jeroen
commented
3 years ago Which operating system are you on? What did you see when you did conda install -c conda-forge r-gert ?
Closed Hrovatin closed 3 years ago
jeroen
commented
3 years ago Which operating system are you on? What did you see when you did conda install -c conda-forge r-gert ?
Hrovatin
commented
3 years ago cat /etc/os-release
NAME=Fedora
VERSION="28 (Twenty Eight)"
ID=fedora
VERSION_ID=28
PLATFORM_ID="platform:f28"
PRETTY_NAME="Fedora 28 (Twenty Eight)"
ANSI_COLOR="0;34"
CPE_NAME="cpe:/o:fedoraproject:fedora:28"
HOME_URL="https://fedoraproject.org/"
SUPPORT_URL="https://fedoraproject.org/wiki/Communicating_and_getting_help"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Fedora"
REDHAT_BUGZILLA_PRODUCT_VERSION=28
REDHAT_SUPPORT_PRODUCT="Fedora"
REDHAT_SUPPORT_PRODUCT_VERSION=28
PRIVACY_POLICY_URL="https://fedoraproject.org/wiki/Legal:PrivacyPolicy"During conda install there were some inconsistencies, but I think some of them should not be even related to gert:
conda install -c conda-forge r-gert
Collecting package metadata (current_repodata.json): done
Solving environment: |
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- conda-forge/linux-64::statsmodels==0.11.1=py38h1e0a361_2
- conda-forge/linux-64::petsc4py==3.13.0=py38h745227e_3
- conda-forge/linux-64::numexpr==2.7.1=py38hcb8c335_1
- conda-forge/linux-64::pytables==3.6.1=py38h1b207d3_2
- bioconda/noarch::cellrank-krylov==1.0.0rc0=pyhd784808_0
- conda-forge/linux-64::anndata==0.7.4=py38h32f6830_0
- conda-forge/linux-64::numba==0.50.1=py38hcb8c335_1
- conda-forge/noarch::seaborn-base==0.10.1=py_1
- conda-forge/linux-64::seaborn==0.10.1=1
- conda-forge/linux-64::matplotlib-base==3.3.0=py38h91b0d89_1
- conda-forge/linux-64::pandas==1.0.5=py38hcb8c335_0
- conda-forge/linux-64::scikit-learn==0.23.1=py38h3a94b23_0
- conda-forge/linux-64::slepc4py==3.13.0=py38h087bb10_1
- bioconda/noarch::cellrank==1.0.0rc0=py_0
- conda-forge/linux-64::umap-learn==0.4.6=py38h32f6830_0
- conda-forge/noarch::patsy==0.5.1=py_0
- conda-forge/linux-64::h5py==2.10.0=nompi_py38hfb01d0b_104
failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: \
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- conda-forge/linux-64::statsmodels==0.11.1=py38h1e0a361_2
- conda-forge/linux-64::petsc4py==3.13.0=py38h745227e_3
- conda-forge/linux-64::numexpr==2.7.1=py38hcb8c335_1
- conda-forge/linux-64::pytables==3.6.1=py38h1b207d3_2
- bioconda/noarch::cellrank-krylov==1.0.0rc0=pyhd784808_0
- conda-forge/linux-64::anndata==0.7.4=py38h32f6830_0
- conda-forge/linux-64::numba==0.50.1=py38hcb8c335_1
- conda-forge/noarch::seaborn-base==0.10.1=py_1
- conda-forge/linux-64::seaborn==0.10.1=1
- conda-forge/linux-64::matplotlib-base==3.3.0=py38h91b0d89_1
- conda-forge/linux-64::pandas==1.0.5=py38hcb8c335_0
- conda-forge/linux-64::scikit-learn==0.23.1=py38h3a94b23_0
- conda-forge/linux-64::slepc4py==3.13.0=py38h087bb10_1
- bioconda/noarch::cellrank==1.0.0rc0=py_0
- conda-forge/linux-64::umap-learn==0.4.6=py38h32f6830_0
- conda-forge/noarch::patsy==0.5.1=py_0
- conda-forge/linux-64::h5py==2.10.0=nompi_py38hfb01d0b_104
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 the existing python installation in your environment:
Specifications:
- attrs -> python[version='2.7.*|3.5.*|3.6.*|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
- bleach -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
- decorator -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.7,<3.8.0a0|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
- defusedxml -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0']
- jinja2 -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
- olefile -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0']
- prometheus_client -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- pyparsing -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
- python-dateutil -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
- setuptools_scm -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|3.4.*|>=3.7,<3.8.0a0']
- testpath -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
Your python: python=3.8
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
The following specifications were found to be incompatible with a past
explicit spec that is not an explicit spec in this operation (r-base):
- r-gert -> r-askpass -> r-base[version='>=3.5,<3.6.0a0|>=3.5.1,<3.5.2.0a0']
- r-gert -> r-base[version='>=3.6,<3.7.0a0|>=4.0,<4.1.0a0']
The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Followed by a long list of package conflicts, from both inside and outside R (e.g. python packages).
jeroen
commented
3 years ago Anaconda is such a mess. Looks like you need to update conda r-base package?
If you're on Fedora, why didn't you sudo yum install libgit2-devel instead of building it in /home/icb/karin.hrovatin/libgit2-1.1.0/?
Hrovatin
commented
3 years ago I work on a server and do not have admin rights. Do you have any suggestions on how to correct the error I initially posted?
jeroen
commented
3 years ago Do you have any suggestions on how to correct the error I initially posted?
I think you would have to set LD_LIBRARY_PATH to the directory of libgit2.so is before loading the package. See also e.g. https://github.com/jeroen/V8/issues/103#issuecomment-716066832
Hrovatin
commented
3 years ago Thank you very much. Executing the below command before running the install worked. I now added it to my conda activate variables script.
export LD_LIBRARY_PATH=/home/icb/karin.hrovatin/libgit2-1.1.0/build:${LD_LIBRARY_PATH}
I want to install gert in my conda env with R4.0.2. After finally sorting out libgit2 my installation now compiles (I assume), but file 00LOCK-gert/00new/gert/libs/gert.so is missing and instalation errors out. This is the command I use:
R CMD INSTALL gert_1.0.2.tar.gz --configure-vars='INCLUDE_DIR=/home/icb/karin.hrovatin/libgit2-1.1.0/include LIB_DIR=/home/icb/karin.hrovatin/libgit2-1.1.0/build'This is the installation output:I also tried installing with
conda install -c conda-forge r-gert, but the package was not installed.