SamStudio8
commented
4 years ago Hi Emma, Looks like you don't have gcc installed for some things to get compiled. If you're on ubuntu, try:
sudo apt-get install build-essential python3-dev
That should install what you need, but let me know if you still have trouble.
On Tue, Jun 16, 2020 at 1:37 PM Emma Doughty notifications@github.com wrote:
Hey Sam,
Hope you're doing well. I thought I'd give reticulatus a go as it looks great- thanks! I ran into some issues with the conda/pip installation as below. I'm sure you've got way more important stuff on right now but figured I'd leave it FYI.
Best wishes, Emma
conda env create --name reticulatus --file environments/base.yaml
Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies. Conda may not use the correct pip to install your packages, and they may end up in the wrong place. Please add an explicit pip dependency. I'm adding one for you, but still nagging you. Collecting package metadata (repodata.json): done Solving environment: done Preparing transaction: done Verifying transaction: done Executing transaction: done Ran pip subprocess with arguments: ['/usr/local/software/conda/envs/reticulatus/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/ESBLEC/Pilot/Nanopore/reticulatus/environments/condaenv.m8j7o093.requirements.txt'] Pip subprocess output: Collecting git+https://github.com/SamStudio8/bondage.git (from -r /home/ESBLEC/Pilot/Nanopore/reticulatus/environments/condaenv.m8j7o093.requirements.txt (line 1)) Cloning https://github.com/SamStudio8/bondage.git to /tmp/pip-req-build-8su13pfp Collecting git+https://github.com/SamStudio8/dehumanizer.git (from -r /home/ESBLEC/Pilot/Nanopore/reticulatus/environments/condaenv.m8j7o093.requirements.txt (line 2)) Cloning https://github.com/SamStudio8/dehumanizer.git to /tmp/pip-req-build-ny89ufbs Collecting git+https://github.com/SamStudio8/ktkit.git (from -r /home/ESBLEC/Pilot/Nanopore/reticulatus/environments/condaenv.m8j7o093.requirements.txt (line 3)) Cloning https://github.com/SamStudio8/ktkit.git to /tmp/pip-req-build-lcz374cj Processing /home/ubuntu/.cache/pip/wheels/c9/72/3f/ebc23f296ed7f71013b99b08d72f8729f6d4a311e152fa3bcd/slackclient-1.3.1-py2.py3-none-any.whl Processing /home/ubuntu/.cache/pip/wheels/79/c1/b2/b6fc2647f693a084da25e1d31328ab3dbb565cc58fea37e973/GPUtil-1.4.0-py3-none-any.whl Collecting mappy Using cached mappy-2.17.tar.gz (199 kB) Requirement already satisfied, skipping upgrade: numpy in /usr/local/software/conda/envs/reticulatus/lib/python3.6/site-packages (from dehumanizer==0.8.0->-r /home/ESBLEC/Pilot/Nanopore/reticulatus/environments/condaenv.m8j7o093.requirements.txt (line 2)) (1.12.1) Requirement already satisfied, skipping upgrade: pysam in /usr/local/software/conda/envs/reticulatus/lib/python3.6/site-packages (from dehumanizer==0.8.0->-r /home/ESBLEC/Pilot/Nanopore/reticulatus/environments/condaenv.m8j7o093.requirements.txt (line 2)) (0.15.0) Collecting websocket-client<0.55.0,>=0.35 Using cached websocket_client-0.54.0-py2.py3-none-any.whl (200 kB) Requirement already satisfied, skipping upgrade: six<2.0a0,>=1.10 in /usr/local/software/conda/envs/reticulatus/lib/python3.6/site-packages (from slackclient==1.3.1->-r /home/ESBLEC/Pilot/Nanopore/reticulatus/environments/condaenv.m8j7o093.requirements.txt (line 4)) (1.15.0) Requirement already satisfied, skipping upgrade: requests<3.0a0,>=2.11 in /usr/local/software/conda/envs/reticulatus/lib/python3.6/site-packages (from slackclient==1.3.1->-r /home/ESBLEC/Pilot/Nanopore/reticulatus/environments/condaenv.m8j7o093.requirements.txt (line 4)) (2.23.0) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /usr/local/software/conda/envs/reticulatus/lib/python3.6/site-packages (from requests<3.0a0,>=2.11->slackclient==1.3.1->-r /home/ESBLEC/Pilot/Nanopore/reticulatus/environments/condaenv.m8j7o093.requirements.txt (line 4)) (2020.4.5.2) Requirement already satisfied, skipping upgrade: chardet<4,>=3.0.2 in /usr/local/software/conda/envs/reticulatus/lib/python3.6/site-packages (from requests<3.0a0,>=2.11->slackclient==1.3.1->-r /home/ESBLEC/Pilot/Nanopore/reticulatus/environments/condaenv.m8j7o093.requirements.txt (line 4)) (3.0.4) Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/software/conda/envs/reticulatus/lib/python3.6/site-packages (from requests<3.0a0,>=2.11->slackclient==1.3.1->-r /home/ESBLEC/Pilot/Nanopore/reticulatus/environments/condaenv.m8j7o093.requirements.txt (line 4)) (1.25.9) Requirement already satisfied, skipping upgrade: idna<3,>=2.5 in /usr/local/software/conda/envs/reticulatus/lib/python3.6/site-packages (from requests<3.0a0,>=2.11->slackclient==1.3.1->-r /home/ESBLEC/Pilot/Nanopore/reticulatus/environments/condaenv.m8j7o093.requirements.txt (line 