##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 BiocHail
###
##############################################################################
##############################################################################
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* preparing ‘BiocHail’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gwas_tut.Rmd’ using rmarkdown
--- finished re-building ‘gwas_tut.Rmd’
--- re-building ‘large_t2t.Rmd’ using rmarkdown
Channels:
- conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.18.0/BiocHail/1.6.0/bsklenv
added / updated specs:
- python=3.10.14
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7
ca-certificates conda-forge/linux-64::ca-certificates-2024.12.14-hbcca054_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_2
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1
libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1
libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1
liblzma conda-forge/linux-64::liblzma-5.6.3-hb9d3cd8_1
liblzma-devel conda-forge/linux-64::liblzma-devel-5.6.3-hb9d3cd8_1
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsqlite conda-forge/linux-64::libsqlite-3.47.2-hee588c1_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
ncurses conda-forge/linux-64::ncurses-6.5-he02047a_1
openssl conda-forge/linux-64::openssl-3.4.0-hb9d3cd8_0
pip conda-forge/noarch::pip-24.3.1-pyh8b19718_2
python conda-forge/linux-64::python-3.10.14-hd12c33a_0_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-75.6.0-pyhff2d567_1
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
xz conda-forge/linux-64::xz-5.6.3-hbcc6ac9_1
xz-gpl-tools conda-forge/linux-64::xz-gpl-tools-5.6.3-hbcc6ac9_1
xz-tools conda-forge/linux-64::xz-tools-5.6.3-hb9d3cd8_1
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-64
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: 24.11.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: linux-64
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: 24.11.1
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/BiocHail/1.6.0/bsklenv
added / updated specs:
- pandas=1.3.5
- python=3.10.14
The following packages will be downloaded:
package | build
---------------------------|-----------------
libblas-3.9.0 |26_linux64_openblas 16 KB conda-forge
libcblas-3.9.0 |26_linux64_openblas 16 KB conda-forge
liblapack-3.9.0 |26_linux64_openblas 16 KB conda-forge
------------------------------------------------------------
Total: 48 KB
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-64::libblas-3.9.0-26_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-26_linux64_openblas
libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_1
libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hd5240d6_1
liblapack conda-forge/linux-64::liblapack-3.9.0-26_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.28-pthreads_h94d23a6_1
libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_1
numpy conda-forge/linux-64::numpy-1.26.4-py310hb13e2d6_0
pandas conda-forge/linux-64::pandas-1.3.5-py310hb5077e9_0
python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1
python_abi conda-forge/linux-64::python_abi-3.10-5_cp310
pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_1
six conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0
The following packages will be SUPERSEDED by a higher-priority channel:
setuptools conda-forge/noarch::setuptools-75.6.0~ --> conda-forge/linux-64::setuptools-59.8.0-py310hff52083_1
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting hail==0.2.108
Using cached hail-0.2.108-py3-none-any.whl.metadata (6.0 kB)
WARNING: Ignoring version 0.2.108 of hail since it has invalid metadata:
Requested hail==0.2.108 from https://files.pythonhosted.org/packages/e0/46/904e5c5cc6981388af95ad482663fd9128a3a790730a2fe5ad09bc8474df/hail-0.2.108-py3-none-any.whl has invalid metadata: .* suffix can only be used with `==` or `!=` operators
google-cloud-storage (>=1.25.*)
~~~~~~~^
Please use pip<24.1 if you need to use this version.
ERROR: Ignored the following yanked versions: 0.2.87, 0.2.121, 0.2.125
ERROR: Could not find a version that satisfies the requirement hail==0.2.108 (from versions: 0.2, 0.2.1, 0.2.2, 0.2.3, 0.2.4, 0.2.5, 0.2.6, 0.2.7, 0.2.8, 0.2.9, 0.2.10, 0.2.11, 0.2.12, 0.2.13, 0.2.14, 0.2.15, 0.2.16, 0.2.17, 0.2.18, 0.2.19, 0.2.20, 0.2.21, 0.2.22, 0.2.23, 0.2.24, 0.2.25, 0.2.26, 0.2.27, 0.2.28, 0.2.29, 0.2.30, 0.2.31, 0.2.32, 0.2.33, 0.2.34, 0.2.35, 0.2.36, 0.2.37, 0.2.38, 0.2.39, 0.2.40, 0.2.41, 0.2.42, 0.2.43, 0.2.44, 0.2.45, 0.2.46, 0.2.47, 0.2.48, 0.2.49, 0.2.50, 0.2.51, 0.2.52, 0.2.53, 0.2.54, 0.2.55, 0.2.56, 0.2.57, 0.2.58, 0.2.59, 0.2.60, 0.2.61, 0.2.62, 0.2.63, 0.2.64, 0.2.65, 0.2.66, 0.2.67, 0.2.68, 0.2.69, 0.2.70, 0.2.71, 0.2.72, 0.2.73, 0.2.74, 0.2.75, 0.2.76, 0.2.77, 0.2.78, 0.2.79, 0.2.80, 0.2.81, 0.2.82, 0.2.83, 0.2.84, 0.2.85, 0.2.86, 0.2.88, 0.2.89, 0.2.90, 0.2.91, 0.2.92, 0.2.93, 0.2.94, 0.2.95, 0.2.96, 0.2.97, 0.2.98, 0.2.99, 0.2.100, 0.2.101, 0.2.102, 0.2.103, 0.2.104, 0.2.105, 0.2.106, 0.2.107, 0.2.108, 0.2.109, 0.2.110, 0.2.111, 0.2.112, 0.2.113, 0.2.114, 0.2.115, 0.2.116, 0.2.117, 0.2.118, 0.2.119, 0.2.120, 0.2.122, 0.2.123, 0.2.124, 0.2.126, 0.2.127, 0.2.127.post1, 0.2.128, 0.2.129, 0.2.130, 0.2.130.post1, 0.2.131, 0.2.132, 0.2.133)
ERROR: No matching distribution found for hail==0.2.108
Quitting from lines 69-79 [do17] (large_t2t.Rmd)
Error: processing vignette 'large_t2t.Rmd' failed with diagnostics:
failed to install additional packages via pip
--- failed re-building ‘large_t2t.Rmd’
--- re-building ‘ukbb.Rmd’ using rmarkdown
--- finished re-building ‘ukbb.Rmd’
SUMMARY: processing the following file failed:
‘large_t2t.Rmd’
Error: Vignette re-building failed.
Execution halted