python 2.7 issue
Opened this issue · 4 comments
Hi,
Thanks for making the package available. I try to use the addOnTargetScore function, but ran into the complain about python 2.7 is not available in current conda channel. Could you please suggest a way to work around it?
Thanks
Xiaoyun
Hi @xguo-nveloptx, which scoring methods are you using (please provide your exact code)? Could you provide your sessionInfo() output as well?
@xguo-nveloptx We have fixed a few bugs today; could you try 1.7.2 of the devel branch to see if you have the same problems?
@xguo-nveloptx Any updates?
Hi, first of all , thank you for making such a detailed tutorial!
I had a similar problem, where azimuth, lindel and other scoring methods that depend on python 2.7 did not work in my local computer. I saw another comment you posted on a previous issue-post refering to how these scoring algorithms cannot be run on a M1 machine and was wondering if that is the issue as my computer is a Apple M1 Max. Is there no work-around?
This is the conda channel on my local computer for your reference :
(base) 01-5651:$ conda install python=2.7
(base) 01-5651:$ conda config --add subdirs osx-64
(base) 01-5651:$ conda search python
Loading channels: done
Name Version Build Channel
python 2.7.13 h32f5f24_13 pkgs/main
python 2.7.13 h89fad4f_16 pkgs/main
python 2.7.13 hdada7c8_15 pkgs/main
python 2.7.14 h001abdc_23 pkgs/main
python 2.7.14 h138c1fe_30 pkgs/main
python 2.7.14 h138c1fe_31 pkgs/main
python 2.7.14 h50fefbe_18 pkgs/main
python 2.7.14 ha6acbcf_22 pkgs/main
python 2.7.14 ha7e29e4_26 pkgs/main
python 2.7.14 hd74e306_15 pkgs/main
python 2.7.14 hde5916a_29 pkgs/main
python 2.7.14 he768d2d_19 pkgs/main
python 2.7.14 hed931fe_16 pkgs/main
python 2.7.15 h138c1fe_0 pkgs/main
python 2.7.15 h8f8e585_2 pkgs/main
python 2.7.15 h8f8e585_4 pkgs/main
python 2.7.15 h8f8e585_6 pkgs/main
python 2.7.16 h97142e2_0 pkgs/main
python 2.7.16 h97142e2_1 pkgs/main
python 2.7.16 h97142e2_2 pkgs/main
python 2.7.16 h97142e2_3 pkgs/main
python 2.7.16 h97142e2_4 pkgs/main
python 2.7.16 h97142e2_5 pkgs/main
python 2.7.16 h97142e2_6 pkgs/main
python 2.7.16 h97142e2_7 pkgs/main
python 2.7.17 h97142e2_0 pkgs/main
python 2.7.18 h441ce09_3 pkgs/main
python 2.7.18 h47d645e_1 pkgs/main
python 2.7.18 hc817775_0 pkgs/main
python 3.5.4 h4bd9b1b_18 pkgs/main
python 3.5.4 h821eb87_14 pkgs/main
python 3.5.4 h8f450c2_22 pkgs/main
python 3.5.4 hb8880cc_19 pkgs/main
python 3.5.4 hc167b69_27 pkgs/main
python 3.5.4 hdd9bdb2_21 pkgs/main
python 3.5.4 he1de2d4_12 pkgs/main
python 3.5.4 he720263_23 pkgs/main
