Issue title: problems with install (louvain)
 Issue body: Hi,

I am trying to install cellOracle on a shared server, which I don't have the sudo permission.
OS: CentOS 7.8. queing system: slurm
I tried first to go through the installation webpage, but failed.

Then I tried to install in the following steps:
ml purge
ml load Python/3.6.6-foss-2018b
virtualenv --system-site-packages /xxx/home/user/cellOracle
source /xxx/home/user/cellOracle/bin/activate
conda install gcc_linux-64 llvm
pip install numpy scipy cython numba matplotlib scikit-learn h5py click pysam 
	pip install velocyto
	git clone https://github.com/velocyto-team/velocyto.py.git
	cd software/velocyto.py/
	pip install -e . #velocyto --help, check install successfully or not
pip install scanpy==1.4.4 umap-learn==0.3.10
pip install genomepy==0.5.5 gimmemotifs==0.13.1
pip install goatools pyarrow tqdm joblib jupyter
All above works.

But when I come to the final step, which is installed cellOracle, stucked.
pip install git+https://github.com/morris-lab/CellOracle.git
It seems related to louvain, which I also tried to install it before install cellOracle:
pip install python-louvain
pip install --user --upgrade python-louvain

The error log:
  ERROR: Failed building wheel for louvain
  Running setup.py clean for louvain
Successfully built celloracle
Failed to build louvain
Installing collected packages: louvain, fa2, celloracle
    Running setup.py install for louvain ... error

Any ideas on how to fix it? thanks a lot!



 Comments: 
 Comment 0: Hi wangmhan, 
Thank you for trying celloracle!

As you said, the problem seems to exist in the louvain package.

Could you please try to install "louvain", instead of "python-louvain" using the following command?
`pip install louvain`


 Comment 1: Hi wangmhan,

Thank you for sending the log file! But I could not find it. 
I think the attached file was automatically removed by the system of GitHub.

Could you please copy and paste the content of log file to the body of message?

Thank you for help. It helps us to improve celloracle!

 Comment 2: yes, sure. It is quite long...

