Issues installing cobrar

[Calvin2077]

Hello! Longtime user of GapSeq and I love how user friendly it is and wide range of metabolic pathways so thanks for making it so awesome.

I recently had to rebuild my miniconda3 environment and when I went to reinstall GapSeq I got these series of errors

conda env create -n gapseq-dev --file gapseq_env.yml
Channels:

• conda-forge
• bioconda
• defaults
• cruizperez
  Platform: osx-64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• nothing provides requested r-renv
• nothing provides requested r-biocmanager
• nothing provides fonts-conda-ecosystem needed by pango-1.50.14-h19c1c8a_2

Could not solve for environment specs
The following packages are incompatible
├─ r-biocmanager does not exist (perhaps a typo or a missing channel);
├─ r-cobrar >=0.1.1 is not installable because it requires
│ └─ r-base [>=4.3,<4.4.0a0 |>=4.4,<4.5.0a0 ], which requires
│ ├─ fonts-conda-ecosystem, which does not exist (perhaps a missing channel);
│ └─ pango >=1.50.14,<2.0a0 , which requires
│ └─ fonts-conda-ecosystem, which does not exist (perhaps a missing channel);
└─ r-renv does not exist (perhaps a typo or a missing channel).

I tried tracking down the issue using this flow chart the error provided me and
R-base version 4.4.1
pango is installed
fonts-conda-ecosystem, r-renv, and r-biocmanager are all PackagesNotFoundError: The following packages are not available from current channels:

Therefore if I could please have some help solving this it would mean a lot so thank you

[Waschina]

What is your conda version?

[Calvin2077]

Hello!
My Conda version is conda 24.11.1

[Calvin2077]

I have tried to install the dependencies independently using
`# Installation of main system dependencies
brew install coreutils binutils git glpk blast bedtools r brewsci/bio/barrnap grep bc gzip parallel curl bc brewsci/bio/libsbml

installation of required R-packages
R -e 'install.packages(c("data.table", "stringr", "getopt", "R.utils", "stringi", "jsonlite", "httr"))'
R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install("Biostrings")'
R -e 'pak::pkg_install("Waschina/cobrar")'

Download latest gapseq version from github
git clone https://github.com/jotech/gapseq && cd gapseq

Download latest reference sequence database
bash ./src/update_sequences.sh`

However I can't install
R -e 'pak::pkg_install("Waschina/cobrar")

and get a very nasty error message