python 3.5.4 hf91e954_15 pkgs/main
python 3.5.5 h0a44026_3 pkgs/main
python 3.5.5 hc167b69_0 pkgs/main
python 3.5.5 hc167b69_1 pkgs/main
python 3.5.6 hc167b69_0 pkgs/main
python 3.6.2 h26d10c0_12 pkgs/main
python 3.6.2 h9e63aee_14 pkgs/main
python 3.6.2 ha11d96e_18 pkgs/main
python 3.6.2 hd04bb42_19 pkgs/main
python 3.6.2 hd0bf7f1_15 pkgs/main
python 3.6.3 h47c878a_7 pkgs/main
python 3.6.3 h5ce8c04_4 pkgs/main
python 3.6.3 h6804ab2_0 pkgs/main
python 3.6.3 h794556d_2 pkgs/main
python 3.6.3 hc655967_3 pkgs/main
python 3.6.4 hc167b69_0 pkgs/main
python 3.6.4 hc167b69_1 pkgs/main
python 3.6.4 hc167b69_3 pkgs/main
python 3.6.5 hc167b69_0 pkgs/main
python 3.6.5 hc167b69_1 pkgs/main
python 3.6.6 hc167b69_0 pkgs/main
python 3.6.7 haf84260_0 pkgs/main
python 3.6.8 haf84260_0 pkgs/main
python 3.6.9 h359304d_0 pkgs/main
python 3.6.10 h359304d_0 pkgs/main
python 3.6.10 hc70fcce_1 pkgs/main
python 3.6.10 hf48f09d_2 pkgs/main
python 3.6.10 hfe9666f_1 pkgs/main
python 3.6.12 h26836e1_2 pkgs/main
python 3.6.13 h88f2d9e_0 pkgs/main
python 3.7.0 hc167b69_0 pkgs/main
python 3.7.1 haf84260_3 pkgs/main
python 3.7.1 haf84260_7 pkgs/main
python 3.7.2 haf84260_0 pkgs/main
python 3.7.3 h359304d_0 pkgs/main
python 3.7.4 h359304d_0 pkgs/main
python 3.7.4 h359304d_1 pkgs/main
python 3.7.5 h359304d_0 pkgs/main
python 3.7.6 h359304d_2 pkgs/main
python 3.7.7 hc70fcce_0_cpython pkgs/main
python 3.7.7 hf48f09d_4 pkgs/main
python 3.7.7 hfe9666f_0_cpython pkgs/main
python 3.7.9 h26836e1_0 pkgs/main
python 3.7.10 h88f2d9e_0 pkgs/main
python 3.7.11 h88f2d9e_0 pkgs/main
python 3.7.13 hdfd78df_0 pkgs/main
python 3.7.13 hdfd78df_1 pkgs/main
python 3.7.15 h218abb5_1 pkgs/main
python 3.7.15 h4319210_0 pkgs/main
python 3.7.16 h218abb5_0 pkgs/main
python 3.8.0 h359304d_0 pkgs/main
python 3.8.0 h359304d_1 pkgs/main
python 3.8.0 h359304d_2 pkgs/main
python 3.8.1 h359304d_1 pkgs/main
python 3.8.2 hc70fcce_0 pkgs/main
python 3.8.2 hf48f09d_13 pkgs/main
python 3.8.2 hfe9666f_0 pkgs/main
python 3.8.3 h26836e1_1 pkgs/main
python 3.8.3 h26836e1_2 pkgs/main
python 3.8.5 h26836e1_0 pkgs/main
python 3.8.5 h26836e1_1 pkgs/main
python 3.8.8 h88f2d9e_4 pkgs/main
python 3.8.8 h88f2d9e_5 pkgs/main
python 3.8.10 h88f2d9e_7 pkgs/main
python 3.8.11 h88f2d9e_1 pkgs/main
python 3.8.12 h88f2d9e_0 pkgs/main
python 3.8.13 hdfd78df_0 pkgs/main
python 3.8.13 hdfd78df_1 pkgs/main
python 3.8.15 h218abb5_2 pkgs/main
python 3.8.15 h4319210_0 pkgs/main
python 3.8.16 h218abb5_2 pkgs/main
python 3.8.16 h218abb5_3 pkgs/main
python 3.8.16 h5ee71fb_4 pkgs/main
python 3.8.17 h218abb5_0 pkgs/main
