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?