Collecting git+https://github.com/morris-lab/CellOracle.git
  Cloning https://github.com/morris-lab/CellOracle.git to
/scratch/pip-req-build-7969rtrw
  Running command git clone -q https://github.com/morris-lab/CellOracle.git
/scratch/pip-req-build-7969rtrw
Requirement already satisfied: numpy in
/scicore/soft/apps/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg
(from celloracle==0.3.7) (1.15.0)
Requirement already satisfied: scipy in
./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (1.5.0)
Requirement already satisfied: cython in
/scicore/soft/apps/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/Cython-0.28.5-py3.6-linux-x86_64.egg
(from celloracle==0.3.7) (0.28.5)
Requirement already satisfied: numba in
./.local/lib/python3.6/site-packages (from celloracle==0.3.7) (0.50.0)
Requirement already satisfied: matplotlib==3.0.* in
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Requirement already satisfied: h5py in ./.local/lib/python3.6/site-packages
(from celloracle==0.3.7) (2.10.0)
Requirement already satisfied: pandas==0.25.* in
./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (0.25.3)
Requirement already satisfied: velocyto>=0.17 in ./software/velocyto.py
(from celloracle==0.3.7) (0.17.16)
Requirement already satisfied: umap-learn==0.3.10 in
./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (0.3.10)
Requirement already satisfied: pyarrow in
./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (0.17.1)
Requirement already satisfied: jupyter in
./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (1.0.0)
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./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (4.46.1)
Requirement already satisfied: python-igraph in
./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (0.8.2)
Collecting louvain==0.6.1
  Using cached louvain-0.6.1.tar.gz (84 kB)
Requirement already satisfied: fa2 in
./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (0.3.5)
Requirement already satisfied: scanpy==1.4.4 in
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Requirement already satisfied: joblib in
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(from celloracle==0.3.7) (0.12.2)
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./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (1.0.6)
Requirement already satisfied: genomepy==0.5.5 in
./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (0.5.5)
Requirement already satisfied: gimmemotifs==0.13.1 in
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(0.33.0)
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(47.3.1)
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(from matplotlib==3.0.*->celloracle==0.3.7) (2.7.3)
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(from matplotlib==3.0.*->celloracle==0.3.7) (2.2.0)
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Requirement already satisfied: pytz>=2017.2 in
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(from pandas==0.25.*->celloracle==0.3.7) (2018.5)
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velocyto>=0.17->celloracle==0.3.7) (3.0.6)
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velocyto>=0.17->celloracle==0.3.7) (116.69.203.115)
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(5.3.0)
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scanpy==1.4.4->celloracle==0.3.7) (1.6.1)
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scanpy==1.4.4->celloracle==0.3.7) (2.4)
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scanpy==1.4.4->celloracle==0.3.7) (0.11.1)
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(2.10.0)
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(5.4.3)
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Requirement already satisfied: wget in
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(from goatools->celloracle==0.3.7) (2.19.1)
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genomepy==0.5.5->celloracle==0.3.7) (0.12.0)
Requirement already satisfied: pyfaidx>=0.5.1 in
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genomepy==0.5.5->celloracle==0.3.7) (0.5.9)
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ipykernel->jupyter->celloracle==0.3.7) (6.1.3)
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bleach->nbconvert->jupyter->celloracle==0.3.7) (0.5.1)
Requirement already satisfied: ptyprocess; os_name != "nt" in
./cellOracle/lib/python3.6/site-packages (from
terminado>=0.8.1->notebook->jupyter->celloracle==0.3.7) (0.6.0)
Requirement already satisfied: parso<0.8.0,>=0.7.0 in
./cellOracle/lib/python3.6/site-packages (from
jedi>=0.10->ipython>=5.0.0->ipykernel->jupyter->celloracle==0.3.7) (0.7.0)
Requirement already satisfied: pyrsistent>=0.14.0 in
./cellOracle/lib/python3.6/site-packages (from
jsonschema!=2.5.0,>=2.4->nbformat>=4.4->nbconvert->jupyter->celloracle==0.3.7)
(0.16.0)
Building wheels for collected packages: celloracle, louvain
  Building wheel for celloracle (setup.py): started
  Building wheel for celloracle (setup.py): finished with status 'done'
  Created wheel for celloracle: filename=celloracle-0.3.7-py3-none-any.whl
size=9666413
sha256=160acc0a858ff7dfdcf1022e8779a151312b8a0824d90e5b9d08d450ea5478d8
  Stored in directory:
/scratch/pip-ephem-wheel-cache-8luk89yk/wheels/61/1c/d4/ddf7ffaf2722290ecc124290240d783aec2b6b4919149f0b34
  Building wheel for louvain (setup.py): started
  Building wheel for louvain (setup.py): still running...
  Building wheel for louvain (setup.py): still running...
  Building wheel for louvain (setup.py): still running...
  Building wheel for louvain (setup.py): still running...
  Building wheel for louvain (setup.py): finished with status 'error'
  ERROR: Command errored out with exit status 1:
   command: /scicore/home/user/cellOracle/bin/python -u -c 'import sys,
setuptools, tokenize; sys.argv[0] =
'"'"'/scratch/pip-install-343eu38b/louvain/setup.py'"'"';
__file__='"'"'/scratch/pip-install-343eu38b/louvain/setup.py'"'"';f=getattr(tokenize,
'"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"',
'"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))'
bdist_wheel -d /scratch/pip-wheel-pcvgp7p9
       cwd: /scratch/pip-install-343eu38b/louvain/
  Complete output (4393 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.6
  creating build/lib.linux-x86_64-3.6/louvain
  copying src/Optimiser.py -> build/lib.linux-x86_64-3.6/louvain
  copying src/VertexPartition.py -> build/lib.linux-x86_64-3.6/louvain
  copying src/__init__.py -> build/lib.linux-x86_64-3.6/louvain
  copying src/_version.py -> build/lib.linux-x86_64-3.6/louvain
  copying src/functions.py -> build/lib.linux-x86_64-3.6/louvain

