Error installing empress

Hi Everyone,

I’m working in qiime2-2021.4 and I have this error message when i ran this:
qiime empress community-plot \

--i-tree rooted_tree.qza \
--i-feature-table table.qza \
--m-sample-metadata-file metadata.tsv \
--m-feature-metadata-file taxonomy.qza \
--o-visualization community-tree-viz.qzv

Error: QIIME 2 has no plugin/command named 'empress'.

but when I wanted to install empress, I got this error message:

ERROR: Command errored out with exit status 1:
command: /home/sitinurmilah/miniconda3/envs/qiime2-2021.4/bin/python3.8 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-xol5cewf/iow_726df99b97844c97848ba4edd2e3ca4c/setup.py'"'"'; file='"'"'/tmp/pip-install-xol5cewf/iow_726df99b97844c97848ba4edd2e3ca4c/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-zy3u2ovo
cwd: /tmp/pip-install-xol5cewf/iow_726df99b97844c97848ba4edd2e3ca4c/
Complete output (47 lines):
running bdist_wheel
running build
running build_py
make: Entering directory '/tmp/pip-install-xol5cewf/iow_726df99b97844c97848ba4edd2e3ca4c/bp/BitArray'
ar -csru libbitarr.a bit_array.o
make: ar: No such file or directory
make: *** [Makefile:25: libbitarr.a] Error 127
make: Leaving directory '/tmp/pip-install-xol5cewf/iow_726df99b97844c97848ba4edd2e3ca4c/bp/BitArray'
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/bp
copying bp/_cli.py -> build/lib.linux-x86_64-3.8/bp
copying bp/_version.py -> build/lib.linux-x86_64-3.8/bp
copying bp/init.py -> build/lib.linux-x86_64-3.8/bp
creating build/lib.linux-x86_64-3.8/bp/BitArray
copying bp/BitArray/AUTHORS -> build/lib.linux-x86_64-3.8/bp/BitArray
copying bp/BitArray/bar.h -> build/lib.linux-x86_64-3.8/bp/BitArray
copying bp/BitArray/bit_array.c -> build/lib.linux-x86_64-3.8/bp/BitArray
copying bp/BitArray/bit_array.h -> build/lib.linux-x86_64-3.8/bp/BitArray
copying bp/BitArray/bit_array.o -> build/lib.linux-x86_64-3.8/bp/BitArray
copying bp/BitArray/bit_macros.h -> build/lib.linux-x86_64-3.8/bp/BitArray
copying bp/BitArray/LICENSE -> build/lib.linux-x86_64-3.8/bp/BitArray
copying bp/BitArray/Makefile -> build/lib.linux-x86_64-3.8/bp/BitArray
copying bp/BitArray/README.md -> build/lib.linux-x86_64-3.8/bp/BitArray
creating build/lib.linux-x86_64-3.8/bp/GPL
copying bp/GPL/Genesis_LICENSE.txt -> build/lib.linux-x86_64-3.8/bp/GPL
copying bp/GPL/_insert.c -> build/lib.linux-x86_64-3.8/bp/GPL
copying bp/GPL/_insert.pyx -> build/lib.linux-x86_64-3.8/bp/GPL
copying bp/GPL/init.py -> build/lib.linux-x86_64-3.8/bp/GPL
UPDATING build/lib.linux-x86_64-3.8/bp/_version.py
set build/lib.linux-x86_64-3.8/bp/_version.py to '1.0.5'
running build_ext
building 'bp._bp' extension
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/bp
/home/sitinurmilah/miniconda3/envs/qiime2-2021.4/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/sitinurmilah/miniconda3/envs/qiime2-2021.4/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/sitinurmilah/miniconda3/envs/qiime2-2021.4/include -fPIC -I/tmp/pip-install-xol5cewf/iow_726df99b97844c97848ba4edd2e3ca4c/bp/BitArray -I/home/sitinurmilah/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/numpy/core/include -I/tmp/pip-install-xol5cewf/iow_726df99b97844c97848ba4edd2e3ca4c/bp/BitArray -I/home/sitinurmilah/miniconda3/envs/qiime2-2021.4/include/python3.8 -c bp/_bp.c -o build/temp.linux-x86_64-3.8/bp/_bp.o
In file included from /home/sitinurmilah/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944,
from /home/sitinurmilah/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/sitinurmilah/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from bp/_bp.c:711:
/home/sitinurmilah/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with "
| ^~~~~~~
x86_64-conda_cos6-linux-gnu-gcc -pthread -shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/home/sitinurmilah/miniconda3/envs/qiime2-2021.4/lib -L/home/sitinurmilah/miniconda3/envs/qiime2-2021.4/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/home/sitinurmilah/miniconda3/envs/qiime2-2021.4/lib -L/home/sitinurmilah/miniconda3/envs/qiime2-2021.4/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/sitinurmilah/miniconda3/envs/qiime2-2021.4/lib -Wl,-rpath-link,/home/sitinurmilah/miniconda3/envs/qiime2-2021.4/lib -L/home/sitinurmilah/miniconda3/envs/qiime2-2021.4/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/sitinurmilah/miniconda3/envs/qiime2-2021.4/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/sitinurmilah/miniconda3/envs/qiime2-2021.4/include build/temp.linux-x86_64-3.8/bp/_bp.o -L/tmp/pip-install-xol5cewf/iow_726df99b97844c97848ba4edd2e3ca4c/bp/BitArray -lbitarr -o build/lib.linux-x86_64-3.8/bp/_bp.cpython-38-x86_64-linux-gnu.so
/home/sitinurmilah/miniconda3/envs/qiime2-2021.4/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lbitarr
collect2: error: ld returned 1 exit status
error: command 'x86_64-conda_cos6-linux-gnu-gcc' failed with exit status 1

ERROR: Failed building wheel for iow

what am I doing wrong?

@Siti_Nurmilah,

It looks like empress was not able to be installed correctly. I was just able to install it on the latest release (2022.2). I think I would create a new install it(here are the install instructions). Then with your new environment activated, you can use these commands to install and check it:

pip install empress
qiime dev refresh-cache
qiime empress

I installed qiime2-2022.2, but it still fails to install empress with the following error message:

error: command 'x86_64-conda_cos6-linux-gnu-gcc' failed with exit status 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> iow

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

Do you have any solutions to this problem?

Hi @Siti_Nurmilah,

I think this is an issue we've seen before, with WSL not having certain libraries installed.

Could you try running sudo apt-get install binutils, and then try re-installing empress? I think this should fix things.

1 Like

I tried, but it didn't appear to work. Is there something I'm missing?

Sorry, my initial response might have been ambiguous. Could you please remove the comma (,) at the end of the command?

So just running

sudo apt-get install binutils

Apologies for the trouble!

Okay, now Empress can be properly installed, thank you! :+1:

2 Likes

@fedarko, thanks for hopping in here, I have not used WSL :face_with_spiral_eyes:

1 Like

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