Closed wangmhan closed 4 years ago
KenjiKamimoto-ac
commented
4 years ago 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
wangmhan
commented
4 years ago Hi Kenji,
Thanks for the suggestion, but it still didn't work. I tried pip install louvain, also tried to assign the specific version: conda install -c conda-forge louvain=0.6.1.
I attached the log file, so you have a close look at what happens when I run: pip install git+https://github.com/morris-lab/CellOracle.git
Hope then we can get a solution. Big thanks!
On Wed, 24 Jun 2020 at 21:03, KenjiKamimoto-wustl122 < notifications@github.com> wrote:
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
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/morris-lab/CellOracle/issues/22#issuecomment-649008485, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJVYTVRBPLJUSVOPDNGVN6TRYJEXZANCNFSM4OG2HZIA .
KenjiKamimoto-ac
commented
4 years ago 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!
wangmhan
commented
4 years ago 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 ./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (3.0.3) Requirement already satisfied: seaborn in ./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (0.10.1) Requirement already satisfied: scikit-learn in ./.local/lib/python3.6/site-packages (from celloracle==0.3.7) (0.23.1) 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) Requirement already satisfied: tqdm>=4.45 in ./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 ./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (1.4.4) Requirement already satisfied: joblib in /scicore/soft/apps/Python/3.6.6-foss-2018b/lib/python3.6/site-packages (from celloracle==0.3.7) (0.12.2) Requirement already satisfied: goatools in ./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 ./cellOracle/lib/python3.6/site-packages (from celloracle==0.3.7) (0.13.1) Requirement already satisfied: llvmlite<0.34,>=0.33.0.dev0 in ./.local/lib/python3.6/site-packages (from numba->celloracle==0.3.7) (0.33.0) Requirement already satisfied: setuptools in ./cellOracle/lib/python3.6/site-packages (from numba->celloracle==0.3.7) (47.3.1) Requirement already satisfied: python-dateutil>=2.1 in /scicore/soft/apps/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/python_dateutil-2.7.3-py3.6.egg (from matplotlib==3.0.->celloracle==0.3.7) (2.7.3) Requirement already satisfied: kiwisolver>=1.0.1 in ./.local/lib/python3.6/site-packages (from matplotlib==3.0.->celloracle==0.3.7) (1.2.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /scicore/soft/apps/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/pyparsing-2.2.0-py3.6.egg (from matplotlib==3.0.->celloracle==0.3.7) (2.2.0) Requirement already satisfied: cycler>=0.10 in ./.local/lib/python3.6/site-packages (from matplotlib==3.0.->celloracle==0.3.7) (0.10.0) Requirement already satisfied: threadpoolctl>=2.0.0 in ./.local/lib/python3.6/site-packages (from scikit-learn->celloracle==0.3.7) (2.1.0) Requirement already satisfied: six in /scicore/soft/apps/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/six-1.11.0-py3.6.egg (from h5py->celloracle==0.3.7) (1.11.0) Requirement already satisfied: pytz>=2017.2 in /scicore/soft/apps/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/pytz-2018.5-py3.6.egg (from pandas==0.25.*->celloracle==0.3.7) (2018.5) Requirement already satisfied: loompy in ./.local/lib/python3.6/site-packages (from velocyto>=0.17->celloracle==0.3.7) (3.0.6) Requirement already satisfied: pysam in ./.local/lib/python3.6/site-packages (from velocyto>=0.17->celloracle==0.3.7) (0.16.0.1) Requirement already satisfied: Click in ./.local/lib/python3.6/site-packages (from velocyto>=0.17->celloracle==0.3.7) (7.1.2) Requirement already satisfied: ipykernel in ./cellOracle/lib/python3.6/site-packages (from jupyter->celloracle==0.3.7) (5.3.0) Requirement already satisfied: nbconvert in ./cellOracle/lib/python3.6/site-packages (from jupyter->celloracle==0.3.7) (5.6.1) Requirement already satisfied: qtconsole in ./cellOracle/lib/python3.6/site-packages (from jupyter->celloracle==0.3.7) (4.7.5) Requirement already satisfied: jupyter-console in ./cellOracle/lib/python3.6/site-packages (from jupyter->celloracle==0.3.7) (6.1.0) Requirement already satisfied: notebook in ./cellOracle/lib/python3.6/site-packages (from jupyter->celloracle==0.3.7) (6.0.3) Requirement already satisfied: ipywidgets in ./cellOracle/lib/python3.6/site-packages (from jupyter->celloracle==0.3.7) (7.5.1) Requirement already satisfied: texttable>=1.6.2 in ./cellOracle/lib/python3.6/site-packages (from python-igraph->celloracle==0.3.7) (1.6.2) Requirement already satisfied: patsy in ./cellOracle/lib/python3.6/site-packages (from scanpy==1.4.4->celloracle==0.3.7) (0.5.1) Requirement already satisfied: tables in ./cellOracle/lib/python3.6/site-packages (from scanpy==1.4.4->celloracle==0.3.7) (3.6.1) 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./cellOracle/lib/python3.6/site-packages (from gimmemotifs==0.13.1->celloracle==0.3.7) (0.5.0) Requirement already satisfied: pyyaml>=3.10 in ./cellOracle/lib/python3.6/site-packages (from gimmemotifs==0.13.1->celloracle==0.3.7) (5.3.1) Requirement already satisfied: future in ./cellOracle/lib/python3.6/site-packages (from gimmemotifs==0.13.1->celloracle==0.3.7) (0.18.2) Requirement already satisfied: numpy-groupies in ./.local/lib/python3.6/site-packages (from loompy->velocyto>=0.17->celloracle==0.3.7) (0+unknown) Requirement already satisfied: jupyter-client in ./cellOracle/lib/python3.6/site-packages (from ipykernel->jupyter->celloracle==0.3.7) (6.1.3) Requirement already satisfied: ipython>=5.0.0 in ./cellOracle/lib/python3.6/site-packages (from ipykernel->jupyter->celloracle==0.3.7) (7.15.0) Requirement already satisfied: tornado>=4.2 in ./cellOracle/lib/python3.6/site-packages (from ipykernel->jupyter->celloracle==0.3.7) (6.0.4) Requirement already satisfied: traitlets>=4.1.0 in 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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
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checking for inttypes.h... yes
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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
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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
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checking how to associate runtime and link libraries... printf %s\n
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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
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checking if : is a manifest tool... no
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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
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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
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checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
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checking whether to build shared libraries... yes
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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
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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.lotest -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.lotest -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.lotest -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.lotest -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.lotest -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.lotest -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.lotest -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.lotest -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.lotest -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.lotest -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
KenjiKamimoto-ac
commented
4 years ago 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.
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.
wangmhan
commented
4 years ago 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
KenjiKamimoto-ac
commented
4 years ago 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!
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!