/scicore/home/user/cellOracle/lib/python3.6/site-packages/setuptools/lib2to3_ex.py:44:
SetuptoolsDeprecationWarning: 2to3 support is deprecated. If the project
still requires Python 2 support, please migrate to a single-codebase
solution or employ an independent conversion process.
    SetuptoolsDeprecationWarning)
  Fixing build/lib.linux-x86_64-3.6/louvain/Optimiser.py
build/lib.linux-x86_64-3.6/louvain/VertexPartition.py
build/lib.linux-x86_64-3.6/louvain/__init__.py
build/lib.linux-x86_64-3.6/louvain/_version.py
build/lib.linux-x86_64-3.6/louvain/functions.py
  Skipping optional fixer: buffer
  Skipping optional fixer: idioms
  Skipping optional fixer: set_literal
  Skipping optional fixer: ws_comma
  Fixing build/lib.linux-x86_64-3.6/louvain/Optimiser.py
build/lib.linux-x86_64-3.6/louvain/VertexPartition.py
build/lib.linux-x86_64-3.6/louvain/__init__.py
build/lib.linux-x86_64-3.6/louvain/_version.py
build/lib.linux-x86_64-3.6/louvain/functions.py
  Skipping optional fixer: buffer
  Skipping optional fixer: idioms
  Skipping optional fixer: set_literal
  Skipping optional fixer: ws_comma
  UPDATING build/lib.linux-x86_64-3.6/louvain/_version.py
  set build/lib.linux-x86_64-3.6/louvain/_version.py to '0.6.1'
  running build_ext
  Cannot find the C core of igraph on this system using pkg-config.
  We will now try to download and compile the C core from scratch.
  Version number of the C core: 0.7.1


