##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data scviR
###
##############################################################################
##############################################################################


* checking for file ‘scviR/DESCRIPTION’ ... OK
* preparing ‘scviR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘citeseq_tut.Rmd’ using rmarkdown
trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/pbmc_citeseq_5k10k.h5ad.gz'
Content type 'application/octet-stream' length 51844928 bytes (49.4 MB)
==================================================
downloaded 49.4 MB

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

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.18.0/scviR/1.6.0/bsklenv

  added / updated specs:
    - python=3.10


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-aarch64::bzip2-1.0.8-h68df207_7 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2025.1.31-hcefe29a_0 
  ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_2 
  libffi             conda-forge/linux-aarch64::libffi-3.4.6-he21f813_0 
  libgcc             conda-forge/linux-aarch64::libgcc-14.2.0-he277a41_1 
  libgcc-ng          conda-forge/linux-aarch64::libgcc-ng-14.2.0-he9431aa_1 
  libgomp            conda-forge/linux-aarch64::libgomp-14.2.0-he277a41_1 
  liblzma            conda-forge/linux-aarch64::liblzma-5.6.4-h86ecc28_0 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.48.0-h5eb1b54_1 
  libuuid            conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0 
  libxcrypt          conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1 
  libzlib            conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 
  ncurses            conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3 
  openssl            conda-forge/linux-aarch64::openssl-3.4.1-hd08dc88_0 
  pip                conda-forge/noarch::pip-25.0.1-pyh8b19718_0 
  python             conda-forge/linux-aarch64::python-3.10.16-h57b00e1_1_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-75.8.0-pyhff2d567_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 
  tzdata             conda-forge/noarch::tzdata-2025a-h78e105d_0 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
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: 25.1.1

Please update conda by running

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



# All requested packages already installed.

Channels:
 - conda-forge
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: 25.1.1

Please update conda by running

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



## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.18.0/scviR/1.6.0/bsklenv

  added / updated specs:
    - numpy=1.24.4
    - pandas=1.5.3
    - python[version='3.10.*,3.10.*']


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libblas-3.9.0              |30_h1a9f1db_openblas          16 KB  conda-forge
    libcblas-3.9.0             |30_hab92f65_openblas          16 KB  conda-forge
    liblapack-3.9.0            |30_h411afd4_openblas          16 KB  conda-forge
    libopenblas-0.3.29         |pthreads_h9d3fd7e_0         4.6 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         4.6 MB

The following NEW packages will be INSTALLED:

  libblas            conda-forge/linux-aarch64::libblas-3.9.0-30_h1a9f1db_openblas 
  libcblas           conda-forge/linux-aarch64::libcblas-3.9.0-30_hab92f65_openblas 
  libgfortran        conda-forge/linux-aarch64::libgfortran-14.2.0-he9431aa_1 
  libgfortran5       conda-forge/linux-aarch64::libgfortran5-14.2.0-hb6113d0_1 
  liblapack          conda-forge/linux-aarch64::liblapack-3.9.0-30_h411afd4_openblas 
  libopenblas        conda-forge/linux-aarch64::libopenblas-0.3.29-pthreads_h9d3fd7e_0 
  libstdcxx          conda-forge/linux-aarch64::libstdcxx-14.2.0-h3f4de04_1 
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-14.2.0-hf1166c9_1 
  numpy              conda-forge/linux-aarch64::numpy-1.24.4-py310h7f380f4_0 
  pandas             conda-forge/linux-aarch64::pandas-1.5.3-py310hc3d6b01_1 
  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1 
  python_abi         conda-forge/linux-aarch64::python_abi-3.10-5_cp310 
  pytz               conda-forge/noarch::pytz-2025.1-pyhd8ed1ab_0 
  six                conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0 



Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting anndata==0.10.1
  Using cached anndata-0.10.1-py3-none-any.whl.metadata (6.4 kB)
Collecting docrep==0.3.2
  Using cached docrep-0.3.2.tar.gz (33 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting flax==0.8.1
  Using cached flax-0.8.1-py3-none-any.whl.metadata (10 kB)
Collecting jax==0.4.23
  Using cached jax-0.4.23-py3-none-any.whl.metadata (24 kB)
Collecting jaxlib==0.4.23
  Using cached jaxlib-0.4.23-cp310-cp310-manylinux2014_aarch64.whl.metadata (2.1 kB)
Collecting optax==0.1.9
  Using cached optax-0.1.9-py3-none-any.whl.metadata (6.7 kB)
Collecting scipy==1.12.0
  Using cached scipy-1.12.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (112 kB)
Collecting scikit-learn==1.4.0
  Using cached scikit_learn-1.4.0-1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (11 kB)
Collecting rich==13.7.1
  Using cached rich-13.7.1-py3-none-any.whl.metadata (18 kB)
Collecting h5py==3.9.0
  Using cached h5py-3.9.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (2.5 kB)
Collecting torch==1.13.1
  Using cached torch-1.13.1-cp310-cp310-manylinux2014_aarch64.whl.metadata (23 kB)
Collecting lightning==2.1.4
  Using cached lightning-2.1.4-py3-none-any.whl.metadata (57 kB)
Collecting torchmetrics==0.11.0
  Using cached torchmetrics-0.11.0-py3-none-any.whl.metadata (16 kB)
Collecting tqdm==4.66.2
  Using cached tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)
Collecting ml-collections==0.1.1
  Using cached ml_collections-0.1.1.tar.gz (77 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting mudata==0.2.3
  Using cached mudata-0.2.3-py3-none-any.whl.metadata (4.7 kB)
Collecting scvi-tools==1.1.2
  Using cached scvi_tools-1.1.2-py3-none-any.whl.metadata (12 kB)
Collecting scanpy==1.9.5
  Using cached scanpy-1.9.5-py3-none-any.whl.metadata (5.9 kB)
Collecting matplotlib==3.7.3
  Using cached matplotlib-3.7.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (5.7 kB)
Collecting scikit-misc==0.3.1
  Using cached scikit_misc-0.3.1.tar.gz (302 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'error'
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [10 lines of output]
      + meson setup /home/biocbuild/tmp/pip-install-ayomgde4/scikit-misc_2d6895365efa498fb97c514046b2cbfa /home/biocbuild/tmp/pip-install-ayomgde4/scikit-misc_2d6895365efa498fb97c514046b2cbfa/.mesonpy-nf9wvdpk -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/home/biocbuild/tmp/pip-install-ayomgde4/scikit-misc_2d6895365efa498fb97c514046b2cbfa/.mesonpy-nf9wvdpk/meson-python-native-file.ini
      The Meson build system
      Version: 1.7.0
      Source dir: /home/biocbuild/tmp/pip-install-ayomgde4/scikit-misc_2d6895365efa498fb97c514046b2cbfa
      Build dir: /home/biocbuild/tmp/pip-install-ayomgde4/scikit-misc_2d6895365efa498fb97c514046b2cbfa/.mesonpy-nf9wvdpk
      Build type: native build
      
      ../meson.build:5:11: ERROR: Command `/home/biocbuild/tmp/pip-install-ayomgde4/scikit-misc_2d6895365efa498fb97c514046b2cbfa/skmisc/_build_utils/version_please.py` failed with status 127.
      
      A full log can be found at /home/biocbuild/tmp/pip-install-ayomgde4/scikit-misc_2d6895365efa498fb97c514046b2cbfa/.mesonpy-nf9wvdpk/meson-logs/meson-log.txt
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Quitting from lines 43-48 [doinit] (citeseq_tut.Rmd)
Error: processing vignette 'citeseq_tut.Rmd' failed with diagnostics:
failed to install additional packages via pip
--- failed re-building ‘citeseq_tut.Rmd’

--- re-building ‘compch12.Rmd’ using rmarkdown
trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/ch12sce.rda'
Content type 'application/octet-stream' length 58079368 bytes (55.4 MB)
==================================================
downloaded 55.4 MB

trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/full_5k10k_totalVI.h5ad'
Content type 'application/octet-stream' length 1216903940 bytes (1160.5 MB)
======================================
downloaded 882.2 MB


Quitting from lines 50-53 [getdat2] (compch12.Rmd)
Error: processing vignette 'compch12.Rmd' failed with diagnostics:
download from 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/full_5k10k_totalVI.h5ad' failed
--- failed re-building ‘compch12.Rmd’

--- re-building ‘scviR.Rmd’ using rmarkdown
--- finished re-building ‘scviR.Rmd’

SUMMARY: processing the following files failed:
  ‘citeseq_tut.Rmd’ ‘compch12.Rmd’

Error: Vignette re-building failed.
Execution halted