install problem with qiime 1.9 and newest Anaconda/Miniconda versions
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Chris Walls
Oct 12, 2017, 2:38:26 PM10/12/17
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Our users have been installing Qiime 1.9 successfully with Anaconda2 or Miniconda2 for many months. This morning a user reported getting errors after following the instructions with use the lastest version of Miniconda. Sure enough, I get the same result when I tried it:
>>print_qiime_config.py -t
Traceback (most recent call last):
File "/home/Username/miniconda3/envs/qiime/bin/print_qiime_config.py", line 4, in <module>
__import__('pkg_resources').run_script('qiime==1.9.1', 'print_qiime_config.py')
File "/home/Username/miniconda3/envs/qiime/lib/python2.7/site-packages/pkg_resources/__init__.py", line 748, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/Username/miniconda3/envs/qiime/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1517, in run_script
exec(code, namespace, namespace)
File "/home/Username/miniconda3/envs/qiime/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/print_qiime_config.py", line 37, in <module>
from skbio.util import remove_files
File "/home/Username/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/__init__.py", line 15, in <module>
import skbio.io
File "/home/Username/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/io/__init__.py", line 309, in <module>
import_module('skbio.io.clustal')
File "/home/Username/miniconda3/envs/qiime/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/home/Username/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/io/clustal.py", line 123, in <module>
from skbio.alignment import Alignment
File "/home/Username/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/alignment/__init__.py", line 230, in <module>
from ._alignment import Alignment, SequenceCollection, StockholmAlignment
File "/home/Username/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/alignment/_alignment.py", line 21, in <module>
from skbio.stats.distance import DistanceMatrix
File "/home/Username/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/stats/__init__.py", line 45, in <module>
from ._subsample import subsample, subsample_counts, isubsample
File "/home/Username/miniconda3/envs/qiime/lib/python2.7/site-packages/skbio/stats/_subsample.py", line 22, in <module>
from .__subsample import _subsample_counts_without_replacement
File "__init__.pxd", line 155, in init skbio.stats.__subsample (skbio/stats/__subsample.c:3964)
ValueError: numpy.dtype has the wrong size, try recompiling
Using pip to update numpy caused a different error. I went to the archives and downloaded version from earlier in the year, qiime installed succesfully.
What has changed?
Christine Walls
Biology Technician/Server Manager
Juniata College
Colin Brislawn
Oct 13, 2017, 7:33:57 PM10/13/17
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Hello Chris,
conda create -n qiime2-2017.9 --file https://data.qiime2.org/distro/core/qiime2-2017.9-conda-linux-64.txt
Good to hear from you. I hope all is well at Juniata College.
Qiime 1.9.1 requires older versions of software, so once the conda environment is made, updating software (using conda or pip) will probably break qiime. The solution is to install qiime 1.9.1 in one conda environment, and newer software (and newer updates!) inside a different conda environment.
For example:
make a conda environment for qiime 1.9.1
conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda
make a second conda environment for qiime 2make a conda environment for qiime 1.9.1
conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda
conda create -n qiime2-2017.9 --file https://data.qiime2.org/distro/core/qiime2-2017.9-conda-linux-64.txt
Does that help answer your question?
Let me know how I can help!
Colin Brislawn
(Juniata College of '14)
Ryan Davis
Mar 20, 2018, 1:24:10 PM3/20/18
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Hi Chris and Colin,
I wanted to use one of the scripts in Qiime 1.9.1 and used conda to install it and received the same error as Chris. I don't have an old version to fall back to and was wondering how to get it working.
Thanks!