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  Extracting igraph-0.7.1.tar.gz...
  Configuring igraph...
  checking for a BSD-compatible install... /usr/bin/install -c
  checking whether build environment is sane... yes
  checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
  checking for gawk... gawk
  checking whether make sets $(MAKE)... yes
  checking whether make supports nested variables... yes
  checking for gcc...
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables...
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether we are using the GNU C compiler... yes
  checking whether
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
accepts -g... yes
  checking for
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
option to accept ISO C89... none needed
  checking whether
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
understands -c and -o together... yes
  checking for style of include used by make... GNU
  checking dependency style of
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc...
gcc3
  checking for g++... g++
  checking whether we are using the GNU C++ compiler... yes
  checking whether g++ accepts -g... yes
  checking dependency style of g++... gcc3
  checking how to run the C++ preprocessor... g++ -E
  checking for flex... flex
  checking lex output file root... lex.yy
  checking lex library... none needed
  checking whether yytext is a pointer... no
  checking for bison... bison -y
  checking how to run the C preprocessor...
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cpp
  checking for grep that handles long lines and -e... /usr/bin/grep
  checking for egrep... /usr/bin/grep -E
  checking for ANSI C header files... yes
  checking for sys/types.h... yes
  checking for sys/stat.h... yes
  checking for stdlib.h... yes
  checking for string.h... yes
  checking for memory.h... yes
  checking for strings.h... yes
  checking for inttypes.h... yes
  checking for stdint.h... yes
  checking for unistd.h... yes
  checking sys/times.h usability... yes
  checking sys/times.h presence... yes
  checking for sys/times.h... yes
  checking build system type... x86_64-unknown-linux-gnu
  checking host system type... x86_64-unknown-linux-gnu
  checking how to print strings... printf
  checking for a sed that does not truncate output... /usr/bin/sed
  checking for fgrep... /usr/bin/grep -F
  checking for ld used by
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc...
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ld
  checking if the linker
(/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ld)
is GNU ld... yes
  checking for BSD- or MS-compatible name lister (nm)...
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-nm
  checking the name lister
(/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-nm)
interface... BSD nm
  checking whether ln -s works... yes
  checking the maximum length of command line arguments... 1572864
  checking whether the shell understands some XSI constructs... yes
  checking whether the shell understands "+="... yes
  checking how to convert x86_64-unknown-linux-gnu file names to
x86_64-unknown-linux-gnu format... func_convert_file_noop
  checking how to convert x86_64-unknown-linux-gnu file names to toolchain
format... func_convert_file_noop
  checking for
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ld
option to reload object files... -r
  checking for objdump...
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-objdump
  checking how to recognize dependent libraries... pass_all
  checking for dlltool... dlltool
  checking how to associate runtime and link libraries... printf %s\n
  checking for archiver @FILE support... @
  checking for strip...
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-strip
  checking for ranlib...
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ranlib
  checking command to parse
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-nm
output from
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
object... ok
  checking for sysroot... no
  checking for mt... no
  checking if : is a manifest tool... no
  checking for dlfcn.h... yes
  checking for objdir... .libs
  checking if
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
supports -fno-rtti -fno-exceptions... no
  checking for
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
option to produce PIC... -fPIC -DPIC
  checking if
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
PIC flag -fPIC -DPIC works... yes
  checking if
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
static flag -static works... yes
  checking if
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
supports -c -o file.o... yes
  checking if
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
supports -c -o file.o... (cached) yes
  checking whether the
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
linker
(/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ld
-m elf_x86_64) supports shared libraries... yes
  checking whether -lc should be explicitly linked in... no
  checking dynamic linker characteristics... GNU/Linux ld.so
  checking how to hardcode library paths into programs... immediate
  checking for shl_load... no
  checking for shl_load in -ldld... no
  checking for dlopen... no
  checking for dlopen in -ldl... yes
  checking whether a program can dlopen itself... yes
  checking whether a statically linked program can dlopen itself... no
  checking whether stripping libraries is possible... yes
  checking if libtool supports shared libraries... yes
  checking whether to build shared libraries... yes
  checking whether to build static libraries... yes
  checking how to run the C++ preprocessor... g++ -E
  checking for ld used by g++...
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ld
-m elf_x86_64
  checking if the linker
(/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ld
-m elf_x86_64) is GNU ld... yes
  checking whether the g++ linker
(/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ld
-m elf_x86_64) supports shared libraries... yes
  checking for g++ option to produce PIC... -fPIC -DPIC
