Failed building wheel for Anvio for installation of version 4

[sipesk]

Hi,
I am aiming to install version 4 on my Ubuntu system. I have been following the directions included in the "Installation with varying levels of pain" tutorial.

I am able to pip install numpy, scipy, and cython, but get an error when trying to install anvio:

gcc -pthread -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/barbara-lloydlab/virtual-envs/anvio-4/lib/python3.5/site-packages/numpy/core/include -I/opt/local/include/ -I/usr/local/include/ -I/home/barbara-lloydlab/.pyenv/versions/3.5.1/include/python3.5m -c ./anvio/extensions/concoct/vbgmm.c -o build/temp.linux-x86_64-3.5/./anvio/extensions/concoct/vbgmm.o
In file included from /usr/lib/gcc/x86_64-linux-gnu/5/include-fixed/syslimits.h:7:0,
from /usr/lib/gcc/x86_64-linux-gnu/5/include-fixed/limits.h:34,
from /home/barbara-lloydlab/.pyenv/versions/3.5.1/include/python3.5m/Python.h:11,
from ./anvio/extensions/concoct/vbgmm.c:4:
/usr/lib/gcc/x86_64-linux-gnu/5/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1

---

Failed building wheel for anvio
Running setup.py clean for anvio
Running setup.py bdist_wheel for psutil ... error
Complete output from command /home/barbara-lloydlab/virtual-envs/anvio-4/bin/python3.5 -u -c "import setuptools, tokenize;file='/tmp/pip-build-ttk565pd/psutil/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/tmpek4k_x3ipip-wheel- --python-tag cp35:
/tmp/tmpgqircnqi.c:1:27: fatal error: linux/ethtool.h: No such file or directory
compilation terminated.
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/psutil
copying psutil/_pssunos.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/init.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_psosx.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_psaix.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_compat.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_pswindows.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_psbsd.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_psposix.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_exceptions.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_pslinux.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_common.py -> build/lib.linux-x86_64-3.5/psutil
creating build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_linux.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/init.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_misc.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_contracts.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_unicode.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_posix.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/main.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_aix.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_connections.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_system.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_bsd.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_osx.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_sunos.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_windows.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_process.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_memory_leaks.py -> build/lib.linux-x86_64-3.5/psutil/tests
running build_ext
building 'psutil._psutil_linux' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/psutil
gcc -pthread -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPSUTIL_POSIX=1 -DPSUTIL_VERSION=543 -DPSUTIL_LINUX=1 -DPSUTIL_ETHTOOL_MISSING_TYPES=1 -I/home/barbara-lloydlab/.pyenv/versions/3.5.1/include/python3.5m -c psutil/_psutil_common.c -o build/temp.linux-x86_64-3.5/psutil/_psutil_common.o
In file included from /usr/lib/gcc/x86_64-linux-gnu/5/include-fixed/syslimits.h:7:0,
from /usr/lib/gcc/x86_64-linux-gnu/5/include-fixed/limits.h:34,
from /home/barbara-lloydlab/.pyenv/versions/3.5.1/include/python3.5m/Python.h:11,
from psutil/_psutil_common.c:9:
/usr/lib/gcc/x86_64-linux-gnu/5/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1