Ryan
Traceback (most recent call last):
File "/home/ryan/miniconda2/envs/qiime1/bin/print_qiime_config.py", line 4, in <module>
__import__('pkg_resources').run_script('qiime==1.9.1', 'print_qiime_config.py')
File "/home/ryan/miniconda2/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 750, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/ryan/miniconda2/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1527, in run_script
exec(code, namespace, namespace)
File "/home/ryan/miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/print_qiime_config.py", line 37, in <module>
from skbio.util import remove_files
File "/home/ryan/miniconda2/envs/qiime1/lib/python2.7/site-packages/skbio/__init__.py", line 15, in <module>
import skbio.io
File "/home/ryan/miniconda2/envs/qiime1/lib/python2.7/site-packages/skbio/io/__init__.py", line 309, in <module>
import_module('skbio.io.clustal')
File "/home/ryan/miniconda2/envs/qiime1/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/home/ryan/miniconda2/envs/qiime1/lib/python2.7/site-packages/skbio/io/clustal.py", line 123, in <module>
from skbio.alignment import Alignment
File "/home/ryan/miniconda2/envs/qiime1/lib/python2.7/site-packages/skbio/alignment/__init__.py", line 230, in <module>
from ._alignment import Alignment, SequenceCollection, StockholmAlignment
File "/home/ryan/miniconda2/envs/qiime1/lib/python2.7/site-packages/skbio/alignment/_alignment.py", line 21, in <module>
from skbio.stats.distance import DistanceMatrix
File "/home/ryan/miniconda2/envs/qiime1/lib/python2.7/site-packages/skbio/stats/__init__.py", line 45, in <module>
from ._subsample import subsample, subsample_counts, isubsample
File "/home/ryan/miniconda2/envs/qiime1/lib/python2.7/site-packages/skbio/stats/_subsample.py", line 22, in <module>
from .__subsample import _subsample_counts_without_replacement
File "__init__.pxd", line 155, in init skbio.stats.__subsample (skbio/stats/__subsample.c:3964)
ValueError: numpy.dtype has the wrong size, try recompiling
(qiime1) ryan@ryan-XPS-8500:~/Desktop/BIOM TABLE$ python
Colin Brislawn
Mar 20, 2018, 6:37:28 PM3/20/18
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Hello Ryan,
I'm not sure why this problem would occur if you didn't install or update software in Qiime's software environment. Do you still get a problem when you perform a clean install?
conda create -n qiime1-clean python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda
source activate qiime1-clean
If the install no longer works in a new conda environment, we can get the devs to take a look at this. While Qiime 1 is no longer being developed, it should still work.
Let me know if the clean install fixes your problem,
Colin
Ryan Davis
Mar 20, 2018, 8:09:55 PM3/20/18
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Hi Colin,
I still get the same error with a clean install:
(qiime1-clean) ryan@ryan-XPS-8500:~$ print_qiime_config.py -t
Traceback (most recent call last):
File "/home/ryan/miniconda2/envs/qiime1-clean/bin/print_qiime_config.py", line 4, in <module>
__import__('pkg_resources').run_script('qiime==1.9.1', 'print_qiime_config.py')
File "/home/ryan/miniconda2/envs/qiime1-clean/lib/python2.7/site-packages/pkg_resources/__init__.py", line 750, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/ryan/miniconda2/envs/qiime1-clean/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1527, in run_script
exec(code, namespace, namespace)
File "/home/ryan/miniconda2/envs/qiime1-clean/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/print_qiime_config.py", line 37, in <module>
from skbio.util import remove_files
File "/home/ryan/miniconda2/envs/qiime1-clean/lib/python2.7/site-packages/skbio/__init__.py", line 15, in <module>
import skbio.io
File "/home/ryan/miniconda2/envs/qiime1-clean/lib/python2.7/site-packages/skbio/io/__init__.py", line 309, in <module>
import_module('skbio.io.clustal')
File "/home/ryan/miniconda2/envs/qiime1-clean/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/home/ryan/miniconda2/envs/qiime1-clean/lib/python2.7/site-packages/skbio/io/clustal.py", line 123, in <module>
from skbio.alignment import Alignment
File "/home/ryan/miniconda2/envs/qiime1-clean/lib/python2.7/site-packages/skbio/alignment/__init__.py", line 230, in <module>
from ._alignment import Alignment, SequenceCollection, StockholmAlignment
File "/home/ryan/miniconda2/envs/qiime1-clean/lib/python2.7/site-packages/skbio/alignment/_alignment.py", line 21, in <module>
from skbio.stats.distance import DistanceMatrix
File "/home/ryan/miniconda2/envs/qiime1-clean/lib/python2.7/site-packages/skbio/stats/__init__.py", line 45, in <module>
from ._subsample import subsample, subsample_counts, isubsample
File "/home/ryan/miniconda2/envs/qiime1-clean/lib/python2.7/site-packages/skbio/stats/_subsample.py", line 22, in <module>
from .__subsample import _subsample_counts_without_replacement
File "__init__.pxd", line 155, in init skbio.stats.__subsample (skbio/stats/__subsample.c:3964)
ValueError: numpy.dtype has the wrong size, try recompiling
Let me know if you need anything else from me. I appreciate the help!
