Comments (4)
gavinmdouglas
commented on July 26, 2024
Is it possible that a different version of pandas had already been installed in that environment with pip? See this error: https://stackoverflow.com/questions/52284234/two-versions-of-pandas-causing-problems
Can you remove the environment and try re-installing?
from picrust2.
itiago
commented on July 26, 2024
I did, same thing:
igor@ubuntu:~$ conda env remove -n picrust2
Remove all packages in environment /home/igor/miniconda2/envs/picrust2:
Package Plan
environment location: /home/igor/miniconda2/envs/picrust2
The following packages will be REMOVED:
_r-mutex: 1.0.0-anacondar_1
atomicwrites: 1.3.0-py_0 conda-forge
attrs: 18.2.0-py_0 conda-forge
biom-format: 2.1.7-py36h3010b51_1002 conda-forge
blas: 1.0-mkl
bzip2: 1.0.6-h470a237_2 conda-forge
ca-certificates: 2018.11.29-ha4d7672_0 conda-forge
cairo: 1.14.12-h276e583_5 conda-forge
certifi: 2018.11.29-py36_1000 conda-forge
click: 7.0-py_0 conda-forge
coverage: 4.5.2-py36h14c3975_1000 conda-forge
curl: 7.61.0-h93b3f91_2 conda-forge
epa-ng: 0.3.4-he860b03_2 bioconda
fontconfig: 2.13.1-h65d0f4c_0 conda-forge
freetype: 2.9.1-h6debe1e_4 conda-forge
future: 0.17.1-py36_1000 conda-forge
gappa: 0.1.0-he860b03_0 bioconda
gettext: 0.19.8.1-h5e8e0c9_1 conda-forge
glib: 2.56.2-h464dc38_1 conda-forge
glpk: 4.65-h16a7912_1 conda-forge
gmp: 6.1.2-hfc679d8_0 conda-forge
graphite2: 1.3.12-hfc679d8_1 conda-forge
gsl: 2.2.1-h0c605f7_3
h5py: 2.7.0-np112py36_1 conda-forge
harfbuzz: 1.9.0-h04dbb29_1 conda-forge
hdf5: 1.8.18-3 conda-forge
hmmer: 3.2.1-hfc679d8_0 bioconda
icu: 58.2-hfc679d8_0 conda-forge
intel-openmp: 2019.1-144
joblib: 0.13.1-py_0 conda-forge
jpeg: 9c-h470a237_1 conda-forge
krb5: 1.14.6-0 conda-forge
libffi: 3.2.1-hfc679d8_5 conda-forge
libgcc-ng: 7.3.0-hdf63c60_0 conda-forge
libgfortran: 3.0.0-1 conda-forge
libgfortran-ng: 7.2.0-hdf63c60_3 conda-forge
libiconv: 1.15-h470a237_3 conda-forge
libpng: 1.6.36-ha92aebf_0 conda-forge
libssh2: 1.8.0-h5b517e9_3 conda-forge
libstdcxx-ng: 7.3.0-hdf63c60_0 conda-forge
libtiff: 4.0.10-he6b73bb_0 conda-forge
libuuid: 2.32.1-h470a237_2 conda-forge
libxcb: 1.13-h470a237_2 conda-forge
libxml2: 2.9.8-h422b904_5 conda-forge
mkl: 2018.0.3-1
more-itertools: 4.3.0-py36_1000 conda-forge
ncurses: 6.1-hfc679d8_2 conda-forge
numpy: 1.12.1-py36he24570b_1
openblas: 0.3.3-ha44fe06_1 conda-forge
openssl: 1.0.2p-h14c3975_1002 conda-forge
pandas: 0.22.0-py36_1 conda-forge
pango: 1.40.14-he752989_2 conda-forge
pcre: 8.41-hfc679d8_3 conda-forge
picrust2: 2.1.0_b-py_0 bioconda
pip: 18.1-py36_1000 conda-forge
pixman: 0.34.0-h470a237_3 conda-forge
pluggy: 0.8.1-py_0 conda-forge
pthread-stubs: 0.4-h470a237_1 conda-forge
py: 1.7.0-py_0 conda-forge
pytest: 4.2.1-py36_0 conda-forge
pytest-cov: 2.6.1-py_0 conda-forge
python: 3.6.7-h5001a0f_1 conda-forge
python-dateutil: 2.8.0-py_0 conda-forge
pytz: 2018.9-py_0 conda-forge
r-base: 3.4.1-h4fe35fd_8 conda-forge
r-castor: 1.3.4-r341hfc679d8_0 conda-forge
r-naturalsort: 0.1.3-r3.4.1_0 conda-forge
r-rcpp: 1.0.0-r341h9d2a408_0 conda-forge
readline: 7.0-haf1bffa_1 conda-forge
scipy: 0.19.1-py36h9976243_3
setuptools: 40.6.3-py36_0 conda-forge
six: 1.12.0-py36_1000 conda-forge
sqlite: 3.26.0-hb1c47c0_0 conda-forge
tk: 8.6.9-ha92aebf_0 conda-forge
wget: 1.19.5-h1ad7b7a_0
wheel: 0.32.3-py36_0 conda-forge
xorg-kbproto: 1.0.7-h470a237_2 conda-forge
xorg-libice: 1.0.9-h470a237_4 conda-forge
xorg-libsm: 1.2.3-h8c8a85c_0 conda-forge
xorg-libx11: 1.6.6-h470a237_0 conda-forge
xorg-libxau: 1.0.8-h470a237_6 conda-forge
xorg-libxdmcp: 1.1.2-h470a237_7 conda-forge
xorg-libxext: 1.3.3-h470a237_4 conda-forge
xorg-libxrender: 0.9.10-h470a237_2 conda-forge
xorg-libxt: 1.1.5-h470a237_2 conda-forge
xorg-renderproto: 0.11.1-h470a237_2 conda-forge
xorg-xextproto: 7.3.0-h470a237_2 conda-forge
xorg-xproto: 7.0.31-h470a237_7 conda-forge
xz: 5.2.4-h470a237_1 conda-forge
zlib: 1.2.11-h470a237_3 conda-forge
Proceed ([y]/n)? y
igor@ubuntu:~$ source activate picrust2
Could not find conda environment: picrust2
You can list all discoverable environments with conda info --envs.
igor@ubuntu:~$ conda create -n picrust2
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.5.11
latest version: 4.6.4
Please update conda by running
$ conda update -n base conda
Package Plan
environment location: /home/igor/miniconda2/envs/picrust2
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
To activate this environment, use
