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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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[BUG] datrie installation in anvio-dev with python 3.10 #2126

Closed semiller10 closed 11 months ago

semiller10 commented 11 months ago

Short description of the problem

In anvio-dev installation, pip failed to build the datrie package, a dependency of snakemake.

anvi'o version

Anvi'o .......................................: hope (v7.1-dev)
Python .......................................: 3.10.12

Profile database .............................: 38
Contigs database .............................: 21
Pan database .................................: 16
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 4
tRNA-seq database ............................: 2

System info

macOS: 13.5.2 (22G91)

Detailed description of the issue

anvio-dev installation with python 3.10 failed at the command pip install -r requirements.txt with failure to build datrie. I think that I fixed the problem by installing the package using mamba rather than pip: mamba install datrie. Therefore, I suggest that datrie be installed by mamba earlier in the installation instructions.

For the record, here was the full error message following the instructions.

Collecting numpy<=1.24 (from -r requirements.txt (line 1))
  Using cached numpy-1.24.0-cp310-cp310-macosx_10_9_x86_64.whl (19.8 MB)
Collecting scipy (from -r requirements.txt (line 2))
  Obtaining dependency information for scipy from https://files.pythonhosted.org/packages/65/da/4d0dfd29379c8ee3ba54b19249f673cc98448e0fd86170339fb02031f0e9/scipy-1.11.2-cp310-cp310-macosx_10_9_x86_64.whl.metadata
  Using cached scipy-1.11.2-cp310-cp310-macosx_10_9_x86_64.whl.metadata (54 kB)
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Collecting pysam (from -r requirements.txt (line 4))
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Collecting ete3 (from -r requirements.txt (line 5))
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Collecting django (from -r requirements.txt (line 7))
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  Using cached Django-4.2.5-py3-none-any.whl.metadata (4.1 kB)
Requirement already satisfied: requests in /usr/local/Caskroom/miniconda/base/envs/anvio-dev/lib/python3.10/site-packages (from -r requirements.txt (line 8)) (2.31.0)
Collecting mistune (from -r requirements.txt (line 9))
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Collecting pandas==1.4.4 (from -r requirements.txt (line 21))
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Collecting snakemake (from -r requirements.txt (line 22))
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Collecting joblib>=1.1.1 (from scikit-learn==1.2.2->-r requirements.txt (line 6))
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Collecting pytz>=2020.1 (from pandas==1.4.4->-r requirements.txt (line 21))
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Collecting asgiref<4,>=3.6.0 (from django->-r requirements.txt (line 7))
  Obtaining dependency information for asgiref<4,>=3.6.0 from https://files.pythonhosted.org/packages/9b/80/b9051a4a07ad231558fcd8ffc89232711b4e618c15cb7a392a17384bbeef/asgiref-3.7.2-py3-none-any.whl.metadata
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Collecting sqlparse>=0.3.1 (from django->-r requirements.txt (line 7))
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Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/Caskroom/miniconda/base/envs/anvio-dev/lib/python3.10/site-packages (from requests->-r requirements.txt (line 8)) (3.2.0)
Requirement already satisfied: idna<4,>=2.5 in /usr/local/Caskroom/miniconda/base/envs/anvio-dev/lib/python3.10/site-packages (from requests->-r requirements.txt (line 8)) (3.4)
Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/local/Caskroom/miniconda/base/envs/anvio-dev/lib/python3.10/site-packages (from requests->-r requirements.txt (line 8)) (2.0.5)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/Caskroom/miniconda/base/envs/anvio-dev/lib/python3.10/site-packages (from requests->-r requirements.txt (line 8)) (2023.7.22)
Collecting contourpy>=1.0.1 (from matplotlib->-r requirements.txt (line 11))
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Collecting kiwisolver>=1.0.1 (from matplotlib->-r requirements.txt (line 11))
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Requirement already satisfied: packaging>=20.0 in /usr/local/Caskroom/miniconda/base/envs/anvio-dev/lib/python3.10/site-packages (from matplotlib->-r requirements.txt (line 11)) (23.1)
Collecting pillow>=6.2.0 (from matplotlib->-r requirements.txt (line 11))
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Collecting pyparsing>=2.3.1 (from matplotlib->-r requirements.txt (line 11))
  Obtaining dependency information for pyparsing>=2.3.1 from https://files.pythonhosted.org/packages/39/92/8486ede85fcc088f1b3dba4ce92dd29d126fd96b0008ea213167940a2475/pyparsing-3.1.1-py3-none-any.whl.metadata
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Collecting patsy>=0.5.2 (from statsmodels->-r requirements.txt (line 12))
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Collecting python-Levenshtein (from illumina-utils->-r requirements.txt (line 14))
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Collecting rich>=11.0.0 (from rich-argparse->-r requirements.txt (line 16))
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Requirement already satisfied: setuptools in /usr/local/Caskroom/miniconda/base/envs/anvio-dev/lib/python3.10/site-packages (from paste->-r requirements.txt (line 18)) (68.2.2)
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Collecting connection-pool>=0.0.3 (from snakemake->-r requirements.txt (line 22))
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  Installing build dependencies ... done
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Building wheels for collected packages: datrie
  Building wheel for datrie (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Building wheel for datrie (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [14 lines of output]
      running bdist_wheel
      running build
      running build_clib
      building 'datrie' library
      creating build
      creating build/temp.macosx-10.9-x86_64-cpython-310
      creating build/temp.macosx-10.9-x86_64-cpython-310/libdatrie
      creating build/temp.macosx-10.9-x86_64-cpython-310/libdatrie/datrie
      clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /usr/local/Caskroom/miniconda/base/envs/anvio-dev/include -fPIC -O2 -isystem /usr/local/Caskroom/miniconda/base/envs/anvio-dev/include -Ilibdatrie -c libdatrie/datrie/alpha-map.c -o build/temp.macosx-10.9-x86_64-cpython-310/libdatrie/datrie/alpha-map.o
      libdatrie/datrie/alpha-map.c:27:10: fatal error: 'ctype.h' file not found
      #include <ctype.h>
               ^~~~~~~~~
      1 error generated.
      error: command '/usr/local/Caskroom/miniconda/base/envs/anvio-dev/bin/clang' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for datrie
Failed to build datrie
ERROR: Could not build wheels for datrie, which is required to install pyproject.toml-based projects
ivagljiva commented 11 months ago