Ryan
Colin Brislawn
Mar 21, 2018, 8:11:05 PM3/21/18
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Hello Ryan,
Looks like this is an issue other folks are having with numpy. I'm not totally sure how to solve this, but updating numpy worked for some.
conda update numpy
You can see what other people have tried over here:
Let me know if you find a fix that works for you, and I can add it into the official qiime 1 documentation (hopefully).
Colin
Susan
Mar 22, 2018, 11:35:00 PM3/22/18
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Same error still exists but conda
update numpy worked for me.
Thanks.
Thanks.
Ryan Davis
Mar 26, 2018, 1:18:29 PM3/26/18
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Hi Colin,
Updating numpy with conda helped! Thanks for the fix
Ryan
Colin Brislawn
Mar 26, 2018, 3:04:15 PM3/26/18
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Ryan, that's great! I can add a note about running
conda update numpy
to that page.
Susan, did this fully solve your error or are you still getting errors after running conda update numpy?
Colin
Melanie Lloyd
May 7, 2018, 11:08:42 AM5/7/18
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I am having this same problem and tried a clean install as well as updating numpy but neither worked.
(qiime1) [mlloyd@pespenilab ~]$ print_qiime_config.py -t
Traceback (most recent call last):
File "/users/m/l/mlloyd/miniconda3/envs/qiime1/bin/print_qiime_config.py", line 4, in <module>
__import__('pkg_resources').run_script('qiime==1.9.1', 'print_qiime_config.py')
File "/users/m/l/mlloyd/miniconda3/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 658, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/users/m/l/mlloyd/miniconda3/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1438, in run_script
exec(code, namespace, namespace)
File "/data/users/m/l/mlloyd/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/print_qiime_config.py", line 37, in <module>
from skbio.util import remove_files
File "/users/m/l/mlloyd/miniconda3/envs/qiime1/lib/python2.7/site-packages/skbio/__init__.py", line 15, in <module>
import skbio.io
File "/users/m/l/mlloyd/miniconda3/envs/qiime1/lib/python2.7/site-packages/skbio/io/__init__.py", line 309, in <module>
import_module('skbio.io.clustal')
File "/users/m/l/mlloyd/miniconda3/envs/qiime1/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/users/m/l/mlloyd/miniconda3/envs/qiime1/lib/python2.7/site-packages/skbio/io/clustal.py", line 123, in <module>
from skbio.alignment import Alignment
File "/users/m/l/mlloyd/miniconda3/envs/qiime1/lib/python2.7/site-packages/skbio/alignment/__init__.py", line 230, in <module>
from ._alignment import Alignment, SequenceCollection, StockholmAlignment
File "/users/m/l/mlloyd/miniconda3/envs/qiime1/lib/python2.7/site-packages/skbio/alignment/_alignment.py", line 21, in <module>
from skbio.stats.distance import DistanceMatrix
File "/users/m/l/mlloyd/miniconda3/envs/qiime1/lib/python2.7/site-packages/skbio/stats/__init__.py", line 45, in <module>
from ._subsample import subsample, subsample_counts, isubsample
File "/users/m/l/mlloyd/miniconda3/envs/qiime1/lib/python2.7/site-packages/skbio/stats/_subsample.py", line 22, in <module>
from .__subsample import _subsample_counts_without_replacement
File "__init__.pxd", line 155, in init skbio.stats.__subsample (skbio/stats/__subsample.c:3964)
ValueError: numpy.dtype has the wrong size, try recompiling
Have any new solutions arisen to address this error?