$ conda activate picrust2
To deactivate an active environment, use
$ conda deactivate
igor@ubuntu:$ source activate picrust2$ conda install -c bioconda -c conda-forge picrust2
(picrust2) igor@ubuntu:
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.5.11
latest version: 4.6.4
Please update conda by running
$ conda update -n base conda
Package Plan
environment location: /home/igor/miniconda2/envs/picrust2
added / updated specs:
- picrust2
The following packages will be downloaded:
package | build
---------------------------|-----------------
icu-58.2 | hf484d3e_1000 22.6 MB conda-forge
fontconfig-2.13.1 | h2176d3f_1000 334 KB conda-forge
libuuid-2.32.1 | h14c3975_1000 26 KB conda-forge
wheel-0.33.0 | py36_0 34 KB conda-forge
glpk-4.65 | ha14ba45_1001 1.2 MB conda-forge
hmmer-3.2.1 | hf484d3e_1 7.1 MB bioconda
r-base-3.4.1 | 4 23.0 MB conda-forge
libssh2-1.8.0 | h1ad7b7a_1003 246 KB conda-forge
xorg-xextproto-7.3.0 | h14c3975_1002 27 KB conda-forge
xz-5.2.4 | h14c3975_1001 366 KB conda-forge
cairo-1.14.12 | he6fea26_5 1.3 MB conda-forge
pango-1.40.14 | h53a7087_1002 521 KB conda-forge
glib-2.55.0 | h464dc38_2 6.1 MB conda-forge
libgcc-7.2.0 | h69d50b8_2 304 KB conda-forge
libpng-1.6.34 | ha92aebf_2 304 KB conda-forge
libffi-3.2.1 | hf484d3e_1005 46 KB conda-forge
xorg-libxdmcp-1.1.2 | h14c3975_1007 18 KB conda-forge
xorg-libx11-1.6.7 | h14c3975_1000 940 KB conda-forge
libiconv-1.15 | h14c3975_1004 2.0 MB conda-forge
xorg-renderproto-0.11.1 | h14c3975_1002 8 KB conda-forge
libtiff-4.0.9 | h648cc4a_1002 566 KB conda-forge
setuptools-40.8.0 | py36_0 626 KB conda-forge
xorg-libxrender-0.9.10 | h14c3975_1002 31 KB conda-forge
xorg-libxau-1.0.9 | h14c3975_0 13 KB conda-forge
freetype-2.9.1 | h3cfcefd_1004 822 KB conda-forge
zlib-1.2.11 | h14c3975_1004 101 KB conda-forge
pip-19.0.2 | py36_0 1.8 MB conda-forge
libcurl-7.64.0 | h01ee5af_0 586 KB conda-forge
curl-7.64.0 | h646f8bb_0 143 KB conda-forge
gettext-0.19.8.1 | h9745a5d_1001 3.7 MB conda-forge
xorg-libxext-1.3.3 | h14c3975_1004 46 KB conda-forge
tk-8.6.9 | h84994c4_1000 3.1 MB conda-forge
pthread-stubs-0.4 | h14c3975_1001 5 KB conda-forge
xorg-libsm-1.2.3 | h4937e3b_1000 25 KB conda-forge
xorg-xproto-7.0.31 | h14c3975_1007 72 KB conda-forge
gmp-6.1.2 | hf484d3e_1000 751 KB conda-forge
xorg-kbproto-1.0.7 | h14c3975_1002 26 KB conda-forge
jpeg-9c | h14c3975_1001 251 KB conda-forge
pixman-0.34.0 | h14c3975_1003 595 KB conda-forge
graphite2-1.3.13 | hf484d3e_1000 109 KB conda-forge
gsl-2.1 | 2 7.3 MB conda-forge
bzip2-1.0.6 | h14c3975_1002 415 KB conda-forge
krb5-1.16.3 | hc83ff2d_1000 1.4 MB conda-forge
harfbuzz-1.9.0 | h08d66d9_0 1.1 MB conda-forge
libxml2-2.9.8 | h143f9aa_1005 2.0 MB conda-forge
libxcb-1.13 | h14c3975_1002 396 KB conda-forge
xorg-libice-1.0.9 | h14c3975_1004 57 KB conda-forge
------------------------------------------------------------
Total: 92.3 MB
The following NEW packages will be INSTALLED:
_r-mutex: 1.0.0-anacondar_1
atomicwrites: 1.3.0-py_0 conda-forge
attrs: 18.2.0-py_0 conda-forge
biom-format: 2.1.7-py36h3010b51_1002 conda-forge
blas: 1.0-mkl
bzip2: 1.0.6-h14c3975_1002 conda-forge
ca-certificates: 2018.11.29-ha4d7672_0 conda-forge
cairo: 1.14.12-he6fea26_5 conda-forge
certifi: 2018.11.29-py36_1000 conda-forge
click: 7.0-py_0 conda-forge
coverage: 4.5.2-py36h14c3975_1000 conda-forge
curl: 7.64.0-h646f8bb_0 conda-forge
epa-ng: 0.3.4-he860b03_2 bioconda
fontconfig: 2.13.1-h2176d3f_1000 conda-forge
freetype: 2.9.1-h3cfcefd_1004 conda-forge
future: 0.17.1-py36_1000 conda-forge
gappa: 0.1.0-he860b03_0 bioconda
gettext: 0.19.8.1-h9745a5d_1001 conda-forge
glib: 2.55.0-h464dc38_2 conda-forge
glpk: 4.65-ha14ba45_1001 conda-forge
gmp: 6.1.2-hf484d3e_1000 conda-forge
graphite2: 1.3.13-hf484d3e_1000 conda-forge
gsl: 2.1-2 conda-forge
h5py: 2.7.0-np112py36_1 conda-forge
harfbuzz: 1.9.0-h08d66d9_0 conda-forge
hdf5: 1.8.18-3 conda-forge
hmmer: 3.2.1-hf484d3e_1 bioconda
icu: 58.2-hf484d3e_1000 conda-forge
intel-openmp: 2019.1-144
joblib: 0.13.1-py_0 conda-forge
jpeg: 9c-h14c3975_1001 conda-forge
krb5: 1.16.3-hc83ff2d_1000 conda-forge
libcurl: 7.64.0-h01ee5af_0 conda-forge
libedit: 3.1.20170329-0 conda-forge
libffi: 3.2.1-hf484d3e_1005 conda-forge
libgcc: 7.2.0-h69d50b8_2 conda-forge
libgcc-ng: 7.3.0-hdf63c60_0 conda-forge
libgfortran: 3.0.0-1 conda-forge
libgfortran-ng: 7.2.0-hdf63c60_3 conda-forge
libiconv: 1.15-h14c3975_1004 conda-forge
libpng: 1.6.34-ha92aebf_2 conda-forge
