AddOnTargetScores unable to run due to error with creating conda environment
benjytan88 opened this issue · 2 comments
benjytan88 commented
Hi developers,
I am having troubles running the AddOnTargetScores command as it produces an error while creating the conda environment. The error seems to be due to incompatible packages as below.
> testSpacer <- addOnTargetScores(testSpacer, methods = c("deephf", "deepspcas9"))
[addOnTargetScores] Adding deephf scores.
/nemo/project/home/tanb/.cache/R/ExperimentHub
does not exist, create directory? (yes/no): yes
|======================================================================| 100%
snapshotDate(): 2022-10-31
see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation
downloading 1 resources
retrieving 1 resource
|======================================================================| 100%
loading from cache
trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-py38_4.12.0-Linux-x86_64.sh'
Content type 'application/x-sh' length 76120962 bytes (72.6 MB)
==================================================
downloaded 72.6 MB
PREFIX=/nemo/project/home/tanb/.cache/R/basilisk/1.10.2/0
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /nemo/project/home/tanb/.cache/R/basilisk/1.10.2/0
added / updated specs:
- _libgcc_mutex==0.1=main
- _openmp_mutex==4.5=1_gnu
- brotlipy==0.7.0=py38h27cfd23_1003
- ca-certificates==2022.3.29=h06a4308_1
- certifi==2021.10.8=py38h06a4308_2
- cffi==1.15.0=py38hd667e15_1
- charset-normalizer==2.0.4=pyhd3eb1b0_0
- colorama==0.4.4=pyhd3eb1b0_0
- conda-content-trust==0.1.1=pyhd3eb1b0_0
- conda-package-handling==1.8.1=py38h7f8727e_0
- conda==4.12.0=py38h06a4308_0
- cryptography==36.0.0=py38h9ce1e76_0
- idna==3.3=pyhd3eb1b0_0
- ld_impl_linux-64==2.35.1=h7274673_9
- libffi==3.3=he6710b0_2
- libgcc-ng==9.3.0=h5101ec6_17
- libgomp==9.3.0=h5101ec6_17
- libstdcxx-ng==9.3.0=hd4cf53a_17
- ncurses==6.3=h7f8727e_2
- openssl==1.1.1n=h7f8727e_0
- pip==21.2.4=py38h06a4308_0
- pycosat==0.6.3=py38h7b6447c_1
- pycparser==2.21=pyhd3eb1b0_0
- pyopenssl==22.0.0=pyhd3eb1b0_0
- pysocks==1.7.1=py38h06a4308_0
- python==3.8.13=h12debd9_0
- readline==8.1.2=h7f8727e_1
- requests==2.27.1=pyhd3eb1b0_0
- ruamel_yaml==0.15.100=py38h27cfd23_0
- setuptools==61.2.0=py38h06a4308_0
- six==1.16.0=pyhd3eb1b0_1
- sqlite==3.38.2=hc218d9a_0
- tk==8.6.11=h1ccaba5_0
- tqdm==4.63.0=pyhd3eb1b0_0
- urllib3==1.26.8=pyhd3eb1b0_0
- wheel==0.37.1=pyhd3eb1b0_0
- xz==5.2.5=h7b6447c_0
- yaml==0.2.5=h7b6447c_0
- zlib==1.2.12=h7f8727e_1
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py38h27cfd23_1003
ca-certificates pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
certifi pkgs/main/linux-64::certifi-2021.10.8-py38h06a4308_2
cffi pkgs/main/linux-64::cffi-1.15.0-py38hd667e15_1
charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
colorama pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
conda pkgs/main/linux-64::conda-4.12.0-py38h06a4308_0
conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.8.1-py38h7f8727e_0
cryptography pkgs/main/linux-64::cryptography-36.0.0-py38h9ce1e76_0
idna pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
libgomp pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
ncurses pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
openssl pkgs/main/linux-64::openssl-1.1.1n-h7f8727e_0
pip pkgs/main/linux-64::pip-21.2.4-py38h06a4308_0
pycosat pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1
pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
pyopenssl pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
pysocks pkgs/main/linux-64::pysocks-1.7.1-py38h06a4308_0
python pkgs/main/linux-64::python-3.8.13-h12debd9_0
readline pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
requests pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.100-py38h27cfd23_0
setuptools pkgs/main/linux-64::setuptools-61.2.0-py38h06a4308_0
six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
sqlite pkgs/main/linux-64::sqlite-3.38.2-hc218d9a_0
tk pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
tqdm pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0
urllib3 pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.12-h7f8727e_1
Preparing transaction: done
Executing transaction: done
installation finished.