  checking if g++ PIC flag -fPIC -DPIC works... yes
  checking if g++ static flag -static works... yes
  checking if g++ supports -c -o file.o... yes
  checking if g++ supports -c -o file.o... (cached) yes
  checking whether the g++ linker
(/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-ld
-m elf_x86_64) supports shared libraries... yes
  checking dynamic linker characteristics... (cached) GNU/Linux ld.so
  checking how to hardcode library paths into programs... immediate
  checking for ANSI C header files... (cached) yes
  checking stdarg.h usability... yes
  checking stdarg.h presence... yes
  checking for stdarg.h... yes
  checking for stdlib.h... (cached) yes
  checking for string.h... (cached) yes
  checking time.h usability... yes
  checking time.h presence... yes
  checking for time.h... yes
  checking for unistd.h... (cached) yes
  checking for stdint.h... (cached) yes
  checking sys/int_types.h usability... no
  checking sys/int_types.h presence... no
  checking for sys/int_types.h... no
  checking for expm1... yes
  checking for rint... yes
  checking for rintf... yes
  checking for finite... yes
  checking for log2... yes
  checking for snprintf... yes
  checking for log1p... yes
  checking for round... yes
  checking for fabsl... yes
  checking for fmin... yes
  checking for strcasecmp... yes
  checking for isnan... yes
  checking for strdup... yes
  checking for _strdup... no
  checking for ftruncate... yes
  checking for stpcpy... yes
  checking whether stpcpy is declared... yes
  checking whether compiler supports -ffloat-store... yes
  checking whether compiler supports -fstore... no
  checking whether compiler accepts -Wall... yes
  checking for xml2-config...
/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/bin/xml2-config
  checking for xmlSAXUserParseFile in -lxml2... yes
  checking libxml/parser.h usability... yes
  checking libxml/parser.h presence... yes
  checking for libxml/parser.h... yes
  checking that generated files are newer than configure... done
  configure: creating ./config.status
  config.status: creating tests/Makefile
  config.status: creating tests/atlocal
  config.status: creating Makefile
  config.status: creating src/Makefile
  config.status: creating igraph.pc
  config.status: creating igraph_Info.plist
  config.status: creating doc/Makefile
  config.status: creating include/igraph_version.h
  config.status: creating include/igraph_threading.h
  config.status: creating config.h
  config.status: executing tests/atconfig commands
  config.status: executing depfiles commands
  config.status: executing libtool commands
  igraph successfully configured.
    GraphML format support -- yes
    GMP library support    -- no
    GLPK library support   -- yes
    Thread-local storage   -- no
    Use internal ARPACK    -- yes
    Use internal LAPACK    -- yes
    Use internal BLAS      -- yes
    Use internal F2C       -- yes
    Use internal GLPK      -- yes
    Debug build            -- no
    Profiling              -- no
  make  all-recursive
  make[1]: Entering directory `/scratch/igraph.4i4wymu7/igraph-0.7.1'
  Making all in src
  make[2]: Entering directory `/scratch/igraph.4i4wymu7/igraph-0.7.1/src'
  /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-fPIC -I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-DNO_FPINIT f2c/arithchk.c -lm -o f2c/arith || \
  /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DNO_LONG_LONG -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-DNO_FPINIT f2c/arithchk.c \
  -Wall -lm -o f2c/arith
  f2c/arith > f2c/arith.h
  make  all-am
  make[3]: Entering directory `/scratch/igraph.4i4wymu7/igraph-0.7.1/src'
  /bin/sh ../libtool  --tag=CC   --mode=compile
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I..   -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-basic_query.lo -MD -MP -MF .deps/libigraph_la-basic_query.Tpo
-c -o libigraph_la-basic_query.lo `test -f 'basic_query.c' || echo
'./'`basic_query.c
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-basic_query.lo -MD -MP -MF .deps/libigraph_la-basic_query.Tpo
-c basic_query.c  -fPIC -DPIC -o .libs/libigraph_la-basic_query.o
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-basic_query.lo -MD -MP -MF .deps/libigraph_la-basic_query.Tpo
-c basic_query.c -o libigraph_la-basic_query.o >/dev/null 2>&1
  mv -f .deps/libigraph_la-basic_query.Tpo
.deps/libigraph_la-basic_query.Plo
  /bin/sh ../libtool  --tag=CC   --mode=compile
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I..   -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-games.lo -MD -MP -MF .deps/libigraph_la-games.Tpo -c -o
libigraph_la-games.lo `test -f 'games.c' || echo './'`games.c
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-games.lo -MD -MP -MF .deps/libigraph_la-games.Tpo -c games.c
 -fPIC -DPIC -o .libs/libigraph_la-games.o
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-games.lo -MD -MP -MF .deps/libigraph_la-games.Tpo -c games.c
-o libigraph_la-games.o >/dev/null 2>&1
  mv -f .deps/libigraph_la-games.Tpo .deps/libigraph_la-games.Plo
  /bin/sh ../libtool  --tag=CC   --mode=compile
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I..   -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-cocitation.lo -MD -MP -MF .deps/libigraph_la-cocitation.Tpo -c
-o libigraph_la-cocitation.lo `test -f 'cocitation.c' || echo
'./'`cocitation.c
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-cocitation.lo -MD -MP -MF .deps/libigraph_la-cocitation.Tpo -c
cocitation.c  -fPIC -DPIC -o .libs/libigraph_la-cocitation.o
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-cocitation.lo -MD -MP -MF .deps/libigraph_la-cocitation.Tpo -c
cocitation.c -o libigraph_la-cocitation.o >/dev/null 2>&1
  mv -f .deps/libigraph_la-cocitation.Tpo .deps/libigraph_la-cocitation.Plo
  /bin/sh ../libtool  --tag=CC   --mode=compile
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I..   -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-iterators.lo -MD -MP -MF .deps/libigraph_la-iterators.Tpo -c
-o libigraph_la-iterators.lo `test -f 'iterators.c' || echo './'`iterators.c