libssh2: 1.8.0-h1ad7b7a_1003 conda-forge
libstdcxx-ng: 7.3.0-hdf63c60_0 conda-forge
libtiff: 4.0.9-h648cc4a_1002 conda-forge
libuuid: 2.32.1-h14c3975_1000 conda-forge
libxcb: 1.13-h14c3975_1002 conda-forge
libxml2: 2.9.8-h143f9aa_1005 conda-forge
mkl: 2018.0.3-1
more-itertools: 4.3.0-py36_1000 conda-forge
ncurses: 5.9-10 conda-forge
numpy: 1.12.1-py36he24570b_1
openssl: 1.0.2p-h14c3975_1002 conda-forge
pandas: 0.22.0-py36_1 conda-forge
pango: 1.40.14-h53a7087_1002 conda-forge
pcre: 8.39-0 conda-forge
picrust2: 2.1.0_b-py_0 bioconda
pip: 19.0.2-py36_0 conda-forge
pixman: 0.34.0-h14c3975_1003 conda-forge
pluggy: 0.8.1-py_0 conda-forge
pthread-stubs: 0.4-h14c3975_1001 conda-forge
py: 1.7.0-py_0 conda-forge
pytest: 4.2.1-py36_0 conda-forge
pytest-cov: 2.6.1-py_0 conda-forge
python: 3.6.5-1 conda-forge
python-dateutil: 2.8.0-py_0 conda-forge
pytz: 2018.9-py_0 conda-forge
r-base: 3.4.1-4 conda-forge
r-castor: 1.3.4-r341hfc679d8_0 conda-forge
r-naturalsort: 0.1.3-r3.4.1_0 conda-forge
r-rcpp: 1.0.0-r341h9d2a408_0 conda-forge
readline: 7.0-0 conda-forge
scipy: 0.19.1-py36h9976243_3
setuptools: 40.8.0-py36_0 conda-forge
six: 1.12.0-py36_1000 conda-forge
sqlite: 3.20.1-2 conda-forge
tk: 8.6.9-h84994c4_1000 conda-forge
wget: 1.19.5-h1ad7b7a_0
wheel: 0.33.0-py36_0 conda-forge
xorg-kbproto: 1.0.7-h14c3975_1002 conda-forge
xorg-libice: 1.0.9-h14c3975_1004 conda-forge
xorg-libsm: 1.2.3-h4937e3b_1000 conda-forge
xorg-libx11: 1.6.7-h14c3975_1000 conda-forge
xorg-libxau: 1.0.9-h14c3975_0 conda-forge
xorg-libxdmcp: 1.1.2-h14c3975_1007 conda-forge
xorg-libxext: 1.3.3-h14c3975_1004 conda-forge
xorg-libxrender: 0.9.10-h14c3975_1002 conda-forge
xorg-renderproto: 0.11.1-h14c3975_1002 conda-forge
xorg-xextproto: 7.3.0-h14c3975_1002 conda-forge
xorg-xproto: 7.0.31-h14c3975_1007 conda-forge
xz: 5.2.4-h14c3975_1001 conda-forge
zlib: 1.2.11-h14c3975_1004 conda-forge
Proceed ([y]/n)? y
Downloading and Extracting Packages
icu-58.2 | 22.6 MB | ##################################### | 100%
fontconfig-2.13.1 | 334 KB | ##################################### | 100%
libuuid-2.32.1 | 26 KB | ##################################### | 100%
wheel-0.33.0 | 34 KB | ##################################### | 100%
glpk-4.65 | 1.2 MB | ##################################### | 100%
hmmer-3.2.1 | 7.1 MB | ##################################### | 100%
r-base-3.4.1 | 23.0 MB | ##################################### | 100%
libssh2-1.8.0 | 246 KB | ##################################### | 100%
xorg-xextproto-7.3.0 | 27 KB | ##################################### | 100%
xz-5.2.4 | 366 KB | ##################################### | 100%
cairo-1.14.12 | 1.3 MB | ##################################### | 100%
pango-1.40.14 | 521 KB | ##################################### | 100%
glib-2.55.0 | 6.1 MB | ##################################### | 100%
libgcc-7.2.0 | 304 KB | ##################################### | 100%
libpng-1.6.34 | 304 KB | ##################################### | 100%
libffi-3.2.1 | 46 KB | ##################################### | 100%
xorg-libxdmcp-1.1.2 | 18 KB | ##################################### | 100%
xorg-libx11-1.6.7 | 940 KB | ##################################### | 100%
libiconv-1.15 | 2.0 MB | ##################################### | 100%
xorg-renderproto-0.1 | 8 KB | ##################################### | 100%
libtiff-4.0.9 | 566 KB | ##################################### | 100%
setuptools-40.8.0 | 626 KB | ##################################### | 100%
xorg-libxrender-0.9. | 31 KB | ##################################### | 100%
xorg-libxau-1.0.9 | 13 KB | ##################################### | 100%
freetype-2.9.1 | 822 KB | ##################################### | 100%
zlib-1.2.11 | 101 KB | ##################################### | 100%
pip-19.0.2 | 1.8 MB | ##################################### | 100%
libcurl-7.64.0 | 586 KB | ##################################### | 100%
curl-7.64.0 | 143 KB | ##################################### | 100%
gettext-0.19.8.1 | 3.7 MB | ##################################### | 100%
xorg-libxext-1.3.3 | 46 KB | ##################################### | 100%
tk-8.6.9 | 3.1 MB | ##################################### | 100%
pthread-stubs-0.4 | 5 KB | ##################################### | 100%
xorg-libsm-1.2.3 | 25 KB | ##################################### | 100%
xorg-xproto-7.0.31 | 72 KB | ##################################### | 100%
