############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data 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/1.19.3/BiocHail/1.7.1/bsklenv added / updated specs: - python=3.12.8 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-2025.1.31-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4 libexpat conda-forge/linux-64::libexpat-2.6.4-h5888daf_0 libffi conda-forge/linux-64::libffi-3.4.6-h2dba641_0 libgcc conda-forge/linux-64::libgcc-14.2.0-h767d61c_2 libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2 libgomp conda-forge/linux-64::libgomp-14.2.0-h767d61c_2 liblzma conda-forge/linux-64::liblzma-5.6.4-hb9d3cd8_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.49.1-hee588c1_2 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-h2d0b736_3 openssl conda-forge/linux-64::openssl-3.4.1-h7b32b05_0 pip conda-forge/noarch::pip-25.0.1-pyh8b19718_0 python conda-forge/linux-64::python-3.12.8-h9e4cc4f_1_cpython readline conda-forge/linux-64::readline-8.2-h8c095d6_2 setuptools conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 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-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.11.3 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-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.11.3 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/1.19.3/BiocHail/1.7.1/bsklenv added / updated specs: - pandas=2.2.3 - python=3.12.8 The following packages will be downloaded: package | build ---------------------------|----------------- pandas-2.2.3 | py312hf9745cd_1 14.7 MB conda-forge python-dateutil-2.9.0.post0| pyhff2d567_1 217 KB conda-forge python-tzdata-2025.1 | pyhd8ed1ab_0 140 KB conda-forge pytz-2024.1 | pyhd8ed1ab_0 184 KB conda-forge six-1.17.0 | pyhd8ed1ab_0 16 KB conda-forge ------------------------------------------------------------ Total: 15.3 MB The following NEW packages will be INSTALLED: libblas conda-forge/linux-64::libblas-3.9.0-31_h59b9bed_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-31_he106b2a_openblas libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_2 libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hf1ad2bd_2 liblapack conda-forge/linux-64::liblapack-3.9.0-31_h7ac8fdf_openblas libopenblas conda-forge/linux-64::libopenblas-0.3.29-pthreads_h94d23a6_0 libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-h8f9b012_2 numpy conda-forge/linux-64::numpy-2.2.4-py312h72c5963_0 pandas conda-forge/linux-64::pandas-2.2.3-py312hf9745cd_1 python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1 python-tzdata conda-forge/noarch::python-tzdata-2025.1-pyhd8ed1ab_0 python_abi conda-forge/linux-64::python_abi-3.12-5_cp312 pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 six conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0 Downloading and Extracting Packages: ...working... pandas-2.2.3 | 14.7 MB | | 0% python-dateutil-2.9. | 217 KB | | 0%  pytz-2024.1 | 184 KB | | 0%  python-tzdata-2025.1 | 140 KB | | 0%  six-1.17.0 | 16 KB | | 0%  pytz-2024.1 | 184 KB | ########## | 100%  six-1.17.0 | 16 KB | ########## | 100%  python-dateutil-2.9. | 217 KB | #########5 | 96%  pandas-2.2.3 | 14.7 MB | | 1% python-tzdata-2025.1 | 140 KB | ########## | 100%  python-tzdata-2025.1 | 140 KB | ########## | 100%  python-dateutil-2.9. | 217 KB | ########## | 100%  six-1.17.0 | 16 KB | ########## | 100%  six-1.17.0 | 16 KB | ########## | 100%  pandas-2.2.3 | 14.7 MB | ####8 | 49% python-dateutil-2.9. | 217 KB | ########## | 100%  pandas-2.2.3 | 14.7 MB | ########## | 100% pandas-2.2.3 | 14.7 MB | ########## | 100% python-tzdata-2025.1 | 140 KB | ########## | 100%  pytz-2024.1 | 184 KB | ########## | 100%  pytz-2024.1 | 184 KB | ########## | 100%  pandas-2.2.3 | 14.7 MB | ########## | 100%     done Preparing transaction: - \ done Verifying transaction: / - \ | / done Executing transaction: \ | / - \ | / - \ | / - \ | / done Collecting hail==0.2.133 Using 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Collecting avro<1.12,>=1.10 (from hail==0.2.133) Using cached avro-1.11.3-py2.py3-none-any.whl Collecting bokeh<3.4,>=3 (from hail==0.2.133) Using cached bokeh-3.3.4-py3-none-any.whl.metadata (12 kB) Collecting decorator<5 (from hail==0.2.133) Using cached decorator-4.4.2-py2.py3-none-any.whl.metadata (4.2 kB) Collecting Deprecated<1.3,>=1.2.10 (from hail==0.2.133) Using cached Deprecated-1.2.18-py2.py3-none-any.whl.metadata (5.7 kB) Collecting numpy<2 (from hail==0.2.133) Using cached numpy-1.26.