@semiller10 , Meren already fixed this problem. Please see the following section from the installation page:

image

We are in the process of updating our installation page to be split into different pages by OS so that the solutions to errors like these are more obvious :)

semiller10 commented 11 months ago

Perfect, should have caught that.

ChunqiJIANG commented 11 months ago

Same error in anvio-8 installation on Mac OSX (pip install anvio-8.tar.gz), can be fixed in the same way, Thanks.

meren commented 11 months ago

Thanks for letting us know, @ChunqiJIANG.

I will make those export statements a mandatory step for macos installation page to avoid further confusion.

ChunqiJIANG commented 11 months ago

Hi, meren

One more thing may need fixation on the installation page (not only Mac OSX I think): 

 command 'anvi-setup-kegg-kofams’ at Setup key resource can not be found in anvio v8, seems should be 'anvi-setup-kegg-data’.

Hope to be helpful.

On Sep 29, 2023, at 16:41, A. Murat Eren (Meren) @.***> wrote:

Thanks for letting us know, @ChunqiJIANG https://github.com/ChunqiJIANG.

I will make those export statements a mandatory step for macos installation page to avoid further confusion.

— Reply to this email directly,, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUJGNQFTA7K4BNN33N3FXVLX4Z3TRANCNFSM6AAAAAA5G2VLNM.

https://github.com/merenlab/anvio/issues/2126#issuecomment-1740452638 You are receiving this because you were mentioned.

ivagljiva commented 11 months ago

command 'anvi-setup-kegg-kofams’ at Setup key resource can not be found in anvio v8, seems should be 'anvi-setup-kegg-data’.

I just fixed this one. Thanks @ChunqiJIANG

ac-simpson commented 9 months ago

FYI, I just got the same "ERROR: Failed building wheel for datrie" on our server running a very fresh installation of Ubuntu 22.04, and had to do a separate "mamba install datrie" before installing anvio. Not sure how common this is, but it may be worth including in 'common problems'.

meren commented 9 months ago

Is this for v8 or anvio-dev, @ac-simpson? And how did you solve the issue? By updating the environment variables for CC/CCX?

nelsonruth11 commented 8 months ago

On an HPC, adding the export CC and export CXX commands before pip install anvio-8.tar.gz did not fix the issue, but as @ac-simpson suggested running mamba install datrie before pip installation did.

jronwalker commented 4 months ago

I had the same issue on Fedora 40 using micromamba. The micromamba install datrie fixed the issue.