gmp-6.1.2 | 751 KB | ##################################### | 100%
xorg-kbproto-1.0.7 | 26 KB | ##################################### | 100%
jpeg-9c | 251 KB | ##################################### | 100%
pixman-0.34.0 | 595 KB | ##################################### | 100%
graphite2-1.3.13 | 109 KB | ##################################### | 100%
gsl-2.1 | 7.3 MB | ##################################### | 100%
bzip2-1.0.6 | 415 KB | ##################################### | 100%
krb5-1.16.3 | 1.4 MB | ##################################### | 100%
harfbuzz-1.9.0 | 1.1 MB | ##################################### | 100%
libxml2-2.9.8 | 2.0 MB | ##################################### | 100%
libxcb-1.13 | 396 KB | ##################################### | 100%
xorg-libice-1.0.9 | 57 KB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(picrust2) igor@ubuntu:~$ pytest
============================= test session starts ==============================
platform linux -- Python 3.6.5, pytest-4.2.1, py-1.7.0, pluggy-0.8.1
rootdir: /home/igor, inifile:
plugins: cov-2.6.1
collected 54 items / 39 errors / 15 selected
========================================================================================= ERRORS =========================================================================================
_______________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_autolink.py _______________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/html/tests/test_autolink.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
________________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_basic.py _________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/html/tests/test_basic.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
________________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_clean.py _________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/html/tests/test_clean.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
_________________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_diff.py _________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/html/tests/test_diff.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
_____________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_elementsoup.py ______________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/html/tests/test_elementsoup.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
___________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_feedparser_data.py ____________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/html/tests/test_feedparser_data.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
_______________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_formfill.py _______________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/html/tests/test_formfill.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
________________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_forms.py _________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/html/tests/test_forms.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
________________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_forms.txt ________________________________________________________________
miniconda2/envs/picrust2/lib/python3.6/doctest.py:669: in get_doctest
return DocTest(self.get_examples(string, name), globs,
miniconda2/envs/picrust2/lib/python3.6/doctest.py:683: in get_examples
return [x for x in self.parse(string, name)
miniconda2/envs/picrust2/lib/python3.6/doctest.py:645: in parse
self._parse_example(m, name, lineno)
miniconda2/envs/picrust2/lib/python3.6/doctest.py:726: in _parse_example
options = self._find_options(source, name, lineno)
miniconda2/envs/picrust2/lib/python3.6/doctest.py:757: in _find_options
(lineno+1, name, option))
E ValueError: line 52 of the doctest for test_forms.txt has an invalid option: '+NOPARSE_MARKUP'