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB) Requirement already satisfied: pandas<3,>=2 in /home/biocbuild/.cache/R/basilisk/1.19.3/BiocHail/1.7.1/bsklenv/lib/python3.12/site-packages (from hail==0.2.133) (2.2.3) Collecting parsimonious<1 (from hail==0.2.133) Using cached parsimonious-0.10.0-py3-none-any.whl.metadata (25 kB) Collecting plotly<6,>=5.18.0 (from hail==0.2.133) Using cached plotly-5.24.1-py3-none-any.whl.metadata (7.3 kB) Collecting protobuf==3.20.2 (from hail==0.2.133) Using cached protobuf-3.20.2-py2.py3-none-any.whl.metadata (720 bytes) Collecting pyspark<3.6,>=3.5.0 (from hail==0.2.133) Using cached pyspark-3.5.5-py2.py3-none-any.whl Collecting requests<3,>=2.31.0 (from hail==0.2.133) Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB) Collecting scipy<1.12,>1.2 (from hail==0.2.133) Using cached scipy-1.11.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) Collecting uvloop<1,>=0.19.0 (from hail==0.2.133) Using cached uvloop-0.21.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.9 kB) Collecting ukbb-common (from ukbb_pan_ancestry==0.0.2) Using cached ukbb_common-0.1.2-py3-none-any.whl.metadata (691 bytes) Collecting msrest>=0.6.21 (from azure-mgmt-storage==20.1.0->hail==0.2.133) Using cached msrest-0.7.1-py3-none-any.whl.metadata (21 kB) Collecting azure-common~=1.1 (from azure-mgmt-storage==20.1.0->hail==0.2.133) Using cached azure_common-1.1.28-py2.py3-none-any.whl.metadata (5.0 kB) Collecting azure-mgmt-core<2.0.0,>=1.3.1 (from azure-mgmt-storage==20.1.0->hail==0.2.133) Using cached azure_mgmt_core-1.5.0-py3-none-any.whl.metadata (4.3 kB) Collecting pycares>=3.0.0 (from aiodns<3,>=2.0.0->hail==0.2.133) Using cached pycares-4.5.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.1 kB) Collecting aiohappyeyeballs>=2.3.0 (from aiohttp<4,>=3.9->hail==0.2.133) Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB) Collecting aiosignal>=1.1.2 (from aiohttp<4,>=3.9->hail==0.2.133) Using cached aiosignal-1.3.2-py2.py3-none-any.whl.metadata (3.8 kB) Collecting attrs>=17.3.0 (from aiohttp<4,>=3.9->hail==0.2.133) Using cached attrs-25.3.0-py3-none-any.whl.metadata (10 kB) Collecting multidict<7.0,>=4.5 (from aiohttp<4,>=3.9->hail==0.2.133) Using cached multidict-6.2.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.9 kB) Collecting propcache>=0.2.0 (from 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typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB) Collecting isodate>=0.6.1 (from azure-storage-blob<13,>=12.11.0->hail==0.2.133) Using cached isodate-0.7.2-py3-none-any.whl.metadata (11 kB) Collecting Jinja2>=2.9 (from bokeh<3.4,>=3->hail==0.2.133) Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB) Collecting contourpy>=1 (from bokeh<3.4,>=3->hail==0.2.133) Using cached contourpy-1.3.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.4 kB) Collecting packaging>=16.8 (from bokeh<3.4,>=3->hail==0.2.133) Using cached packaging-24.2-py3-none-any.whl.metadata (3.2 kB) Collecting pillow>=7.1.0 (from bokeh<3.4,>=3->hail==0.2.133) Using cached pillow-11.1.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (9.1 kB) Collecting tornado>=5.1 (from bokeh<3.4,>=3->hail==0.2.133) Using cached tornado-6.4.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) Collecting xyzservices>=2021.09.1 (from bokeh<3.4,>=3->hail==0.2.133) Using cached xyzservices-2025.1.0-py3-none-any.whl.metadata (4.3 kB) Collecting jmespath<2.0.0,>=0.7.1 (from boto3<2.0,>=1.17->hail==0.2.133) Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB) Collecting s3transfer<0.12.0,>=0.11.0 (from boto3<2.0,>=1.17->hail==0.2.133) Using cached s3transfer-0.11.4-py3-none-any.whl.metadata (1.7 kB) Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/biocbuild/.cache/R/basilisk/1.19.3/BiocHail/1.7.1/bsklenv/lib/python3.12/site-packages (from botocore<2.0,>=1.20->hail==0.2.133) (2.9.0.post0) Collecting urllib3!