Closed gsilvaarias closed 7 months ago
bodkan
commented
7 months ago Haha, oh man, not another Python/conda problem! 🤣
More seriously though - hello, Gustavo! Thanks for checking out slendr and for reporting back!
First — this is going to sound a bit strange but can you try (in a freshly restarted R session) to type these, one by one, separately one after another, and report the entire output you get from each command? Thank you.
library(slendr)
init_env()
check_env()
gsilvaarias
commented
7 months ago Hi, thanks for the reply. Here the output of :
> library(slendr)The 'slim' binary could not be found in your $PATH. Most of
the functionality of slendr will work without any issues but
you will not be able to simulate data with the `slim()` function.
If you want to run SLiM simulations, make sure to modify the $PATH
variable so that it points to the directory containing the slim
command-line program. One easy way to do this is to add this:
PATH="path/to/directory/with/slim/binary"
to your ~/.Renviron file.
Alternatively, use the `slim_path` argument of the `slim()` function.
--------------------
In order to use spatial features of slendr, packages 'sf', 'stars',
and 'rnaturalearth' are required but not all are present.
You can install all of them with
`install.packages(c("sf", "stars", "rnaturalearth"))`.
--------------------init_env()Error in py_run_file_impl(file, local, convert) :
ModuleNotFoundError: No module named 'numpy'
Run `reticulate::py_last_error()` for details.check_env()Summary of the currently active Python environment:
Python binary: /Users/guta/Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2/bin/python
Python version: 3.12.2 | packaged by conda-forge | (main, Feb 16 2024, 20:54:21) [Clang 16.0.6 ]
slendr requirements:
- tskit: MISSING ❌
- msprime: MISSING ❌
- pyslim: MISSING ❌
- tspop: MISSING ❌
Note that due to the technical limitations of embedded Python, if you
want to switch to another Python environment you will need to restart
your R session first.Yikes. Yeah, that’s a Python installation issue. As in, even if you were to run the installation of tskit, msprime, et al. in a plain shell terminal for Python only (which is actually exactly what happens when you peek into the setup_env() log that you helpfully posted in full), it would fail as well.
I am currently sort of on sick leave without access to my computer but as soon as I have access to it, I will dig in.
It has happened in the past that either tskit or msprime failed to build, particularly on M Macs, but given that stuff worked very recently on my M1 Mac, I would assume M2 should also be OK.
I will give you an update hopefully soon.
In the meantime, you could try this:
clear_env(all = TRUE)followed by (in a fresh R session):
setup_env(pip = FALSE)Switching off pip forces setup_env() to install slendr Python dependencies using conda which has been unfortunately broken on M Macs for tskit / msprime for a long time, so this is unlikely to help here. (I actually added the pip= option precisely to workaround conda being broken on those systems with pip working basically always.)
That said, it’s worth trying because as I said, I run M1 and you have M2 Mac, so perhaps the situation for M2 setups is different and the pip workaround isn’t need edge anymore.
In any case, dealing with Python installation is a traditional nightmare but I can confidently say that I got slendr running pretty much on any machine and setup ever, so don’t despair. :)
gsilvaarias
commented
7 months ago Hello. Thank you for your advice and the enormous effort to keep slendr running for everyone.
I tried to generate the new environment as you indicated, but as you expected, it didn't work. You can see below the outputs after executing these last two steps.
If I manage to create an environment that includes the needed packages/versions (Python-3.12, msprime-1.3.1, tskit-0.5.6, pyslim-1.0.4, and tspop-0.0.2), is it possible to run the setup_env() by pointing to my custom environment?
Best, Gustavo
> clear_env(all = TRUE)
The following slendr-looking Python environments have been identified:
- [#1] Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2
You will be asked for confirmation before any of them are deleted.
To remove all of them at once, you can call `clear_env(force = TRUE, all = TRUE)`.
Do you want to delete Python environment [#1]? (Hit ESC to cancel.)