---

Failed building wheel for psutil
Running setup.py clean for psutil
Failed to build anvio psutil
Installing collected packages: psutil, mistune, python-dateutil, pandas, anvio
Running setup.py install for psutil ... error
Complete output from command /home/barbara-lloydlab/virtual-envs/anvio-4/bin/python3.5 -u -c "import setuptools, tokenize;file='/tmp/pip-build-ttk565pd/psutil/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-t_f502ck-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/barbara-lloydlab/virtual-envs/anvio-4/include/site/python3.5/psutil:
/tmp/tmpz44bvamv.c:1:27: fatal error: linux/ethtool.h: No such file or directory
compilation terminated.
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/psutil
copying psutil/_pssunos.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/init.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_psosx.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_psaix.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_compat.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_pswindows.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_psbsd.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_psposix.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_exceptions.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_pslinux.py -> build/lib.linux-x86_64-3.5/psutil
copying psutil/_common.py -> build/lib.linux-x86_64-3.5/psutil
creating build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_linux.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/init.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_misc.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_contracts.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_unicode.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_posix.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/main.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_aix.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_connections.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_system.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_bsd.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_osx.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_sunos.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_windows.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_process.py -> build/lib.linux-x86_64-3.5/psutil/tests
copying psutil/tests/test_memory_leaks.py -> build/lib.linux-x86_64-3.5/psutil/tests
running build_ext
building 'psutil._psutil_linux' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/psutil
gcc -pthread -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPSUTIL_POSIX=1 -DPSUTIL_VERSION=543 -DPSUTIL_LINUX=1 -DPSUTIL_ETHTOOL_MISSING_TYPES=1 -I/home/barbara-lloydlab/.pyenv/versions/3.5.1/include/python3.5m -c psutil/_psutil_common.c -o build/temp.linux-x86_64-3.5/psutil/_psutil_common.o
In file included from /usr/lib/gcc/x86_64-linux-gnu/5/include-fixed/syslimits.h:7:0,
from /usr/lib/gcc/x86_64-linux-gnu/5/include-fixed/limits.h:34,
from /home/barbara-lloydlab/.pyenv/versions/3.5.1/include/python3.5m/Python.h:11,
from psutil/_psutil_common.c:9:
/usr/lib/gcc/x86_64-linux-gnu/5/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1

----------------------------------------

Command "/home/barbara-lloydlab/virtual-envs/anvio-4/bin/python3.5 -u -c "import setuptools, tokenize;file='/tmp/pip-build-ttk565pd/psutil/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-t_f502ck-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/barbara-lloydlab/virtual-envs/anvio-4/include/site/python3.5/psutil" failed with error code 1 in /tmp/pip-build-ttk565pd/psutil/

Any suggestions? Thanks!

[meren]

giampaolo/psutil#1143

It seems running this first should solve this:

sudo apt-get install python-dev

Please report back if it does.

[sipesk]

I first had to run sudo apt-get -f install to met dependencies (it was complaining about not having Python 2.7). Following this, sudo apt-get install python-dev worked perfectly!

Thanks a bunch, Meren!

-Joy and Katie

[cpalacios98]

Hi. I´m trying to install anvio7.1 following the official instructions (https://anvio.org/install/) and I get to the same error as @sipesk. I´ve already done sudo apt-get install python-dev but it´s still failing. What should I do @meren? Thank you very much in advance.

[meren]

Did you open a new terminal once you were done with sudo apt-get install python-dev, @cpalacios98?

PS: sorry for incorrectly mentioning @sipesk in the original message!

[cpalacios98]

It´s allright now. I tried to close conda env and reopen a new one and it worked. Thank you very much for your prompt response @meren
Greetings from Spain

[meren]

Great! I'm very glad things worked out. Thanks for reporting back.

[cpalacios98]

Hi @meren. I am sorry to disturb you again but today I tried to run anvio and my Linux terminal couldn´t find it. I activated the conda env where I installed anvio yesterday (conda activate anvio-7.1) but it is not there. I tried to pip install the final tar file again (succesfully) but when running the program, prodigal and the rest of conda packages installed yesterday don´t exist. Do you know what might be happening? Thanks again in advance.

[meren]

@cpalacios98, you nee dot find a way to activate your conda environment. pip installations outside of the relevant environment will not solve your problem. you can perhaps start with

conda env list

to see what conda environments are there and whether your inability to activate it is a typo :)

[cpalacios98]

Thank you again for the prompt response and the advice. I´ll make sure that my conda environment is always activated. Regards,

César

[cpalacios98]

Hello Meren. It´s me, your favourite Spanish annoying guy. I have already installed anvio and run a phylogenomic analysis following the online tutorial (https://merenlab.org/2017/06/07/phylogenomics/) which helped me a lot. Thank u so much for that.

Now, I was trying to extend the display of my tree with the -d argument of anvi-interactive command but the program keeps telling me that "The probability that myfile.txt is a tab-delimited file is zero." I am 100% sure that my file is tab delimited, I have already checked that in various ways. What can I do?

Thank you again. Regards,

César

[meren]

Hey César, this is not the best place to discuss these because this is not a technical issue.

Can you come to anvi'o slack and send your TAB-delmited file there by mentioning that anvi'o doesn't think it is a TAB-delimited file?

[cpalacios98]

Sure thing. I´ll do it right now