[Bug] Unable to install R API through conda or through R

[Dzhan4]

Hello, I'm trying to install tiledbsoma R API to use for cellxgene census.

I have a custom conda environment with R 4.3.1 and Python 3.12.0 and all other dependencies installed except for tiledbsoma. I have already installed tiledb through conda as well. When I try to install either tiledbsoma or cellxgene.census, I get errors when I try to install through conda or through R. Any help would be greatly appreciated!

Errors below:

conda install error:

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libgcc-ng conflicts for:
r-tiledbsoma -> libgcc-ng[version='>=12']
r-tiledbsoma -> r-arrow -> libgcc-ng[version='7.2.0.*|>=11.2.0|>=7.3.0|>=7.2.0']

Package libstdcxx-ng conflicts for:
r-tiledbsoma -> r-arrow -> libstdcxx-ng[version='7.2.0.*|>=11.2.0|>=7.3.0|>=7.2.0']
r-tiledbsoma -> libstdcxx-ng[version='>=12']

Package _libgcc_mutex conflicts for:
r-tiledbsoma -> libgcc-ng[version='>=12'] -> _libgcc_mutex==0.1=conda_forge
python=3.12 -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='*|0.1',build='main|main|conda_forge']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
  - python=3.12 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.17

R install error:

x86_64-conda-linux-gnu-c++ -std=gnu++17 -shared -L/home1/05833/dzhan4/miniconda3/envs/RSeurat/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home1/05833/dzhan4/miniconda3/envs/RSeurat/lib -Wl,-rpath-link,/home1/05833/dzhan4/miniconda3/envs/RSeurat/lib -L/home1/05833/dzhan4/miniconda3/envs/RSeurat/lib -o tiledbsoma.so RcppExports.o nanoarrow.o rinterface.o riterator.o rutilities.o -ltiledb -L../inst/tiledb/lib -ltiledbsoma -L../inst/tiledbsoma/lib -Wl,-rpath,$ORIGIN/../tiledb/lib -Wl,-rpath,$ORIGIN/../tiledbsoma/lib -L/home1/05833/dzhan4/miniconda3/envs/RSeurat/lib/R/lib -lR
/opt/apps/gcc/12.2.0/bin/ld: cannot find -ltiledbsoma
collect2: error: ld returned 1 exit status
make: *** [/home1/05833/dzhan4/miniconda3/envs/RSeurat/lib/R/share/make/shlib.mk:10: tiledbsoma.so] Error 1
ERROR: compilation failed for package ‘tiledbsoma’
* removing ‘/home1/05833/dzhan4/miniconda3/envs/RSeurat/lib/R/library/tiledbsoma’

To Reproduce
conda install -c tiledb r-tiledbsoma

In R: install.packages("tiledbsoma")

Versions (please complete the following information):

• TileDB-SOMA version: 1.4.3
• Language and language version (e.g. Python 3.8, R 4.2.2): Python 3.12.0, R 4.3.1
• OS (e.g. MacOS, Ubuntu Linux): Ubuntu Linux

[johnkerl]

@Dzhan4 thank you for your note! Our TileDB-SOMA R install is in a little flux until our 1.5.0 release, which is coming.

A verified install scenario may be found here:
https://github.com/single-cell-data/TileDB-SOMA/wiki/R-quick-start
with the caveat that this will soon become simpler.

[Dzhan4]

Thank you for the quick response! Will keep an eye out for 1.5.0 release.

[jdblischak]

@Dzhan4 Are you still having trouble installing r-tiledbsoma with conda? I confirmed that I was unable to install r-tiledbsoma 1.4.3 with R 4.3.1 (because 1.4.3 was only built against R 4.2). However, I was able to install r-tiledbsoma 1.5.0 and the latest (1.7.2)

mamba create --dry-run -n test \
  --override-channels -c conda-forge -c tiledb \
  python=3.12.0 \
  r-base=4.3.1 \
  r-tiledbsoma=1.4.3
## Could not solve for environment specs
## The following packages are incompatible
## ├─ r-base 4.3.1**  is requested and can be installed;
## └─ r-tiledbsoma 1.4.3**  is not installable because it requires
##    └─ r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported.

mamba create --dry-run -n test \
  --override-channels -c conda-forge -c tiledb \
  python=3.12.0 \
  r-base=4.3.1 \
  r-tiledbsoma=1.5.0
# solves

mamba create --dry-run -n test \
  --override-channels -c conda-forge -c tiledb \
  python=3.12.0 \
  r-base=4.3.1 \
  r-tiledbsoma
# installs r-tiledbsoma 1.7.2

[johnkerl]

@Dzhan4 I believe this is resolved -- please let me know if I'm mistaken and I'll happily re-open -- thank you!