/Users/guta/Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2/
1: No
2: Yes
Selection: 2
+ /Users/guta/Library/r-miniconda-arm64/bin/conda 'remove' '--yes' '--name' 'Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2' '--all'
Remove all packages in environment /Users/guta/Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2:
## Package Plan ##
environment location: /Users/guta/Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2
The following packages will be REMOVED:
bzip2-1.0.8-h93a5062_5
ca-certificates-2024.2.2-hf0a4a13_0
libexpat-2.6.1-hebf3989_0
libffi-3.4.2-h3422bc3_5
libsqlite-3.45.1-h091b4b1_0
libzlib-1.2.13-h53f4e23_5
ncurses-6.4-h463b476_2
openssl-3.2.1-h0d3ecfb_0
pip-24.0-pyhd8ed1ab_0
python-3.12.2-hdf0ec26_0_cpython
readline-8.2-h92ec313_1
setuptools-69.1.1-pyhd8ed1ab_0
tk-8.6.13-h5083fa2_1
tzdata-2024a-h0c530f3_0
wheel-0.42.0-pyhd8ed1ab_0
xz-5.2.6-h57fd34a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
slendr environment 'Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2' has been sucessfully removed.... and after starting a new fresh R session and loading slendr,
> setup_env(pip = FALSE)
This function will install a completely isolated Miniconda Python distribution
just for slendr and create an environment with all required Python modules.
Everything will be installed into a completely separate location into an
isolated environment in an R library directory. This won't affect your other
Python installations at all. You can always wipe out the automatically created
environment by running clear_env().
Do you wish to proceed with the automated Python environment setup?
1: No
2: Yes
Selection: 2
=======================================================================
Installing slendr's Python environment. Please wait until
the installation procedure finishes. Do NOT interrupt the
process while the installation is still running.
======================================================================
+ /Users/guta/Library/r-miniconda-arm64/bin/conda 'create' '--yes' '--name' 'Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2' 'python=3.12' '--quiet' '-c' 'conda-forge'
Channels:
- conda-forge
- defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/guta/Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2
added / updated specs:
- python=3.12
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h93a5062_5
ca-certificates conda-forge/osx-arm64::ca-certificates-2024.2.2-hf0a4a13_0
libexpat conda-forge/osx-arm64::libexpat-2.6.1-hebf3989_0
libffi conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
libsqlite conda-forge/osx-arm64::libsqlite-3.45.1-h091b4b1_0
libzlib conda-forge/osx-arm64::libzlib-1.2.13-h53f4e23_5
ncurses conda-forge/osx-arm64::ncurses-6.4-h463b476_2
openssl conda-forge/osx-arm64::openssl-3.2.1-h0d3ecfb_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-arm64::python-3.12.2-hdf0ec26_0_cpython
readline conda-forge/osx-arm64::readline-8.2-h92ec313_1
setuptools conda-forge/noarch::setuptools-69.1.1-pyhd8ed1ab_0
tk conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0
xz conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ /Users/guta/Library/r-miniconda-arm64/bin/conda 'install' '--yes' '--name' 'Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2' '-c' 'conda-forge' 'msprime==1.3.1' 'tskit==0.5.6' 'pyslim==1.0.4'
Channels:
- conda-forge
- defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- nothing provides kastore needed by pyslim-1.0.4-pyhd8ed1ab_0
Could not solve for environment specs
The following package could not be installed
└─ pyslim 1.0.4 is not installable because it requires
└─ kastore, which does not exist (perhaps a missing channel).
Error: one or more Python packages failed to install [error code 1]Thanks again for the detailed report.
I can think of three things to try to fix this, but to do that I would need access to my machine… I can only do that once I recover from this virus. 🤕
I will be back later this week.
To your question — there is a way to do the Python setup outside slendr and link the environment afterwards but this would also require a bit of slendr hacking in the background I think. Plus, as I said, the error that you got happened by running this command in your first report:
/Users/guta/Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2/bin/python -m pip install --upgrade --no-user 'msprime==1.3.1' 'tskit==0.5.6' 'pyslim==1.0.4'
Note that this happened outside R anyway (on a normal shell in the background) so I suspect the same Python issue would happen regardless.
I have also someone with an M2 Mac in the office so I’ll be also able to do better testing there. Worst case, will ask one if the tskit/msprime/pyslim folks for help.