Colin Brislawn
May 7, 2018, 11:45:54 AM5/7/18
to Qiime 1 Forum
Hello Melanie,
This looks like the same error, but so I'm not sure why neither the simple qiime 1 install or the qiime 1 + conda update numpy does not fix this problem.
Hopefully Tony has more ideas.
Colin
P.S. Of maybe it's a sign to switch to Qiime 2!
Melanie Lloyd
May 7, 2018, 11:54:06 AM5/7/18
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Thank you for your swift reply, Colin.
Yes, I think the switch to Qiime 2 is in the future but I need the old version to fix a few small things in an analysis I did a few months about in Qiime 1.
Thanks
Colin Brislawn
May 7, 2018, 11:59:57 AM5/7/18
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I totally understand.
Ok, after additional googleing, it looks like 'conda update numpy' needs to be run with 'conda update pandas' to so the software matches. Because you have already do the numpy update, just updateing pandas should work:
conda update pandas
Colin
Melanie Lloyd
May 7, 2018, 12:25:45 PM5/7/18
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Hi Colin,
Thanks for the tip but that didn't work either.
Here is the list of all the packages and their version numbers I'm running, in case this info is helpful:
(qiime1) [mlloyd@pespenilab ~]$ conda list
# packages in environment at /users/m/l/mlloyd/miniconda3/envs/qiime1:
#
# Name Version Build Channel
backports 1.0 py27h63c9359_1
backports.shutil_get_terminal_size 1.0.0 py27h5bc021e_2
biom-format 2.1.6 py27_0 bioconda
burrito 0.9.1 py27_0 bioconda
burrito-fillings 0.1.1 py27_0 bioconda
ca-certificates 2018.03.07 0
cairo 1.12.18 6
certifi 2018.4.16 py27_0
click 6.7 py27h4225b90_0
cogent 1.5.3 py27_1 bioconda
decorator 4.3.0 py27_0
emperor 0.9.51 py27_0 bioconda
enum34 1.1.6 py27h99a27e9_1
fontconfig 2.11.1 6
freetype 2.5.5 1
funcsigs 1.0.2 py27h83f16ab_0
future 0.16.0 py27_1
gdata 2.0.18 py27_0
h5py 2.7.1 py27h2697762_0
hdf5 1.10.1 h9caa474_1
icu 58.2 h9c2bf20_1
intel-openmp 2018.0.0 8
ipython 5.6.0 py27_0
ipython_genutils 0.2.0 py27h89fb69b_0
libedit 3.1 heed3624_0
libffi 3.2.1 hd88cf55_4
libgcc 7.2.0 h69d50b8_2
libgcc-ng 7.2.0 hdf63c60_3
libgfortran-ng 7.2.0 hdf63c60_3
libpng 1.6.17 0
libstdcxx-ng 7.2.0 hdf63c60_3
libxml2 2.9.8 hf84eae3_0
matplotlib 1.4.3 np19py27_2
mkl 2018.0.2 1
mock 2.0.0 py27h0c0c831_0
mpi4py 2.0.0 py27_2
mpich2 1.4.1p1 0
mysql-python 1.2.5 py27_0
natsort 3.5.0 py27_0
ncurses 6.0 h9df7e31_2
nose 1.3.7 py27heec2199_2
numpy 1.9.3 py27h7e35acb_3
openssl 1.0.2o h20670df_0
pandas 0.21.1 py27h38cdd7d_0
pathlib2 2.3.2 py27_0
pbr 4.0.2 py27_0
pexpect 4.5.0 py27_0
pickleshare 0.7.4 py27h09770e1_0
pip 10.0.1 py27_0
pixman 0.32.6 0
prompt_toolkit 1.0.15 py27h1b593e1_0
ptyprocess 0.5.2 py27h4ccb14c_0
py2cairo 1.10.0 py27_2
pygments 2.2.0 py27h4a8b6f5_0
pynast 1.2.2 py27_0 bioconda
pyparsing 2.0.3 py27_0
pyqi 0.3.2 py27_0 bioconda
pyqt 4.11.4 py27_4
python 2.7.15 h1571d57_0
python-dateutil 2.3 py27_0 bioconda
pytz 2018.4 py27_0
qcli 0.1.1 py27_0 bioconda
qiime 1.9.1 py27_0 bioconda
qiime-default-reference 0.1.3 py27_0 bioconda
qt 4.8.7 3
readline 7.0 ha6073c6_4
scandir 1.7 py27h14c3975_0
scikit-bio 0.2.3 py27_0 bioconda