python 3.8.17 h5ee71fb_0 pkgs/main
python 3.8.18 h218abb5_0 pkgs/main
python 3.8.18 h5ee71fb_0 pkgs/main
python 3.9.0 h88f2d9e_1 pkgs/main
python 3.9.0 h88f2d9e_2 pkgs/main
python 3.9.1 h88f2d9e_2 pkgs/main
python 3.9.2 h88f2d9e_0 pkgs/main
python 3.9.4 h88f2d9e_0 pkgs/main
python 3.9.5 h88f2d9e_3 pkgs/main
python 3.9.6 h88f2d9e_0 pkgs/main
python 3.9.6 h88f2d9e_1 pkgs/main
python 3.9.7 h88f2d9e_1 pkgs/main
python 3.9.11 hdfd78df_1 pkgs/main
python 3.9.11 hdfd78df_2 pkgs/main
python 3.9.12 hdfd78df_0 pkgs/main
python 3.9.12 hdfd78df_1 pkgs/main
python 3.9.13 hdfd78df_1 pkgs/main
python 3.9.13 hdfd78df_2 pkgs/main
python 3.9.15 h218abb5_2 pkgs/main
python 3.9.15 hdfd78df_0 pkgs/main
python 3.9.16 h218abb5_0 pkgs/main
python 3.9.16 h218abb5_1 pkgs/main
python 3.9.16 h218abb5_2 pkgs/main
python 3.9.16 h5ee71fb_3 pkgs/main
python 3.9.17 h218abb5_0 pkgs/main
python 3.9.17 h5ee71fb_0 pkgs/main
python 3.9.18 h218abb5_0 pkgs/main
python 3.9.18 h5ee71fb_0 pkgs/main
python 3.10.0 h88f2d9e_0 pkgs/main
python 3.10.0 h88f2d9e_1 pkgs/main
python 3.10.0 hdfd78df_2 pkgs/main
python 3.10.0 hdfd78df_3 pkgs/main
python 3.10.0 hdfd78df_5 pkgs/main
python 3.10.3 hdfd78df_5 pkgs/main
python 3.10.4 hdfd78df_0 pkgs/main
python 3.10.6 hdfd78df_0 pkgs/main
python 3.10.6 hdfd78df_1 pkgs/main
python 3.10.8 h218abb5_1 pkgs/main
python 3.10.8 hdfd78df_0 pkgs/main
python 3.10.9 h218abb5_0 pkgs/main
python 3.10.9 h218abb5_1 pkgs/main
python 3.10.9 h218abb5_2 pkgs/main
python 3.10.10 h218abb5_2 pkgs/main
python 3.10.11 h218abb5_2 pkgs/main
python 3.10.11 h5ee71fb_3 pkgs/main
python 3.10.12 h218abb5_0 pkgs/main
python 3.10.12 h5ee71fb_0 pkgs/main
python 3.10.13 h218abb5_0 pkgs/main
python 3.10.13 h5ee71fb_0 pkgs/main
python 3.11.0 h1fd4e5f_2 pkgs/main
python 3.11.0 h1fd4e5f_3 pkgs/main
python 3.11.2 h1fd4e5f_0 pkgs/main
python 3.11.3 h1fd4e5f_0 pkgs/main
python 3.11.3 hf27a42d_1 pkgs/main
python 3.11.4 h1fd4e5f_0 pkgs/main
python 3.11.4 hf27a42d_0 pkgs/main
python 3.11.5 h1fd4e5f_0 pkgs/main
python 3.11.5 hf27a42d_0 pkgs/main
python 3.11.7 hf27a42d_0 pkgs/main
python 3.11.8 hf27a42d_0 pkgs/main
python 3.12.0 hd58486a_0 pkgs/main
python 3.12.1 hd58486a_0 pkgs/main
python 3.12.2 hd58486a_0 pkgs/main
and even after downloading the development version of crisprScore (v.1.7.2) and crisprScoreData from this github
I still faced similar errors, shown below, please help!
guideSet <- addOnTargetScores(guideSet, methods = c("azimuth", "ruleset1", "ruleset3", "lindel", "deephf", "deepspcas9", "crisprater"))
[addOnTargetScores] Adding azimuth scores.