Stay tuned and thanks for your patience.
bodkan
commented
7 months ago OK, so curiously, even on my Mac I get errors stating that pyslim cannot be installed via conda because kastore isn't available, same situation as you have. I suspect it's because the kastore/pyslim modules aren't properly built for every platform (Windows / Linux / Mac), and the Mac version is somehow missing? Sadly, I don't know anything about Python packaging, so I have no means of verifying this. In any case, this is not slendr's problem so it's more productive to try to work with what we have.
Given how frequently Python installations fail under various circumstances, I have now changed the setup_env() internal logic to behave like this:
setup_env(pip = FALSE) (i.e. the default setup_env() call) -- use conda to only install msprime and tskit, but always install pyslim and tspop using pip. tspop isn't available on conda anyway (so it was always installed by pip) and given the issue we've now discovered, pyslim is not installable from conda anyway in a cross-platform way -- it actually doesn't matter to me whether this is a Mac-specific thing or not. slendr must operate on Windows/Linux/macOS in the same way.
setup_env(pip = TRUE) -- in this situation, conda is only used to pull the Python interpreter binary but no Python modules are installed from conda. I.e., all msprime, tskit, pyslim, tspop are installed via pip.
@gsilvaarias could you test the new update but running this again in a fresh R session, one command at a time, and post the outputs of the commands # 3, 4, 5?
devtools::install_github("bodkan/slendr")library(slendr)clear_env(all = TRUE) to remove whatever remains of slendr Python environments are on your system.setup_env() -- this will pull msprime and tskit from conda (equivalent of pip = FALSE above) but pyslim and tspop using pipinit_env()check_env()gsilvaarias
commented
7 months ago Hi, it is working now. Many thanks!
> setup_env()This function will install a completely isolated Miniconda Python distribution
just for slendr and create an environment with all required Python modules.
Everything will be installed into a completely separate location into an
isolated environment in an R library directory. This won't affect your other
Python installations at all. You can always wipe out the automatically created
environment by running clear_env().
Do you wish to proceed with the automated Python environment setup?
1: No
2: Yes
Selection: 2
=======================================================================
Installing slendr's Python environment. Please wait until
the installation procedure finishes. Do NOT interrupt the
process while the installation is still running.
======================================================================
+ /Users/guta/Library/r-miniconda-arm64/bin/conda 'create' '--yes' '--name' 'Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2' 'python=3.12' '--quiet' '-c' 'conda-forge'
Retrieving notices: ...working... done
Channels:
- conda-forge
- defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/guta/Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2
added / updated specs:
- python=3.12
The following packages will be downloaded:
package | build
---------------------------|-----------------
libsqlite-3.45.2 | h091b4b1_0 806 KB conda-forge
setuptools-69.2.0 | pyhd8ed1ab_0 460 KB conda-forge
------------------------------------------------------------
Total: 1.2 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h93a5062_5
ca-certificates conda-forge/osx-arm64::ca-certificates-2024.2.2-hf0a4a13_0
libexpat conda-forge/osx-arm64::libexpat-2.6.1-hebf3989_0
libffi conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
libsqlite conda-forge/osx-arm64::libsqlite-3.45.2-h091b4b1_0
libzlib conda-forge/osx-arm64::libzlib-1.2.13-h53f4e23_5
ncurses conda-forge/osx-arm64::ncurses-6.4-h463b476_2