________________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_frames.py ________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/html/tests/test_frames.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
_____________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_html5parser.py ______________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/html/tests/test_html5parser.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
_____________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_rewritelinks.py _____________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/html/tests/test_rewritelinks.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
________________________________________________________________ ERROR collecting lxml/src/lxml/html/tests/test_xhtml.py _________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/html/tests/test_xhtml.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
__________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_builder.py __________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_builder.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_builder.py:9: in
from lxml import etree
E ImportError: cannot import name 'etree'
________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_classlookup.py ________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_classlookup.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_classlookup.py:14: in
from common_imports import etree, HelperTestCase, SillyFileLike, fileInTestDir
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
____________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_css.py ____________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_css.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_css.py:3: in
import lxml.html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
______________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_doctestcompare.py _______________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_doctestcompare.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_doctestcompare.py:4: in
from lxml import etree
E ImportError: cannot import name 'etree'
____________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_dtd.py ____________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_dtd.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_dtd.py:13: in
from common_imports import etree, html, BytesIO, _bytes, _str
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_elementpath.py ________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_elementpath.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_elementpath.py:11: in
from .common_imports import etree, HelperTestCase
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_elementtree.py ________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_elementtree.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_elementtree.py:18: in
from common_imports import BytesIO, etree
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
__________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_errors.py ___________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_errors.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_errors.py:10: in
from lxml import etree
E ImportError: cannot import name 'etree'
___________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_etree.py ___________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_etree.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_etree.py:25: in
from .common_imports import etree, StringIO, BytesIO, HelperTestCase
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
_____________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_external_document.py _____________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_external_document.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_external_document.py:11: in
from .common_imports import HelperTestCase, etree, skipIf
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_htmlparser.py _________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_htmlparser.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_htmlparser.py:14: in
from common_imports import etree, html, StringIO, BytesIO, fileInTestDir, _bytes, _str
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
__________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_http_io.py __________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_http_io.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_http_io.py:19: in
from .common_imports import (
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
____________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_incremental_xmlfile.py ____________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_incremental_xmlfile.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_incremental_xmlfile.py:16: in
from lxml.etree import LxmlSyntaxError
