OS: Ubuntu 20.04, 16 cores, ~ 256 GB RAM. Python: Python 3.9.16
I got the follow error attempting to run the Demo, following the Quickstart instructions:
git clone https://github.com/dib-lab/charcoal
cd ./charcoal/
conda env create -f environment.yml -n charcoal
conda activate charcoal
pip install -e .
(charcoal) cooperjo@nkusa1:charcoal$python -m charcoal run demo/demo.conf -j 4
** read 3 provided lineages
** config file checks PASSED!
** from here on out, it's all snakemake...
Building DAG of jobs...
Creating conda environment charcoal/conf/env-sourmash.yml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /home/hh.nku.edu/cooperjo/software/charcoal/charcoal/conf/env-sourmash.yml:
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Installing pip dependencies: ...working... Pip subprocess error:
Running command git clone --filter=blob:none --quiet https://github.com/dib-lab/charcoal.git /tmp/pip-req-build-g6pba77p
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [29 lines of output]
running bdist_wheel
running build
running build_ext
using unix compiler
building 'crlibm' extension
creating build
creating build/temp.linux-x86_64-cpython-39
creating build/temp.linux-x86_64-cpython-39/ext
/home/hh.nku.edu/cooperjo/miniconda3/envs/metagenome/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include -fPIC -O2 -isystem /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/hh.nku.edu/cooperjo/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/hh.nku.edu/cooperjo/miniconda3/include -fPIC -Ibuild/crlibm/include -I/home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include/python3.9 -c ext/crlibmmodule.c -o build/temp.linux-x86_64-cpython-39/ext/crlibmmodule.o
invoking: ['make', 'crlibm-notest']
(cd crlibm; CFLAGS='-fPIC' ./configure --prefix=/tmp/pip-install-0vow1iho/crlibm_6fa4e4c480fc477a8d0cb56a247b6d4f/build/crlibm)
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-conda-linux-gnu
checking host system type... x86_64-conda-linux-gnu
checking whether make sets $(MAKE)... (cached) yes
checking for x86_64-conda-linux-gnu-gcc... /home/hh.nku.edu/cooperjo/miniconda3/envs/metagenome/bin/x86_64-conda-linux-gnu-cc
checking for C compiler default output file name...
configure: error: in /tmp/pip-install-0vow1iho/crlibm_6fa4e4c480fc477a8d0cb56a247b6d4f/crlibm': configure: error: C compiler cannot create executables See config.log' for more details.
Makefile:26: recipe for target 'crlibm/crlibm_config.h' failed
make: *** [crlibm/crlibm_config.h] Error 77
building 'crlibm' extension
/home/hh.nku.edu/cooperjo/miniconda3/envs/metagenome/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include -fPIC -O2 -isystem /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/hh.nku.edu/cooperjo/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/hh.nku.edu/cooperjo/miniconda3/include -fPIC -Ibuild/crlibm/include -I/home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include/python3.9 -c ext/crlibmmodule.c -o build/temp.linux-x86_64-cpython-39/ext/crlibmmodule.o
error: command '/home/hh.nku.edu/cooperjo/miniconda3/envs/metagenome/bin/x86_64-conda-linux-gnu-cc' failed: No such file or directory
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for crlibm
error: subprocess-exited-with-error
× Building wheel for datrie (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [10 lines of output]
running bdist_wheel
running build
running build_clib
building 'datrie' library
creating build
creating build/temp.linux-x86_64-cpython-39
creating build/temp.linux-x86_64-cpython-39/libdatrie
creating build/temp.linux-x86_64-cpython-39/libdatrie/datrie
/home/hh.nku.edu/cooperjo/miniconda3/envs/metagenome/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include -fPIC -O2 -isystem /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/hh.nku.edu/cooperjo/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/hh.nku.edu/cooperjo/miniconda3/include -fPIC -Ilibdatrie -c libdatrie/datrie/alpha-map.c -o build/temp.linux-x86_64-cpython-39/libdatrie/datrie/alpha-map.o
error: command '/home/hh.nku.edu/cooperjo/miniconda3/envs/metagenome/bin/x86_64-conda-linux-gnu-cc' failed: No such file or directory
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for datrie
ERROR: Could not build wheels for datrie, which is required to install pyproject.toml-based projects
failed
CondaEnvException: Pip failed
File "/home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages/snakemake/deployment/conda.py", line 387, in create
Error in snakemake invocation: Command '['snakemake', '-s', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/Snakefile', '--use-conda', '-j', '1', '-j', '4', '--configfile', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/conf/defaults.conf', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/conf/system.conf', 'demo/demo.conf']' returned non-zero exit status 1.