scipy 1.0.1 py27hfc37229_0
setuptools 39.1.0 py27_0
simplegeneric 0.8.1 py27_2
sip 4.18 py27_0
six 1.11.0 py27h5f960f1_1
sqlalchemy 1.2.7 py27h6b74fdf_0
sqlite 3.23.1 he433501_0
tk 8.6.7 hc745277_3
traitlets 4.3.2 py27hd6ce930_0
wcwidth 0.1.7 py27h9e3e1ab_0
wheel 0.31.0 py27_0
xz 5.2.3 h5e939de_4
zlib 1.2.11 ha838bed_2
Melanie Lloyd
May 7, 2018, 1:40:05 PM5/7/18
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Another update,
I tried uninstalling qiime and reinstalling with miniconda (didn't help) as well as the alternative pip install (instructions here: http://qiime.org/install/alternative.html).
I ran sudo pip install numpy
and this was returned:
Requirement already satisfied: numpy in /usr/lib64/python2.7/site-packages (1.14.3)
ancomp 0.0.1 has requirement scikit-bio>=0.4.0, but you'll have scikit-bio 0.2.3 which is incompatible.
cyvcf2 0.4.0 has requirement cython>=0.22.1, but you'll have cython 0.19 which is incompatible.
I then tried to update scikit-bio by running:
sudo pip upgrade scikit-bio
and this returned:
Collecting scikit-bio
Downloading https://files.pythonhosted.org/packages/98/ee/08995b89efccf2bf8a0307a1eb7825dceb199e64a3db24cec832c0ca0baf/scikit-bio-0.5.2.tar.gz (8.3MB)
100% |████████████████████████████████| 8.3MB 3.8MB/s
Complete output from command python setup.py egg_info:
scikit-bio can only be used with Python 3. You are currently running Python 2.
Do you think there is an incompatibility because the most recent version of scikit-bio works with Pythin 3 but Qiime1 works with Python 2?
Thank you for all of your help
Colin Brislawn
May 7, 2018, 2:34:42 PM5/7/18
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Thank you for your time! I'm sorry I've not got a good answer.
Do you think there is an incompatibility because the most recent version of scikit-bio works with Pythin 3 but Qiime1 works with Python 2?
Yes, that's correct. Qiime 1 depends on older software, but that's why we use mini conda to consistently install the older software we need. Being able to 'conda update numpy' to exactly the version you should be our goal. Looks like we updated too far forward!
Our goal here is to install the right versions of numpy and pandas. Here are the versions I have:
numpy: mine is 1.10.4, yours is 1.9.3
pandas: mine is 0.19.0, yours is 0.21.1
So in your qiime environent, try installing the versions that work for me, and see if that also works well on your system.
conda install numpy=1.10.4 pandas=0.19.0 -c bioconda
I hope we figure this out!
Colin
Melanie Lloyd
May 8, 2018, 10:58:08 AM5/8/18
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Hi Colin,
Thank you so much for your help. Back tracking to older versions of numpy and pandas, as well as making sure matplot was the correct version seemed to work. I also needed to make sure matplot was configured to work without a display (see here: https://forum.qiime2.org/t/error-in-qiime-feature-table-summarize/308/2?u=thermokarst)
Gregory Putzel
May 9, 2018, 9:44:56 AM5/9/18
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I am getting the same error message (`numpy.dtype has the wrong size, try recompiling`).