openssl conda-forge/osx-arm64::openssl-3.2.1-h0d3ecfb_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-arm64::python-3.12.2-hdf0ec26_0_cpython
readline conda-forge/osx-arm64::readline-8.2-h92ec313_1
setuptools conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
tk conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0
xz conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ /Users/guta/Library/r-miniconda-arm64/bin/conda 'install' '--yes' '--name' 'Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2' '-c' 'conda-forge' 'msprime==1.3.1' 'tskit==0.5.6'
Channels:
- conda-forge
- defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 23.11.0
latest version: 24.1.2
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /Users/guta/Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2
added / updated specs:
- msprime==1.3.1
- tskit==0.5.6
The following packages will be downloaded:
package | build
---------------------------|-----------------
attrs-23.2.0 | pyh71513ae_0 53 KB conda-forge
demes-0.2.3 | pyhd8ed1ab_0 40 KB conda-forge
gsl-2.7 | h6e638da_0 2.6 MB conda-forge
importlib_resources-6.3.0 | pyhd8ed1ab_0 30 KB conda-forge
jsonschema-4.21.1 | pyhd8ed1ab_0 71 KB conda-forge
jsonschema-specifications-2023.12.1| pyhd8ed1ab_0 16 KB conda-forge
msprime-1.3.1 | py312h0767fef_0 410 KB conda-forge
numpy-1.26.4 | py312h8442bc7_0 5.8 MB conda-forge
pkgutil-resolve-name-1.3.10| pyhd8ed1ab_1 11 KB conda-forge
pyparsing-3.1.2 | pyhd8ed1ab_0 87 KB conda-forge
python_abi-3.12 | 4_cp312 6 KB conda-forge
referencing-0.33.0 | pyhd8ed1ab_0 38 KB conda-forge
rpds-py-0.18.0 | py312h77200ec_0 288 KB conda-forge
ruamel.yaml-0.18.6 | py312he37b823_0 262 KB conda-forge
ruamel.yaml.clib-0.2.8 | py312he37b823_0 109 KB conda-forge
svgwrite-1.4.3 | pyhd8ed1ab_0 52 KB conda-forge
tskit-0.5.6 | py312hf635c46_0 536 KB conda-forge
zipp-3.17.0 | pyhd8ed1ab_0 19 KB conda-forge
------------------------------------------------------------
Total: 10.4 MB
The following NEW packages will be INSTALLED:
attrs conda-forge/noarch::attrs-23.2.0-pyh71513ae_0
demes conda-forge/noarch::demes-0.2.3-pyhd8ed1ab_0
gsl conda-forge/osx-arm64::gsl-2.7-h6e638da_0
importlib_resourc~ conda-forge/noarch::importlib_resources-6.3.0-pyhd8ed1ab_0
jsonschema conda-forge/noarch::jsonschema-4.21.1-pyhd8ed1ab_0
jsonschema-specif~ conda-forge/noarch::jsonschema-specifications-2023.12.1-pyhd8ed1ab_0
libblas conda-forge/osx-arm64::libblas-3.9.0-21_osxarm64_openblas
libcblas conda-forge/osx-arm64::libcblas-3.9.0-21_osxarm64_openblas
libcxx conda-forge/osx-arm64::libcxx-16.0.6-h4653b0c_0
libgfortran conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3
libgfortran5 conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3
liblapack conda-forge/osx-arm64::liblapack-3.9.0-21_osxarm64_openblas
libopenblas conda-forge/osx-arm64::libopenblas-0.3.26-openmp_h6c19121_0
llvm-openmp conda-forge/osx-arm64::llvm-openmp-17.0.6-hcd81f8e_0
msprime conda-forge/osx-arm64::msprime-1.3.1-py312h0767fef_0
numpy conda-forge/osx-arm64::numpy-1.26.4-py312h8442bc7_0
pkgutil-resolve-n~ conda-forge/noarch::pkgutil-resolve-name-1.3.10-pyhd8ed1ab_1
pyparsing conda-forge/noarch::pyparsing-3.1.2-pyhd8ed1ab_0
python_abi conda-forge/osx-arm64::python_abi-3.12-4_cp312
referencing conda-forge/noarch::referencing-0.33.0-pyhd8ed1ab_0
rpds-py conda-forge/osx-arm64::rpds-py-0.18.0-py312h77200ec_0
ruamel.yaml conda-forge/osx-arm64::ruamel.yaml-0.18.6-py312he37b823_0
ruamel.yaml.clib conda-forge/osx-arm64::ruamel.yaml.clib-0.2.8-py312he37b823_0
svgwrite conda-forge/noarch::svgwrite-1.4.3-pyhd8ed1ab_0
tskit conda-forge/osx-arm64::tskit-0.5.6-py312hf635c46_0
zipp conda-forge/noarch::zipp-3.17.0-pyhd8ed1ab_0
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ . /Users/guta/Library/r-miniconda-arm64/bin/activate
+ conda activate 'Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2'