4)) (2.9) Building wheels for collected packages: bondage, dehumanizer, mappy, ktkit Building wheel for bondage (setup.py): started Building wheel for bondage (setup.py): finished with status 'done' Created wheel for bondage: filename=bondage-0.0.1-py3-none-any.whl size=4381 sha256=d06f7dcc6ea6b68f43bb57b5dc1fbc1a062fb1a992344795114ddd24279fe4bd Stored in directory: /tmp/pip-ephem-wheel-cache-_ci_t2z2/wheels/06/61/69/1df9af0e88ee51931698719bd4eed07016ff2d0aaa60d29f2f Building wheel for dehumanizer (setup.py): started Building wheel for dehumanizer (setup.py): finished with status 'done' Created wheel for dehumanizer: filename=dehumanizer-0.8.0-py3-none-any.whl size=5915 sha256=d458c8881f55fade73c12f104947b015dc1981ec5804b8ed99828a29be7d9bcd Stored in directory: /tmp/pip-ephem-wheel-cache-_ci_t2z2/wheels/c6/a8/66/e43189ab31f500c043303e8897a58ba4d741c76b40017325d2 Building wheel for mappy (setup.py): started Building wheel for mappy (setup.py): finished with status 'error' Running setup.py clean for mappy Building wheel for ktkit (setup.py): started Building wheel for ktkit (setup.py): finished with status 'done' Created wheel for ktkit: filename=ktkit-0.0.0-py3-none-any.whl size=6530 sha256=e9daaddbaeb31a95c630fc0349fea9ef15e9905dbbbb316ed9b21fa069050ac8 Stored in directory: /tmp/pip-ephem-wheel-cache-_ci_t2z2/wheels/11/d0/db/0ace68af0902e464e07c9b2ee253ca2e20d7efb69861482ddb Successfully built bondage dehumanizer ktkit Failed to build mappy Installing collected packages: websocket-client, slackclient, GPUtil, bondage, mappy, dehumanizer, ktkit Running setup.py install for mappy: started Running setup.py install for mappy: finished with status 'error'
Pip subprocess error: Running command git clone -q https://github.com/SamStudio8/bondage.git /tmp/pip-req-build-8su13pfp Running command git clone -q https://github.com/SamStudio8/dehumanizer.git /tmp/pip-req-build-ny89ufbs Running command git clone -q https://github.com/SamStudio8/ktkit.git /tmp/pip-req-build-lcz374cj ERROR: Command errored out with exit status 1: command: /usr/local/software/conda/envs/reticulatus/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uhn2esml/mappy/setup.py'"'"'; file='"'"'/tmp/pip-install-uhn2esml/mappy/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 /tmp/pip-wheel-6e6dwgw2 cwd: /tmp/pip-install-uhn2esml/mappy/ Complete output (10 lines): running bdist_wheel running build running build_ext building 'mappy' extension creating build creating build/temp.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/python gcc -pthread -B /usr/local/software/conda/envs/reticulatus/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I. -I/usr/local/software/conda/envs/reticulatus/include/python3.6m -c python/mappy.c -o build/temp.linux-x86_64-3.6/python/mappy.o -DHAVE_KALLOC -msse4.1 unable to execute 'gcc': No such file or directory error: command 'gcc' failed with exit status 1
ERROR: Failed building wheel for mappy ERROR: Command errored out with exit status 1: command: /usr/local/software/conda/envs/reticulatus/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uhn2esml/mappy/setup.py'"'"'; file='"'"'/tmp/pip-install-uhn2esml/mappy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-fe5mma2k/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/software/conda/envs/reticulatus/include/python3.6m/mappy cwd: /tmp/pip-install-uhn2esml/mappy/ Complete output (10 lines): running install running build running build_ext building 'mappy' extension creating build creating build/temp.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/python gcc -pthread -B /usr/local/software/conda/envs/reticulatus/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I. -I/usr/local/software/conda/envs/reticulatus/include/python3.6m -c python/mappy.c -o build/temp.linux-x86_64-3.6/python/mappy.o -DHAVE_KALLOC -msse4.1 unable to execute 'gcc': No such file or directory error: command 'gcc' failed with exit status 1
ERROR: Command errored out with exit status 1: /usr/local/software/conda/envs/reticulatus/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uhn2esml/mappy/setup.py'"'"'; file='"'"'/tmp/pip-install-uhn2esml/mappy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-fe5mma2k/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/software/conda/envs/reticulatus/include/python3.6m/mappy Check the logs for full command output.
CondaEnvException: Pip failed
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emmadoughty
Hey Sam,
Hope you're doing well. I thought I'd give reticulatus a go as it looks great- thanks! I ran into some issues with the conda/pip installation as below. I'm sure you've got way more important stuff on right now but figured I'd leave it FYI.
Best wishes, Emma