation: no
Bye...
Aborted (core dumped)
Hi,
Within the pyscenic conda environment (activate conda pyscenic), could you try to install and properly configure hdf5 with the following command and try pyscenic again?
conda install -c anaconda hdf5
Hope this helps, Bram
Unfortunately that does not help even though I installed hdf5
(pysenic) bioinfo@bioinfo-pc:~/Downloads/pySCENIC$ conda list
# packages in environment at /home/bioinfo/miniconda2/envs/pysenic:
#
# Name Version Build Channel
arboreto 0.1.5 pypi_0 pypi
attrs 19.1.0 pypi_0 pypi
boltons 19.1.0 pypi_0 pypi
ca-certificates 2019.1.23 0 anaconda
certifi 2019.3.9 py36_0 anaconda
click 7.0 pypi_0 pypi
cloudpickle 0.8.1 pypi_0 pypi
cytoolz 0.9.0.1 pypi_0 pypi
dask 1.0.0 pypi_0 pypi
decorator 4.4.0 pypi_0 pypi
dill 0.2.9 pypi_0 pypi
distributed 1.27.1 pypi_0 pypi
frozendict 1.2 pypi_0 pypi
h5py 2.9.0 pypi_0 pypi
hdf5 1.10.4 hb1b8bf9_0 anaconda
heapdict 1.0.0 pypi_0 pypi
interlap 0.2.6 pypi_0 pypi
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 8.2.0 hdf63c60_1
libgfortran-ng 7.3.0 hdf63c60_0 anaconda
libstdcxx-ng 8.2.0 hdf63c60_1
llvmlite 0.28.0 pypi_0 pypi
loompy 2.0.2 pypi_0 pypi
msgpack 0.6.1 pypi_0 pypi
multiprocessing-on-dill 3.5.0a4 pypi_0 pypi
ncurses 6.1 hf484d3e_1002 conda-forge
networkx 2.3 pypi_0 pypi
numba 0.43.1 pypi_0 pypi
numpy 1.16.3 pypi_0 pypi
openssl 1.1.1 h7b6447c_0 anaconda
pandas 0.23.4 pypi_0 pypi
pip 19.1 py36_0 conda-forge
psutil 5.6.2 pypi_0 pypi
pyarrow 0.13.0 pypi_0 pypi
pyscenic 0.9.8+2.g0a44830 pypi_0 pypi
python 3.6.7 h381d211_1004 conda-forge
python-dateutil 2.8.0 pypi_0 pypi
pytz 2019.1 pypi_0 pypi
pyyaml 5.1 pypi_0 pypi
readline 7.0 hf8c457e_1001 conda-forge
scikit-learn 0.20.3 pypi_0 pypi
scipy 1.2.1 pypi_0 pypi
setuptools 41.0.1 py36_0 conda-forge
six 1.12.0 pypi_0 pypi
sortedcontainers 2.1.0 pypi_0 pypi
sqlite 3.26.0 h67949de_1001 conda-forge
tblib 1.4.0 pypi_0 pypi
tk 8.6.9 h84994c4_1001 conda-forge
toolz 0.9.0 pypi_0 pypi
tornado 6.0.2 pypi_0 pypi
tqdm 4.31.1 pypi_0 pypi
typing 3.6.6 pypi_0 pypi
umap-learn 0.3.8 pypi_0 pypi
wheel 0.33.1 py36_0 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zict 0.1.4 pypi_0 pypi
zlib 1.2.11 h14c3975_1004 conda-forge