+ '/Users/guta/Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2/bin/python' -m pip install --upgrade --no-user 'pyslim==1.0.4' 'tspop==0.0.2' pyarrow
Collecting pyslim==1.0.4
Using cached pyslim-1.0.4-py3-none-any.whl.metadata (1.3 kB)
Collecting tspop==0.0.2
Downloading tspop-0.0.2-py3-none-any.whl.metadata (1.1 kB)
Collecting pyarrow
Downloading pyarrow-15.0.1-cp312-cp312-macosx_11_0_arm64.whl.metadata (3.0 kB)
Requirement already satisfied: msprime>=1.0.1 in ./Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2/lib/python3.12/site-packages (from pyslim==1.0.4) (1.3.1)
Requirement already satisfied: numpy in ./Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2/lib/python3.12/site-packages (from pyslim==1.0.4) (1.26.4)
Requirement already satisfied: tskit in ./Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2/lib/python3.12/site-packages (from pyslim==1.0.4) (0.5.6)
Collecting pandas>=1.2.0 (from tspop==0.0.2)
Downloading pandas-2.2.1-cp312-cp312-macosx_11_0_arm64.whl.metadata (19 kB)
Collecting matplotlib>=3.4.0 (from tspop==0.0.2)
Downloading matplotlib-3.8.3-cp312-cp312-macosx_11_0_arm64.whl.metadata (5.8 kB)
Collecting contourpy>=1.0.1 (from matplotlib>=3.4.0->tspop==0.0.2)
Downloading contourpy-1.2.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (5.8 kB)
Collecting cycler>=0.10 (from matplotlib>=3.4.0->tspop==0.0.2)
Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib>=3.4.0->tspop==0.0.2)
Downloading fonttools-4.49.0-cp312-cp312-macosx_10_9_universal2.whl.metadata (159 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 159.1/159.1 kB 3.6 MB/s eta 0:00:00
Collecting kiwisolver>=1.3.1 (from matplotlib>=3.4.0->tspop==0.0.2)
Downloading kiwisolver-1.4.5-cp312-cp312-macosx_11_0_arm64.whl.metadata (6.4 kB)
Collecting packaging>=20.0 (from matplotlib>=3.4.0->tspop==0.0.2)
Using cached packaging-24.0-py3-none-any.whl.metadata (3.2 kB)
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Collecting six>=1.5 (from python-dateutil>=2.7->matplotlib>=3.4.0->tspop==0.0.2)
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Installing collected packages: pytz, tzdata, six, pyarrow, pillow, packaging, newick, kiwisolver, fonttools, cycler, contourpy, python-dateutil, pandas, matplotlib, tspop, pyslim
Successfully installed contourpy-1.2.0 cycler-0.12.1 fonttools-4.49.0 kiwisolver-1.4.5 matplotlib-3.8.3 newick-1.9.0 packaging-24.0 pandas-2.2.1 pillow-10.2.0 pyarrow-15.0.1 pyslim-1.0.4 python-dateutil-2.9.0.post0 pytz-2024.1 six-1.16.0 tspop-0.0.2 tzdata-2024.1
======================================================================
Python environment for slendr has been successfuly created, and the R
interface to msprime, tskit, and pyslim modules has been activated.
In future sessions, activate this environment by calling init_env().
=======================================================================> init_env()The interface to all required Python modules has been activated.> check_env()Summary of the currently active Python environment:
Python binary: /Users/guta/Library/r-miniconda-arm64/envs/Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2/bin/python
Python version: 3.12.2 | packaged by conda-forge | (main, Feb 16 2024, 20:54:21) [Clang 16.0.6 ]
slendr requirements:
- tskit: version 0.5.6 ✓
- msprime: version 1.3.1 ✓
- pyslim: version 1.0.4 ✓
- tspop: present ✓ Beautiful! Thank you so much for these detailed log outputs. This made developing a more robust way to deal with various conda / pip issues much easier.
I will make a new release soon so that others may also benefit from this.
Hi, I have trouble installing slendr on R version 4.3.1 (macOS 14.2.1, Apple M2).
slendrinstallation seems to work fine, but have problem installingtskitduring thesetup_env(). Please find the full report below.I appreciate your help.
Best, Gustavo