OS: Ubuntu 20.04, 16 cores, ~ 256 GB RAM. Python: Python 3.9.16
I got the follow error attempting to run the Demo, following the Quickstart instructions:
git clone https://github.com/dib-lab/charcoal
cd ./charcoal/
conda env create -f environment.yml -n charcoal
conda activate charcoal
pip install -e .
(charcoal) cooperjo@nkusa1:charcoal$python -m charcoal run demo/demo.conf -j 4
** read 3 provided lineages
** config file checks PASSED!
** from here on out, it's all snakemake...
Building DAG of jobs...
Creating conda environment charcoal/conf/env-sourmash.yml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /home/hh.nku.edu/cooperjo/software/charcoal/charcoal/conf/env-sourmash.yml:
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Installing pip dependencies: ...working... Pip subprocess error:
Running command git clone --filter=blob:none --quiet https://github.com/dib-lab/charcoal.git /tmp/pip-req-build-g6pba77p
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [29 lines of output]
running bdist_wheel
running build
running build_ext
using unix compiler
building 'crlibm' extension
creating build
creating build/temp.linux-x86_64-cpython-39
creating build/temp.linux-x86_64-cpython-39/ext
/home/hh.nku.edu/cooperjo/miniconda3/envs/metagenome/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include -fPIC -O2 -isystem /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/hh.nku.edu/cooperjo/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/hh.nku.edu/cooperjo/miniconda3/include -fPIC -Ibuild/crlibm/include -I/home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include/python3.9 -c ext/crlibmmodule.c -o build/temp.linux-x86_64-cpython-39/ext/crlibmmodule.o
invoking: ['make', 'crlibm-notest']
(cd crlibm; CFLAGS='-fPIC' ./configure --prefix=/tmp/pip-install-0vow1iho/crlibm_6fa4e4c480fc477a8d0cb56a247b6d4f/build/crlibm)
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-conda-linux-gnu
checking host system type... x86_64-conda-linux-gnu
checking whether make sets $(MAKE)... (cached) yes
checking for x86_64-conda-linux-gnu-gcc... /home/hh.nku.edu/cooperjo/miniconda3/envs/metagenome/bin/x86_64-conda-linux-gnu-cc
checking for C compiler default output file name...
configure: error: in
/tmp/pip-install-0vow1iho/crlibm_6fa4e4c480fc477a8d0cb56a247b6d4f/crlibm': configure: error: C compiler cannot create executables Seeconfig.log' for more details.Makefile:26: recipe for target 'crlibm/crlibm_config.h' failed
make: *** [crlibm/crlibm_config.h] Error 77
building 'crlibm' extension
/home/hh.nku.edu/cooperjo/miniconda3/envs/metagenome/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include -fPIC -O2 -isystem /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/hh.nku.edu/cooperjo/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/hh.nku.edu/cooperjo/miniconda3/include -fPIC -Ibuild/crlibm/include -I/home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include/python3.9 -c ext/crlibmmodule.c -o build/temp.linux-x86_64-cpython-39/ext/crlibmmodule.o
error: command '/home/hh.nku.edu/cooperjo/miniconda3/envs/metagenome/bin/x86_64-conda-linux-gnu-cc' failed: No such file or directory
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for crlibm
error: subprocess-exited-with-error
× Building wheel for datrie (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [10 lines of output]
running bdist_wheel
running build
running build_clib
building 'datrie' library
creating build
creating build/temp.linux-x86_64-cpython-39
creating build/temp.linux-x86_64-cpython-39/libdatrie
creating build/temp.linux-x86_64-cpython-39/libdatrie/datrie
/home/hh.nku.edu/cooperjo/miniconda3/envs/metagenome/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include -fPIC -O2 -isystem /home/hh.nku.edu/cooperjo/software/charcoal/.snakemake/conda/2f8996c5733077dbf60189f4fe4cdad4/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/hh.nku.edu/cooperjo/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/hh.nku.edu/cooperjo/miniconda3/include -fPIC -Ilibdatrie -c libdatrie/datrie/alpha-map.c -o build/temp.linux-x86_64-cpython-39/libdatrie/datrie/alpha-map.o
error: command '/home/hh.nku.edu/cooperjo/miniconda3/envs/metagenome/bin/x86_64-conda-linux-gnu-cc' failed: No such file or directory
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for datrie
ERROR: Could not build wheels for datrie, which is required to install pyproject.toml-based projects
failed
CondaEnvException: Pip failed
File "/home/hh.nku.edu/cooperjo/miniconda3/envs/charcoal/lib/python3.9/site-packages/snakemake/deployment/conda.py", line 387, in create
Error in snakemake invocation: Command '['snakemake', '-s', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/Snakefile', '--use-conda', '-j', '1', '-j', '4', '--configfile', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/conf/defaults.conf', '/home/hh.nku.edu/cooperjo/software/charcoal/charcoal/conf/system.conf', 'demo/demo.conf']' returned non-zero exit status 1.