WARNING:
You currently have a PYTHONPATH environment variable set. This may cause
unexpected behavior when running the Python interpreter in Miniconda3.
For best results, please verify that your PYTHONPATH only points to
directories of packages that are compatible with the Python interpreter
in Miniconda3: /nemo/project/home/tanb/.cache/R/basilisk/1.10.2/0
+ /nemo/project/home/tanb/.cache/R/basilisk/1.10.2/0/bin/conda 'create' '--yes' '--prefix' '/nemo/project/home/tanb/.cache/R/basilisk/1.10.2/crisprScore/1.2.0/deephf_basilisk' 'python=3.6' '--quiet' '-c' 'conda-forge' '-c' 'bioconda'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /nemo/project/home/tanb/.cache/R/basilisk/1.10.2/crisprScore/1.2.0/deephf_basilisk
added / updated specs:
- python=3.6
The following packages will be downloaded:
package | build
---------------------------|-----------------
certifi-2016.9.26 | py36_0 217 KB conda-forge
openssl-1.1.1v | hd590300_0 1.9 MB conda-forge
pip-20.0.2 | py36_1 1.9 MB conda-forge
python-3.6.15 |hb7a2778_0_cpython 38.4 MB conda-forge
setuptools-49.6.0 | py36h5fab9bb_3 936 KB conda-forge
wheel-0.36.2 | pyhd3deb0d_0 31 KB conda-forge
------------------------------------------------------------
Total: 43.3 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2023.7.22-hbcca054_0
certifi conda-forge/linux-64::certifi-2016.9.26-py36_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.1.0-he5830b7_0
libgomp conda-forge/linux-64::libgomp-13.1.0-he5830b7_0
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libsqlite conda-forge/linux-64::libsqlite-3.42.0-h2797004_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.1.0-hfd8a6a1_0
libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5
ncurses conda-forge/linux-64::ncurses-6.4-hcb278e6_0
openssl conda-forge/linux-64::openssl-1.1.1v-hd590300_0
pip conda-forge/linux-64::pip-20.0.2-py36_1
python conda-forge/linux-64::python-3.6.15-hb7a2778_0_cpython
python_abi conda-forge/linux-64::python_abi-3.6-2_cp36m
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/linux-64::setuptools-49.6.0-py36h5fab9bb_3
sqlite conda-forge/linux-64::sqlite-3.42.0-h2c6b66d_0
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
wheel conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: ...working...