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-iterators.lo -MD -MP -MF .deps/libigraph_la-iterators.Tpo -c
iterators.c  -fPIC -DPIC -o .libs/libigraph_la-iterators.o
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-iterators.lo -MD -MP -MF .deps/libigraph_la-iterators.Tpo -c
iterators.c -o libigraph_la-iterators.o >/dev/null 2>&1
  mv -f .deps/libigraph_la-iterators.Tpo .deps/libigraph_la-iterators.Plo
  /bin/sh ../libtool  --tag=CC   --mode=compile
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I..   -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-structural_properties.lo -MD -MP -MF
.deps/libigraph_la-structural_properties.Tpo -c -o
libigraph_la-structural_properties.lo `test -f 'structural_properties.c' ||
echo './'`structural_properties.c
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-structural_properties.lo -MD -MP -MF
.deps/libigraph_la-structural_properties.Tpo -c structural_properties.c
 -fPIC -DPIC -o .libs/libigraph_la-structural_properties.o
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-structural_properties.lo -MD -MP -MF
.deps/libigraph_la-structural_properties.Tpo -c structural_properties.c -o
libigraph_la-structural_properties.o >/dev/null 2>&1
  mv -f .deps/libigraph_la-structural_properties.Tpo
.deps/libigraph_la-structural_properties.Plo
  /bin/sh ../libtool  --tag=CC   --mode=compile
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I..   -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-components.lo -MD -MP -MF .deps/libigraph_la-components.Tpo -c
-o libigraph_la-components.lo `test -f 'components.c' || echo
'./'`components.c
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-components.lo -MD -MP -MF .deps/libigraph_la-components.Tpo -c
components.c  -fPIC -DPIC -o .libs/libigraph_la-components.o
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-components.lo -MD -MP -MF .deps/libigraph_la-components.Tpo -c
components.c -o libigraph_la-components.o >/dev/null 2>&1
  mv -f .deps/libigraph_la-components.Tpo .deps/libigraph_la-components.Plo
  /bin/sh ../libtool  --tag=CC   --mode=compile
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I..   -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-layout.lo -MD -MP -MF .deps/libigraph_la-layout.Tpo -c -o
libigraph_la-layout.lo `test -f 'layout.c' || echo './'`layout.c
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-layout.lo -MD -MP -MF .deps/libigraph_la-layout.Tpo -c
layout.c  -fPIC -DPIC -o .libs/libigraph_la-layout.o
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-layout.lo -MD -MP -MF .deps/libigraph_la-layout.Tpo -c
layout.c -o libigraph_la-layout.o >/dev/null 2>&1
  mv -f .deps/libigraph_la-layout.Tpo .deps/libigraph_la-layout.Plo
  /bin/sh ../libtool  --tag=CC   --mode=compile
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I..   -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-structure_generators.lo -MD -MP -MF
.deps/libigraph_la-structure_generators.Tpo -c -o
libigraph_la-structure_generators.lo `test -f 'structure_generators.c' ||
echo './'`structure_generators.c
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-structure_generators.lo -MD -MP -MF
.deps/libigraph_la-structure_generators.Tpo -c structure_generators.c
 -fPIC -DPIC -o .libs/libigraph_la-structure_generators.o
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-structure_generators.lo -MD -MP -MF
.deps/libigraph_la-structure_generators.Tpo -c structure_generators.c -o
libigraph_la-structure_generators.o >/dev/null 2>&1
  mv -f .deps/libigraph_la-structure_generators.Tpo
.deps/libigraph_la-structure_generators.Plo
  /bin/sh ../libtool  --tag=CC   --mode=compile
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I..   -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-conversion.lo -MD -MP -MF .deps/libigraph_la-conversion.Tpo -c
-o libigraph_la-conversion.lo `test -f 'conversion.c' || echo
'./'`conversion.c
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-conversion.lo -MD -MP -MF .deps/libigraph_la-conversion.Tpo -c
conversion.c  -fPIC -DPIC -o .libs/libigraph_la-conversion.o
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-conversion.lo -MD -MP -MF .deps/libigraph_la-conversion.Tpo -c
conversion.c -o libigraph_la-conversion.o >/dev/null 2>&1
  mv -f .deps/libigraph_la-conversion.Tpo .deps/libigraph_la-conversion.Plo
  /bin/sh ../libtool  --tag=CC   --mode=compile
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I..   -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-type_indexededgelist.lo -MD -MP -MF
.deps/libigraph_la-type_indexededgelist.Tpo -c -o
libigraph_la-type_indexededgelist.lo `test -f 'type_indexededgelist.c' ||
echo './'`type_indexededgelist.c
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-type_indexededgelist.lo -MD -MP -MF
.deps/libigraph_la-type_indexededgelist.Tpo -c type_indexededgelist.c
 -fPIC -DPIC -o .libs/libigraph_la-type_indexededgelist.o
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-type_indexededgelist.lo -MD -MP -MF
.deps/libigraph_la-type_indexededgelist.Tpo -c type_indexededgelist.c -o
libigraph_la-type_indexededgelist.o >/dev/null 2>&1
  mv -f .deps/libigraph_la-type_indexededgelist.Tpo
.deps/libigraph_la-type_indexededgelist.Plo
  /bin/sh ../libtool  --tag=CC   --mode=compile
/scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I..   -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-spanning_trees.lo -MD -MP -MF
.deps/libigraph_la-spanning_trees.Tpo -c -o libigraph_la-spanning_trees.lo
`test -f 'spanning_trees.c' || echo './'`spanning_trees.c
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2 -MT
libigraph_la-spanning_trees.lo -MD -MP -MF
.deps/libigraph_la-spanning_trees.Tpo -c spanning_trees.c  -fPIC -DPIC -o
.libs/libigraph_la-spanning_trees.o
  libtool: compile:
 /scicore/home/user/software/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc
-DHAVE_CONFIG_H -I. -I.. -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
-I../include -I../include -Wall -I../optional/glpk -I../src/prpack
-DPRPACK_IGRAPH_SUPPORT -fPIC
-I/scicore/soft/apps/libxml2/2.9.8-GCCcore-7.3.0/include/libxml2
 Comment 3: Hi wangmhan,