E ModuleNotFoundError: No module named 'lxml.etree'
____________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_io.py _____________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_io.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_io.py:14: in
from common_imports import etree, ElementTree, _str, _bytes
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
_______________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_isoschematron.py _______________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_isoschematron.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_isoschematron.py:8: in
from lxml import isoschematron
lxml/src/lxml/isoschematron/init.py:7: in
from lxml import etree as _etree # due to validator init signature
E ImportError: cannot import name 'etree'
_________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_nsclasses.py _________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_nsclasses.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_nsclasses.py:14: in
from common_imports import etree, HelperTestCase, _bytes
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
_________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_objectify.py _________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_objectify.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_objectify.py:14: in
from common_imports import etree, HelperTestCase, fileInTestDir
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
_______________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_pyclasslookup.py _______________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_pyclasslookup.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_pyclasslookup.py:14: in
from common_imports import etree, StringIO, HelperTestCase, fileInTestDir
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
__________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_relaxng.py __________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_relaxng.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_relaxng.py:13: in
from common_imports import etree, BytesIO, _bytes, HelperTestCase, fileInTestDir
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
____________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_sax.py ____________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_sax.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_sax.py:13: in
from common_imports import HelperTestCase, make_doctest, BytesIO, _bytes
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_schematron.py _________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_schematron.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_schematron.py:13: in
from common_imports import etree, HelperTestCase, fileInTestDir
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
_________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_threading.py _________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_threading.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_threading.py:17: in
from common_imports import etree, HelperTestCase, BytesIO, _bytes
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
__________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_unicode.py __________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_unicode.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_unicode.py:10: in
from common_imports import StringIO, etree, SillyFileLike, HelperTestCase
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
_________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_xmlschema.py _________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_xmlschema.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_xmlschema.py:13: in
from common_imports import etree, BytesIO, HelperTestCase, fileInTestDir
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
______________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_xpathevaluator.py _______________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_xpathevaluator.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_xpathevaluator.py:13: in
from common_imports import etree, HelperTestCase, _bytes, BytesIO
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
