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Install from bioconda installs 2.2.10 and yields numpy error #519

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ahrimj21 opened this issue Feb 7, 2025 · 10 comments
Open

Install from bioconda installs 2.2.10 and yields numpy error #519

ahrimj21 opened this issue Feb 7, 2025 · 10 comments

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@ahrimj21
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ahrimj21 commented Feb 7, 2025 •
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I have raised this issue before but it still persists. I have uninstalled anaconda3 and reinstalled, then tried to build a crispresso environment by running :
CONDA_SUBDIR=osx-64 conda create -n AlleleCallerEnv -c bioconda crispresso2

This sucessfully installs CRISPResso2 but the version is 2.2.10 not the latest 2.3.2. When I run the follow command :

CRISPResso --fastq_r1 /Users/ahrim/Desktop/Ahrim_SummerWork/2025-01-31/fastqs/Red/DH20240828RedV4A01_L001-ds.6527e917ae654cf28b5036ac6bd781fe/DH20240828RedV4A01_S289_L001_R1_001.fastq.gz --fastq_r2 /Users/ahrim/Desktop/Ahrim_SummerWork/2025-01-31/fastqs/Red/DH20240828RedV4A01_L001-ds.6527e917ae654cf28b5036ac6bd781fe/DH20240828RedV4A01_S289_L001_R2_001.fastq.gz --amplicon_seq gactcagaaacacagcctgatgaggaggaagaagaagaagaagaaaaagtttctcaaccagaggtgggagctgccattaagatcattcggcagttaatggagaagtttaacttggatctatcaacagttacacaggccttcctaaaaaatagtggtgagctggaggctacttccgccttcttagcgtctggtcagagagctgatggatatcccatttggtcccgacaaga -g GAGCTGCCATTAAGATCATT

the software runs through generation of 1c.Alignment_barplot.png and then errors out with:

ERROR: module 'numpy' has no attribute 'float'. np.floatwas a deprecated alias for the builtinfloat. To avoid this error in existing code, use floatby itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, usenp.float64 here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

Current numpy version should be compatible with Crispresso2:
# Name Version Build Channel numpy 1.24.4 py38h9a4a08f_0 conda-forge

When i try conda uninstall numpy this prompts me to remove crispresso2 as well.

When I try to install an older version of Crispresso2 directly (ie 2.2.7) it gives me a 'seaborn-base' error even though seaborn is installed.

Here is my full conda env:
`(AlleleCallerEnv) ahrim@wifi-10-41-219-145 ~ % conda list

packages in environment at /Users/ahrim/anaconda3/envs/AlleleCallerEnv:

Name Version Build Channel

bowtie2 2.5.4 he4764aa_5 bioconda
brotli 1.1.0 h00291cd_2 conda-forge
brotli-bin 1.1.0 h00291cd_2 conda-forge
bzip2 1.0.8 hfdf4475_7 conda-forge
c-ares 1.34.4 hf13058a_0 conda-forge
ca-certificates 2025.1.31 h8857fd0_0 conda-forge
certifi 2022.6.15 py38h50d1736_0 conda-forge
cffi 1.17.0 py38hc8bcfa4_0 conda-forge
chardet 3.0.4 py38h5347e94_1008 conda-forge
contourpy 1.1.1 py38h15a1a5b_1 conda-forge
crispresso2 2.2.10 py38habe91e9_0 bioconda
cryptography 43.0.0 py38h09e535d_0 conda-forge
cycler 0.10.0 py38_0
flash 1.2.11 0 bioconda
fonttools 4.51.0 py38h6c40b1e_0
freetype 2.12.1 h60636b9_2 conda-forge
htslib 1.21 h9f635df_1 bioconda
idna 2.9 py38_0 conda-forge
jinja2 3.1.4 py38hecd8cb5_0
kiwisolver 1.4.5 py38h15a1a5b_1 conda-forge
krb5 1.21.3 h37d8d59_0 conda-forge
lcms2 2.16 ha2f27b4_0 conda-forge
lerc 4.0.0 hb486fe8_0 conda-forge
libblas 3.9.0 20_osx64_openblas conda-forge
libbrotlicommon 1.1.0 h00291cd_2 conda-forge
libbrotlidec 1.1.0 h00291cd_2 conda-forge
libbrotlienc 1.1.0 h00291cd_2 conda-forge
libcblas 3.9.0 20_osx64_openblas conda-forge
libcurl 8.11.1 h5dec5d8_0 conda-forge
libcxx 19.1.7 hf95d169_0 conda-forge
libdeflate 1.23 he65b83e_0 conda-forge
libedit 3.1.20250104 pl5321ha958ccf_0 conda-forge
libev 4.33 h10d778d_2 conda-forge
libffi 3.4.2 h0d85af4_5 conda-forge
libgfortran 5.0.0 13_2_0_h97931a8_3 conda-forge
libgfortran5 13.2.0 h2873a65_3 conda-forge
libjpeg-turbo 3.0.0 h0dc2134_1 conda-forge
liblapack 3.9.0 20_osx64_openblas conda-forge
liblzma 5.6.4 hd471939_0 conda-forge
liblzma-devel 5.6.4 hd471939_0 conda-forge
libnghttp2 1.64.0 hc7306c3_0 conda-forge
libopenblas 0.3.25 openmp_hfef2a42_0 conda-forge
libpng 1.6.46 h3c4a55f_0 conda-forge
libsqlite 3.48.0 hdb6dae5_1 conda-forge
libssh2 1.11.1 h3dc7d44_0 conda-forge
libtiff 4.7.0 hb77a491_3 conda-forge
libwebp-base 1.5.0 h6cf52b4_0 conda-forge
libxcb 1.17.0 hf1f96e2_0 conda-forge
libzlib 1.3.1 hd23fc13_2 conda-forge
llvm-openmp 19.1.7 ha54dae1_0 conda-forge
markupsafe 2.1.5 py38hae2e43d_0 conda-forge
matplotlib-base 3.6.3 py38hcb346ec_0 conda-forge
ncurses 6.5 h0622a9a_3 conda-forge
numpy 1.24.4 py38h9a4a08f_0 conda-forge
openjdk 23.0.2 h18c9476_0 conda-forge
openjpeg 2.5.3 h7fd6d84_0 conda-forge
openssl 3.4.0 hc426f3f_1 conda-forge
packaging 24.1 py38hecd8cb5_0
pandas 1.5.3 py38hec72209_1 conda-forge
perl 5.32.1 7_h10d778d_perl5 conda-forge
pillow 10.4.0 py38hf802781_0 conda-forge
pip 20.0.2 py38_1 conda-forge
platformdirs 3.10.0 py38hecd8cb5_0
plotly 5.24.1 py38h20db666_0
pooch 1.7.0 py38hecd8cb5_0
pthread-stubs 0.4 h00291cd_1002 conda-forge
pycparser 2.19 py38_1 conda-forge
pyopenssl 24.2.1 py38hecd8cb5_0
pyparsing 3.1.2 py38hecd8cb5_0
pysocks 1.7.1 py38h50d1736_5 conda-forge
python 3.8.20 h4f978b9_2_cpython conda-forge
python-dateutil 2.9.0post0 py38hecd8cb5_2
python_abi 3.8 5_cp38 conda-forge
pytz 2024.1 py38hecd8cb5_0
readline 8.2 h9e318b2_1 conda-forge
requests 2.23.0 py38h32f6830_1 conda-forge
samtools 1.21 ha21ef43_1 bioconda
scipy 1.10.1 py38h9cf86d3_3 conda-forge
seaborn 0.13.2 py38hecd8cb5_0
setuptools 65.3.0 py38h50d1736_0 conda-forge
six 1.14.0 py38_0 conda-forge
tenacity 6.2.0 py38h32f6830_0 conda-forge
tk 8.6.13 h1abcd95_1 conda-forge
trimmomatic 0.36 5 bioconda
unicodedata2 15.1.0 py38hcafd530_0 conda-forge
urllib3 1.25.8 py38h32f6830_1 conda-forge
wheel 0.34.2 py38_0 conda-forge
xorg-libxau 1.0.12 h6e16a3a_0 conda-forge
xorg-libxdmcp 1.1.5 h00291cd_0 conda-forge
xz 5.6.4 h357f2ed_0 conda-forge
xz-gpl-tools 5.6.4 h357f2ed_0 conda-forge
xz-tools 5.6.4 hd471939_0 conda-forge
zstd 1.5.6 h915ae27_0 conda-forge`
@ahrimj21
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ahrimj21 commented Feb 7, 2025

@shayanhoss

@Colelyman
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Hi @ahrimj21,

Sorry to hear that you are running into these issues! They are very frustrating. Have you tried running conda install crispresso2=2.3.2? Alternatively, if you can't get the newest version of CRISPResso to install, you can install an older version of numpy (like 1.19.5).

Also, it looks like you are on an Apple Silicon Mac. If that is true, bioconda has recently supported native packages for CRISPResso, so you no longer have to add the CONDA_SUBDIR=osx-64. So, it may also be worth trying conda create -n AlleleCallerEnv-2.3.2 -c bioconda crispresso2=2.3.2.

I hope this helps! And please let us know if this works.

Thanks,
Cole

@ahrimj21
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ahrimj21 commented Feb 10, 2025 •
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I have tried all the solutions you suggested and am still running into issues. I first tried to run the following command line:

conda install crispresso2=2.3.2 and this is the error I face:

(base) ahrim@Ahrims-MacBook-Pro Ahrim_SummerWork % conda install crispresso2=2.3.2
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

InvalidSpec: The package "pkgs/main/osx-arm64::_anaconda_depends==2024.10=py312_openblas_0" is not available for the specified platform

I then tried to downgrade to numpy version 1.19.5 by creating a conda environment with python version 3.6 (as this python version was compatible was numpy ver 1.19.5). I then ran into this error:

(crispresso2_env) ahrim@Ahrims-MacBook-Pro Ahrim_SummerWork % pip install -U numpy==1.19.5
Collecting numpy==1.19.5
 Downloading numpy-1.19.5-cp36-cp36m-macosx_10_9_x86_64.whl (15.6 MB)
    |████████████████████████████████| 15.6 MB 3.1 MB/s
Installing collected packages: numpy
Successfully installed numpy-1.19.5
(crispresso2_env) ahrim@Ahrims-MacBook-Pro Ahrim_SummerWork % CONDA_SUBDIR=osx-64 conda install crispresso2=2.3.2
Channels:
- conda-forge
- bioconda
- defaults
Platform: osx-64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
 - nothing provides seaborn-base needed by crispresso2-2.3.2-py310h6e131d9_0

Could not solve for environment specs
The following package could not be installed
└─ crispresso2 2.3.2**  is not installable because it requires
  └─ seaborn-base, which does not exist (perhaps a missing channel).

(crispresso2_env) ahrim@Ahrims-MacBook-Pro Ahrim_SummerWork % numpy --version
zsh: command not found: numpy
(crispresso2_env) ahrim@Ahrims-MacBook-Pro Ahrim_SummerWork % pip show numpy
Name: numpy
Version: 1.19.5
Summary: NumPy is the fundamental package for array computing with Python.
Home-page: https://www.numpy.org
Author: Travis E. Oliphant et al.
Author-email: None
License: BSD
Location: /Users/ahrim/anaconda3/envs/crispresso2_env/lib/python3.6/site-packages
Requires:

I finally tried to run conda create -n AlleleCallerEnv-2.3.2 -c bioconda crispresso2=2.3.2 and ran into this error (even though seaborn is installed):

(base) ahrim@Ahrims-MacBook-Pro Ahrim_SummerWork % conda create -n crispresso2_env-2.3.2 -c bioconda crispresso2=2.3.2
Retrieving notices: ...working... done
Channels:
 - bioconda
 - conda-forge
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides seaborn-base needed by crispresso2-2.3.2-py310h6e131d9_0

Could not solve for environment specs
The following package could not be installed
└─ crispresso2 2.3.2**  is not installable because it requires
   └─ seaborn-base, which does not exist (perhaps a missing channel).

@Colelyman
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Hi @ahrimj21,

So sorry you are still having trouble with this, but I think you are close! Could you try the last command again, but add the conda-forge channel? Like this: conda create -n AlleleCallerEnv-2.3.2 -c bioconda -c conda-forge crispresso2=2.3.2.

Alternatively, I forgot to mention in the previous comment, if this doesn't work it might be worth trying to use Docker (see here for instructions).

@ahrimj21
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I still seem to be running into issues. This is the error I get (still linked to seaborn):

(base) ahrim@Ahrims-MacBook-Pro Ahrim_SummerWork % conda create -n crispresso2_new-2.3.2 -c bioconda -c conda-forge crispresso2=2.3.2
Channels:
 - bioconda
 - conda-forge
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides seaborn-base needed by crispresso2-2.3.2-py310h6e131d9_0

Could not solve for environment specs
The following package could not be installed
└─ crispresso2 2.3.2**  is not installable because it requires
   └─ seaborn-base, which does not exist (perhaps a missing channel).

@Colelyman
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Interesting, I'm not sure why this is happening. Maybe try explicitly adding seaborn-base? Like conda create -n crispresso2_new-2.3.2 -c bioconda -c conda-forge crispresso2=2.3.2 seaborn-base. You could also try install seaborn by adding the -c anacoda channel.

@ahrimj21
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When I try to install seaborn. This is the issue I run into:

(base) ahrim@Ahrims-MacBook-Pro Ahrim_SummerWork % conda install -c anaconda seaborn

Channels:
 - anaconda
 - conda-forge
 - bioconda
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

InvalidSpec: The package "pkgs/main/osx-arm64::_anaconda_depends==2024.10=py312_openblas_0" is not available for the specified platform

@Colelyman
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Ah, I see. Looks like seaborn doesn't support the Apple Silicon architecture yet. If you try this, does it fix it? CONDA_SUBDIR=osx-64 conda create -n crispresso2_new-2.3.2 -c bioconda -c conda-forge crispresso2=2.3.2

@ahrimj21
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Just tried it! It seems like it is still giving me the same error..

(base) ahrim@Ahrims-MacBook-Pro Ahrim_SummerWork % CONDA_SUBDIR=osx-64 conda create -n crispresso2_new-2.3.2 -c bioconda -c conda-forge crispresso2=2.3.2
Channels:
 - bioconda
 - conda-forge
 - defaults
Platform: osx-64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides seaborn-base needed by crispresso2-2.3.2-py310h6e131d9_0

Could not solve for environment specs
The following package could not be installed
└─ crispresso2 2.3.2**  is not installable because it requires
   └─ seaborn-base, which does not exist (perhaps a missing channel).

@Colelyman
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Hi @ahrimj21,

I'm sorry that isn't working, I'm not sure what else to suggest other than trying Docker!

Thanks,
Cole

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