When I try to remedy this by doing
conda install numpy=1.10.4 pandas=0.19.0 -c bioconda
I get this error:
Solving environment: failed
UnsatisfiableError: The following specifications were found to be in conflict:
- numpy=1.10.4
- pandas=0.19.0 -> numpy=1.11
This is all within a conda environment that I created using
conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda
On a Linux system. I'm not 100% sure about the distribution, but when I do `cat /proc/version` I get
Linux version 2.6.32-642.13.1.el6.x86_64 (mock...@c1bm.rdu2.centos.org) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC) ) #1 SMP Wed Jan 11 20:56:24 UTC 2017
Gregory Putzel
May 9, 2018, 10:04:06 AM5/9/18
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For those who are having the same problem, I was able to install qiime1 successfully on the same system using
conda create -n qiime1 python=2.7
source activate qiime1
pip install numpy
pip install qiime
print_qiime_config.py -t
Colin Brislawn
May 9, 2018, 1:07:58 PM5/9/18
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Hello Gregory,
I'm glad you got this working.
Can you please post the version of numpy and pandas you have installed? On my machine I have numpy=1.10.4 pandas=0.19.0 and this works OK, so I want to figure out the versions that work for you.
Thanks!
Colin
Gregory Putzel
May 10, 2018, 9:41:11 AM5/10/18
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I have it working in an environment with numpy=1.14.2 and pandas=0.19.0.
I should mention that it does give the following warning when it starts up:
FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
from ._conv import register_converters as _register_converters
It seems like this is closely related to the error that started this discussion thread, but at least it's just a warning - if anyone is aware of a reason to take this warning seriously, please let me know!
Thanks
Greg
Colin Brislawn
May 10, 2018, 10:31:00 AM5/10/18
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Hello Greg,
I'm glad those versions of numpy and pandas work well on your computer.
The FutureWarning is a friendly warning to let the developers know that software will change in the future. Because only Qiime 2 is being updated in the future, we can ignore these warnings.
Colin
Irene Villa
Jul 30, 2018, 1:22:16 PM7/30/18
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Dear users,
I´m trying to install qiime1 with anaconda but i get the following messages:
print_qiime_config.py -t
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/sparse/lil.py:19: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from . import _csparsetools
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:165: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from ._shortest_path import shortest_path, floyd_warshall, dijkstra,\
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/sparse/csgraph/_validation.py:5: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from ._tools import csgraph_to_dense, csgraph_from_dense,\
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:167: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from ._traversal import breadth_first_order, depth_first_order, \
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:169: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from ._min_spanning_tree import minimum_spanning_tree
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:170: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from ._reordering import reverse_cuthill_mckee, maximum_bipartite_matching, \
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/spatial/__init__.py:95: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from .ckdtree import *
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/spatial/__init__.py:96: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from .qhull import *
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/spatial/_spherical_voronoi.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from . import _voronoi
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/spatial/distance.py:122: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from . import _hausdorff
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/linalg/basic.py:17: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from ._solve_toeplitz import levinson
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/linalg/__init__.py:207: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from ._decomp_update import *
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/special/__init__.py:640: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from ._ufuncs import *
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/special/_ellip_harm.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/interpolate/_bsplines.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from . import _bspl
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/optimize/_trlib/__init__.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from ._trlib import TRLIBQuadraticSubproblem
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/optimize/_numdiff.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from ._group_columns import group_dense, group_sparse
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/scipy/stats/_continuous_distns.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from . import _stats
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/_libs/__init__.py:4: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/__init__.py:26: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from pandas._libs import (hashtable as _hashtable,