Although I'm still not 100% sure why you got that error, I tried to update our code to solve the problem.

We updated celloracle codes to support the latest version of louvain. 
Also, we updated celloracle to version 0.4.0 in order to support the packages below. 

![Screen Shot 2020-06-28 at 15 14 45](https://user-images.githubusercontent.com/42547768/85957359-54d62a80-b952-11ea-96d1-c94d89257cb6.png)

Besides, we updated our documentation for installation.
https://morris-lab.github.io/CellOracle.documentation/installation/index.html

Could you please try to install these dependent packages again?
I recommend installing them from beginning again as the package dependencies have changed significantly.

I hope this update helps you solve your issue.



 Comment 4: Hi Kenji,

I am now trying to run the whole workflow. And the genomepy install did not work with the version 0.5.5.
While if I change to version 0.8.3, there is no problem. I also asked the author, the new version is more flexible.
But I wonder if it is compatible with cellOracle or not.

Thanks & best regards,
Menghan
 Comment 5: Thank you! The reason why I was using 0.5.5 was I got serious error with ver 0.6 or something. 
I'll check the new version 0.8.3 asap Thank you!

{'source': 'GithubIssues', 'repo_name_with_owner': 'morris-lab/CellOracle', 'issue_id': 644742979, 'repo_stars': 104.0}