done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ /nemo/project/home/tanb/.cache/R/basilisk/1.10.2/0/bin/conda 'install' '--yes' '--prefix' '/nemo/project/home/tanb/.cache/R/basilisk/1.10.2/crisprScore/1.2.0/deephf_basilisk' 'python=3.6'
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.7.2
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
+ /nemo/project/home/tanb/.cache/R/basilisk/1.10.2/0/bin/conda 'install' '--yes' '--prefix' '/nemo/project/home/tanb/.cache/R/basilisk/1.10.2/crisprScore/1.2.0/deephf_basilisk' '-c' 'conda-forge' '-c' 'bioconda' 'python=3.6' 'python=3.6' 'viennarna=2.4.5' 'absl-py=0.12.0' 'astor=0.8.1' 'biopython=1.71' 'bleach=1.5.0' 'certifi=2020.12.5' 'cycler=0.10.0' 'decorator=4.4.2' 'dotmap=1.2.20' 'gast=0.4.0' 'GPy=1.9.8' 'GPyOpt=1.2.6' 'grpcio=1.36.1' 'h5py=2.9.0' 'html5lib=0.9999999' 'importlib-metadata=3.7.2' 'Keras=2.1.6' 'kiwisolver=1.3.1' 'Mako=1.1.4' 'Markdown=3.3.4' 'MarkupSafe=1.1.1' 'matplotlib=3.1.1' 'numpy=1.14.0' 'pandas=0.25.3' 'paramz=0.9.5' 'pip=21.0.1' 'protobuf=3.15.5' 'pygpu=0.7.6' 'pyparsing=2.4.7' 'python-dateutil=2.8.1' 'pytz=2021.1' 'PyYAML=5.4.1' 'scikit-learn=0.19.1' 'scipy=1.1.0' 'setuptools=49.6.0' 'six=1.15.0' 'tensorboard=1.8.0' 'tensorflow=1.8.0' 'termcolor=1.1.0' 'Theano=1.0.5' 'tornado=6.1' 'typing-extensions=3.7.4.3' 'webencodings=0.5.1' 'Werkzeug=1.0.1' 'wheel=0.36.2' 'zipp=3.4.1'
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed \ \
UnsatisfiableError: The following specifications were found to be incompatible with a past
explicit spec that is not an explicit spec in this operation (python):
What follows after that code chunk is a long list of incompatible packages which ends with this code chunk.
Package libedit conflicts for:
sqlite -> libedit[version='>=3.1.20170329,<3.2.0a0|>=3.1.20181209,<3.2.0a0|>=3.1.20191231,<3.2.0a0']
python[version='3.6.*,3.6.*'] -> sqlite[version='>=3.33.0,<4.0a0'] -> libedit[version='>=3.1.20170329,<3.2.0a0|>=3.1.20181209,<3.2.0a0|>=3.1.20191231,<3.2.0a0']The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.17=0
- feature:|@/linux-64::__glibc==2.17=0
- biopython=1.71 -> libgcc-ng[version='>=7.2.0'] -> __glibc[version='>=2.17']
- gpy=1.9.8 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- grpcio=1.36.1 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- h5py=2.9.0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- keras=2.1.6 -> tensorflow -> __cuda
- keras=2.1.6 -> tensorflow -> __glibc[version='>=2.17']
- kiwisolver=1.3.1 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- libffi -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
- libnsl -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
- libstdcxx-ng -> __glibc[version='>=2.17']
- libzlib -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
- markupsafe=1.1.1 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- matplotlib=3.1.1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- ncurses -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
- numpy=1.14.0 -> libgcc-ng[version='>=7.2.0'] -> __glibc[version='>=2.17']
- openssl -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
- pandas=0.25.3 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- protobuf=3.15.5 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pygpu=0.7.6 -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
- python[version='3.6.*,3.6.*'] -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
- pyyaml=5.4.1 -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
- readline -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- scikit-learn=0.19.1 -> libgcc-ng[version='>=7.2.0'] -> __glibc[version='>=2.17']
- scipy=1.1.0 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- sqlite -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
- tensorboard=1.8.0 -> libgcc-ng[version='>=7.2.0'] -> __glibc[version='>=2.17']
- tk -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
- tornado=6.1 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
- viennarna=2.4.5 -> libgcc-ng[version='>=4.9'] -> __glibc[version='>=2.17']
- xz -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.17
Note that strict channel priority may have removed packages required for satisfiability.
Error: one or more Python packages failed to install [error code 1]
Could you please advise how to fix this issue? Thank you.
Jfortin1 commented
Hi @nicodemus88, we fixed a few bugs today in crisprScore; could you install version 1.7.2 of the devel branch of crisprScore to see if you have the same problems?
Jfortin1 commented
@nicodemus88 Any updates from your side?