___________________________________________________________________ ERROR collecting lxml/src/lxml/tests/test_xslt.py ____________________________________________________________________
ImportError while importing test module '/home/igor/lxml/src/lxml/tests/test_xslt.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
lxml/src/lxml/tests/test_xslt.py:33: in
from .common_imports import etree, BytesIO, HelperTestCase, fileInTestDir
lxml/src/lxml/tests/common_imports.py:18: in
from lxml import etree, html
lxml/src/lxml/html/init.py:54: in
from .. import etree
E ImportError: cannot import name 'etree'
==================================================================================== warnings summary ====================================================================================
miniconda2/envs/picrust2/lib/python3.6/site-packages/h5py/tests/old/test_attrs_data.py:251
/home/igor/miniconda2/envs/picrust2/lib/python3.6/site-packages/h5py/tests/old/test_attrs_data.py:251: DeprecationWarning: invalid escape sequence \H
s = b"Hello\x00\Hello"
-- Docs: https://docs.pytest.org/en/latest/warnings.html
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 39 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
========================================================================= 1 warnings, 39 error in 22.37 seconds ==========================================================================
(picrust2) igor@ubuntu:~$
from picrust2.
gavinmdouglas
commented on July 26, 2024
I just realized the problem -pytest will search all subdirectories for files starting with "test" and run them. Since you're running this in your home directory you're running this on tests meant for the lxml python package, which is unrelated to PICRUSt2. Note that this step is only in the install instructions when installing from source since it doesn't work when installing from bioconda.
The test folder is not downloaded with PICRUSt2 when installed through bioconda anyway, so I believe earlier you were running tests meant for a different version of PICRUSt2. However, if you want to run the proper PICRUSt2 tests you just need to download the source and run pytest in the picrust2 directory.
Gavin
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itiago
commented on July 26, 2024
Great. Sorry about the alarm.
Thanks for the light speed replies!
Best
Igor
Em 14/02/2019 17:42, "Gavin Douglas" <[email protected]> escreveu:
I just realized the problem -pytest will search all subdirectories for
files starting with "test" and run them. Since you're running this in your
home directory you're running this on tests meant for the lxml python
package, which is unrelated to PICRUSt2. Note that this step is only in the
install instructions when installing from source since it doesn't work when
installing from bioconda.
The test folder is not downloaded with PICRUSt2 when installed through
bioconda anyway, so I believe earlier you were running tests meant for a
different version of PICRUSt2. However, if you want to run the proper
PICRUSt2 tests you just need to download the source and run pytest in the
picrust2 directory.
Gavin
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You are receiving this because you authored the thread.
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Related Issues (20)
- COG3512 was eliminated in the latest COG database (2020) HOT 1
- Retrieving more Fungi genomes for ITS and 18S predictions HOT 3
- Error picrust2 picrust2_pipeline.py HOT 3
- i get "1 failed, 60 passed" when i run the tests to verify the installation after installed picrust2-2.5.0 from source HOT 12
- Invalid model name error HOT 3
- PICRUSt2 with other database(e.g. cowpi) HOT 2
- warning line 341 "metagenome_pipeline.py" HOT 1
- Unable to install v2.5.1 on MackBook M1 with Monterey HOT 11
- Running PICRUSt on ITS sequences HOT 1
- Calling in ITS reference HOT 5
- Getting Reverse Complementary Seqs HOT 1
- q2-picrust2 Tutorial error_ "pro_ref.raxml_info" could not be found. HOT 1
- "Stopping - no ASV ids overlap between input FASTA and sequence abundance table" despite having exact ASV id matching. HOT 3
- PICRUSt2 Data and STAMP HOT 1
- use --per_sequence_contrib but find some functions have empty 'norm_taxon_function_contrib' HOT 1
- q2-picrust2-2021.11_0 will not install with qiime 2023.2 HOT 3
- Missing metacyc nitrogen pathways? HOT 2
- Missing default_files HOT 4
- pathway_pipeline.py operation failed on a column HOT 4
- Error with epa-ng HOT 1
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