##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiCool
###
##############################################################################
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* checking for file ‘HiCool/DESCRIPTION’ ... OK
* preparing ‘HiCool’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HiCool.Rmd’ using rmarkdown
Channels:
 - conda-forge
 - bioconda
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.17.2/HiCool/1.5.0/env

  added / updated specs:
    - python=3.7.12


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2024.7.4-hcefe29a_0 
  ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h9fc2d93_7 
  libffi             conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5 
  libgcc-ng          conda-forge/linux-aarch64::libgcc-ng-14.1.0-he277a41_0 
  libgomp            conda-forge/linux-aarch64::libgomp-14.1.0-he277a41_0 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.46.0-hf51ef55_0 
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-14.1.0-h3f4de04_0 
  libzlib            conda-forge/linux-aarch64::libzlib-1.3.1-h68df207_1 
  ncurses            conda-forge/linux-aarch64::ncurses-6.5-h0425590_0 
  openssl            conda-forge/linux-aarch64::openssl-3.3.1-h68df207_2 
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.7.12-h47f6e27_100_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-69.0.3-pyhd8ed1ab_0 
  sqlite             conda-forge/linux-aarch64::sqlite-3.46.0-hdc7ab3c_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 
  wheel              conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0 
  xz                 conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
 - bioconda
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.3.0
    latest version: 24.7.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



# All requested packages already installed.

Channels:
 - conda-forge
 - bioconda
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides requested samtools 1.16.1**
  - nothing provides requested bowtie2 2.5.0**
  - package hicstuff-3.1.5-pyhdfd78af_0 requires pysam, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ bowtie2 2.5.0**  does not exist (perhaps a typo or a missing channel);
├─ hicstuff 3.1.5**  is installable and it requires
│  └─ pysam with the potential options
│     ├─ pysam [0.22.0|0.22.1] would require
│     │  ├─ python >=3.10,<3.11.0a0 , which can be installed;
│     │  └─ python_abi 3.10.* *_cp310, which can be installed;
│     ├─ pysam [0.22.0|0.22.1] would require
│     │  ├─ python >=3.8,<3.9.0a0 , which can be installed;
│     │  └─ python_abi 3.8.* *_cp38, which can be installed;
│     ├─ pysam [0.22.0|0.22.1] would require
│     │  ├─ python >=3.9,<3.10.0a0 , which can be installed;
│     │  └─ python_abi 3.9.* *_cp39, which can be installed;
│     ├─ pysam 0.22.1 would require
│     │  ├─ python >=3.11,<3.12.0a0 , which can be installed;
│     │  └─ python_abi 3.11.* *_cp311, which can be installed;
│     └─ pysam 0.22.1 would require
│        └─ python_abi 3.12.* *_cp312, which can be installed;
├─ python 3.7.12.*,3.7.12.*  is not installable because there are no viable options
│  ├─ python 3.7.12 conflicts with any installable versions previously reported;
│  └─ python 3.7.12 would require
│     └─ python_abi 3.7.* *_cp37m, which conflicts with any installable versions previously reported;
└─ samtools 1.16.1**  does not exist (perhaps a typo or a missing channel).


Quitting from lines 71-80 [unnamed-chunk-3] (HiCool.Rmd)
Error: processing vignette 'HiCool.Rmd' failed with diagnostics:
one or more Python packages failed to install [error code 1]
--- failed re-building ‘HiCool.Rmd’

SUMMARY: processing the following file failed:
  ‘HiCool.Rmd’

Error: Vignette re-building failed.
Execution halted