- /Users/dskuen/Library/Caches/org.R-project.R/R/basilisk/1.14.3/0/bin/conda 'create' '--yes' '--prefix' '/Users/dskuen/Library/Caches/org.R-project.R/R/basilisk/1.14.3/crisprScore/1.7.2/azimuth_basilisk' 'python=2.7' '--quiet' '-c' 'bioconda' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Package Plan
environment location: /Users/dskuen/Library/Caches/org.R-project.R/R/basilisk/1.14.3/crisprScore/1.7.2/azimuth_basilisk
added / updated specs:
- python=2.7
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/osx-64::ca-certificates-2024.2.2-h8857fd0_0
certifi conda-forge/osx-64::certifi-2019.11.28-py27h8c360ce_1
libcxx conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0
libffi bioconda/osx-64::libffi-3.2.1-1
libsqlite conda-forge/osx-64::libsqlite-3.45.1-h92b6c6a_0
libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5
ncurses conda-forge/osx-64::ncurses-6.4-h93d8f39_2
openssl conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0
pip conda-forge/osx-64::pip-20.0.2-py27_1
python conda-forge/osx-64::python-2.7.15-h8e446fc_1011_cpython
python_abi conda-forge/osx-64::python_abi-2.7-1_cp27m
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/osx-64::setuptools-44.0.0-py27_0
sqlite conda-forge/osx-64::sqlite-3.45.1-h7461747_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
wheel conda-forge/osx-64::wheel-0.34.2-py27_0
zlib conda-forge/osx-64::zlib-1.2.13-h8a1eda9_5
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
- /Users/dskuen/Library/Caches/org.R-project.R/R/basilisk/1.14.3/0/bin/conda 'install' '--yes' '--prefix' '/Users/dskuen/Library/Caches/org.R-project.R/R/basilisk/1.14.3/crisprScore/1.7.2/azimuth_basilisk' 'python=2.7'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.1.2
Please update conda by running
$ conda update -n base -c defaults conda
Package Plan
environment location: /Users/dskuen/Library/Caches/org.R-project.R/R/basilisk/1.14.3/crisprScore/1.7.2/azimuth_basilisk
added / updated specs:
- python=2.7
The following packages will be UPDATED:
openssl conda-forge::openssl-1.1.1w-h8a1eda9_0 --> pkgs/main::openssl-3.0.13-hca72f7f_0
python conda-forge::python-2.7.15-h8e446fc_1~ --> pkgs/main::python-2.7.18-hc817775_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates conda-forge::ca-certificates-2024.2.2~ --> pkgs/main::ca-certificates-2023.12.12-hecd8cb5_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
- /Users/dskuen/Library/Caches/org.R-project.R/R/basilisk/1.14.3/0/bin/conda 'install' '--yes' '--prefix' '/Users/dskuen/Library/Caches/org.R-project.R/R/basilisk/1.14.3/crisprScore/1.7.2/azimuth_basilisk' '-c' 'bioconda' '-c' 'conda-forge' 'python=2.7' 'python=2.7' 'biopython=1.74' 'certifi=2019.11.28' 'cycler=0.10.0' 'futures=3.3.0' 'kiwisolver=1.1.0' 'matplotlib=2.2.3' 'mmtf-python=1.1.2' 'nose=1.3.7' 'numpy=1.11.3' 'olefile=0.46' 'pandas=0.23.4' 'Pillow=6.2.1' 'pip=20.1.1' 'pyparsing=2.4.7' 'python-dateutil=2.8.1' 'pytz=2020.1' 'reportlab=3.5.42' 'scipy=1.2.1' 'setuptools=44.0.0' 'six=1.15.0' 'subprocess32=3.5.4' 'tornado=5.1.1' 'wheel=0.36.2'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- mmtf-python=1.1.2
- pytz=2020.1
- pyparsing=2.4.7
- wheel=0.36.2
- python-dateutil=2.8.1
Current channels:
- https://conda.anaconda.org/bioconda/osx-64
- https://conda.anaconda.org/conda-forge/osx-64
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/r/osx-64
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
Error: one or more Python packages failed to install [error code 1]