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/core/dtypes/common.py:6: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from pandas._libs import algos, lib
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/core/util/hashing.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from pandas._libs import hashing, tslib
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/core/indexes/base.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from pandas._libs import (lib, index as libindex, tslib as libts,
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/tseries/offsets.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
import pandas._libs.tslibs.offsets as liboffsets
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/core/ops.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from pandas._libs import algos as libalgos, ops as libops
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/core/indexes/interval.py:32: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from pandas._libs.interval import (
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/core/internals.py:14: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from pandas._libs import internals as libinternals
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/core/sparse/array.py:33: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
import pandas._libs.sparse as splib
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/core/window.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
import pandas._libs.window as _window
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/core/groupby/groupby.py:68: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from pandas._libs import (lib, reduction,
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/core/reshape/reshape.py:30: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from pandas._libs import algos as _algos, reshape as _reshape
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/io/parsers.py:45: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
import pandas._libs.parsers as parsers
/home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/pandas/io/pytables.py:50: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
from pandas._libs import algos, lib, writers as libwriters
System information
==================
Platform: linux2
Python version: 2.7.15 |Anaconda, Inc.| (default, May 1 2018, 23:32:55) [GCC 7.2.0]
Python executable: /home/rjb/ivilla/anaconda2/envs/qiime1-clean/bin/python
QIIME default reference information
===================================
For details on what files are used as QIIME's default references, see here:
Dependency versions
===================
QIIME library version: 1.9.1
QIIME script version: 1.9.1
qiime-default-reference version: 0.1.3
NumPy version: 1.15.0
SciPy version: 1.1.0
pandas version: 0.23.3
matplotlib version: 2.2.2
biom-format version: 2.1.6
h5py version: Not installed.
qcli version: 0.1.1
pyqi version: 0.3.2
scikit-bio version: 0.2.3
PyNAST version: 1.2.2
Emperor version: 0.9.61
burrito version: 0.9.1
burrito-fillings version: 0.1.1
sortmerna version: SortMeRNA version 2.0, 29/11/2014
sumaclust version: SUMACLUST Version 1.0.00
swarm version: Swarm 1.2.19 [Jul 28 2018 23:09:37]
gdata: Installed.
QIIME config values
===================
For definitions of these settings and to learn how to configure QIIME, see here:
blastmat_dir: None
pick_otus_reference_seqs_fp: /home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
sc_queue: all.q
topiaryexplorer_project_dir: None
pynast_template_alignment_fp: /home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
cluster_jobs_fp: start_parallel_jobs.py
pynast_template_alignment_blastdb: None
assign_taxonomy_reference_seqs_fp: /home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue: friendlyq
jobs_to_start: 1
slurm_time: None
denoiser_min_per_core: 50
assign_taxonomy_id_to_taxonomy_fp: /home/rjb/ivilla/anaconda2/envs/qiime1-clean/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir: /tmp/
slurm_memory: None
slurm_queue: None
blastall_fp: blastall
seconds_to_sleep: 1
QIIME base install test results
===============================
.........
----------------------------------------------------------------------
Ran 9 tests in 0.040s
OK
According to the early messages , it seem to have a problem with numpy (" RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88"), but I update the version that you recommend above and it does not work.
At the end, the test seem to be right, but I don't understand the messages at the beginning. Does anybody knows how to resolve?
Thanks for your help,
Irene
Colin Brislawn
Jul 30, 2018, 4:23:01 PM7/30/18
to Qiime 1 Forum
Hello Irene,
As far as I can see, these are all warnings which means that the your Qiime configuration might work fine. Have you had a chance to try one of the tutorials and see if the analysis and graphing scripts work out OK?
While Errors are problems that must be solved, Warnings are just friendly reminders to the developers about possible issues and things to improve. As you only have warning, I think you could be totally fine!
Colin
Irene Villa
Aug 30, 2018, 7:03:01 AM8/30/18
to Qiime 1 Forum
Hello Colin,
You're right, it does seem to work fine. However I'm going to try the tutorial!
Thank you so much for your advice.
Irene
You're right, it does seem to work fine. However I'm going to try the tutorial!
Thank you so much for your advice.
Irene
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