=2.2.0,<3,>=1.25.4 (from botocore<2.0,>=1.20->hail==0.2.133) Using cached urllib3-2.3.0-py3-none-any.whl.metadata (6.5 kB) Collecting wrapt<2,>=1.10 (from Deprecated<1.3,>=1.2.10->hail==0.2.133) Using cached wrapt-1.17.2-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB) Collecting cachetools<6.0,>=2.0.0 (from google-auth<3,>=2.14.1->hail==0.2.133) Using cached cachetools-5.5.2-py3-none-any.whl.metadata (5.4 kB) Collecting pyasn1-modules>=0.2.1 (from google-auth<3,>=2.14.1->hail==0.2.133) Using cached pyasn1_modules-0.4.1-py3-none-any.whl.metadata (3.5 kB) Collecting rsa<5,>=3.1.4 (from google-auth<3,>=2.14.1->hail==0.2.133) Using cached rsa-4.9-py3-none-any.whl.metadata (4.2 kB) Collecting requests-oauthlib>=0.7.0 (from google-auth-oauthlib<1,>=0.5.2->hail==0.2.133) Using cached requests_oauthlib-2.0.0-py2.py3-none-any.whl.metadata (11 kB) Requirement already satisfied: six~=1.13 in /home/biocbuild/.cache/R/basilisk/1.19.3/BiocHail/1.7.1/bsklenv/lib/python3.12/site-packages (from jproperties<3,>=2.1.1->hail==0.2.133) (1.17.0) Requirement already satisfied: pytz>=2020.1 in /home/biocbuild/.cache/R/basilisk/1.19.3/BiocHail/1.7.1/bsklenv/lib/python3.12/site-packages (from pandas<3,>=2->hail==0.2.133) (2024.1) Requirement already satisfied: tzdata>=2022.7 in /home/biocbuild/.cache/R/basilisk/1.19.3/BiocHail/1.7.1/bsklenv/lib/python3.12/site-packages (from pandas<3,>=2->hail==0.2.133) (2025.1) Collecting regex>=2022.3.15 (from parsimonious<1->hail==0.2.133) Using cached regex-2024.11.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (40 kB) Collecting tenacity>=6.2.0 (from plotly<6,>=5.18.0->hail==0.2.133) Using cached tenacity-9.0.0-py3-none-any.whl.metadata (1.2 kB) Collecting py4j==0.10.9.7 (from pyspark<3.6,>=3.5.0->hail==0.2.133) Using cached py4j-0.10.9.7-py2.py3-none-any.whl.metadata (1.5 kB) Collecting charset-normalizer<4,>=2 (from requests<3,>=2.31.0->hail==0.2.133) Using cached charset_normalizer-3.4.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB) Collecting idna<4,>=2.5 (from requests<3,>=2.31.0->hail==0.2.133) Using cached idna-3.10-py3-none-any.whl.metadata (10 kB) Collecting certifi>=2017.4.17 (from requests<3,>=2.31.0->hail==0.2.133) Using cached certifi-2025.1.31-py3-none-any.whl.metadata (2.5 kB) Collecting commonmark<0.10.0,>=0.9.0 (from rich<13,>=12.6.0->hail==0.2.133) Using cached commonmark-0.9.1-py2.py3-none-any.whl.metadata (5.7 kB) Collecting pygments<3.0.0,>=2.6.0 (from rich<13,>=12.6.0->hail==0.2.133) Using cached pygments-2.19.1-py3-none-any.whl.metadata (2.5 kB) Collecting click>=8.0.0 (from typer<1,>=0.9.0->hail==0.2.133) Using cached click-8.1.8-py3-none-any.whl.metadata (2.3 kB) Collecting shellingham>=1.3.0 (from typer<1,>=0.9.0->hail==0.2.133) Using cached shellingham-1.5.4-py2.py3-none-any.whl.metadata (3.5 kB) Collecting cffi>=1.12 (from cryptography>=2.5->azure-identity<2,>=1.6.0->hail==0.2.133) Using cached cffi-1.17.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.5 kB) Collecting MarkupSafe>=2.0 (from Jinja2>=2.9->bokeh<3.4,>=3->hail==0.2.133) Using cached MarkupSafe-3.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB) Collecting PyJWT<3,>=1.0.0 (from PyJWT[crypto]<3,>=1.0.0->msal>=1.30.0->azure-identity<2,>=1.6.0->hail==0.2.133) Using cached PyJWT-2.10.1-py3-none-any.whl.metadata (4.0 kB) Collecting pyasn1<0.7.0,>=0.4.6 (from pyasn1-modules>=0.2.1->google-auth<3,>=2.14.1->hail==0.2.133) Using cached pyasn1-0.6.1-py3-none-any.whl.metadata (8.4 kB) Collecting oauthlib>=3.0.0 (from requests-oauthlib>=0.7.0->google-auth-oauthlib<1,>=0.5.2->hail==0.2.133) Using cached oauthlib-3.2.2-py3-none-any.whl.metadata (7.5 kB) Collecting pycparser (from cffi>=1.12->cryptography>=2.5->azure-identity<2,>=1.6.0->hail==0.2.133) Using cached pycparser-2.22-py3-none-any.whl.metadata (943 bytes) Using cached hail-0.2.133-py3-none-any.whl (144.7 MB) Using cached ukbb_pan_ancestry-0.0.2-py3-none-any.whl (13 kB) Using cached azure_mgmt_storage-20.1.0-py3-none-any.whl (2.3 MB) Using cached protobuf-3.20.2-py2.py3-none-any.whl (162 kB) Using cached aiodns-2.0.0-py2.py3-none-any.whl (4.8 kB) Using cached aiohttp-3.11.14-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.7 MB) Using cached azure_identity-1.21.0-py3-none-any.whl (189 kB) Using cached azure_storage_blob-12.25.0-py3-none-any.whl (406 kB) Using cached bokeh-3.3.4-py3-none-any.whl (6.8 MB) Downloading boto3-1.37.18-py3-none-any.whl (139 kB) Downloading botocore-1.37.18-py3-none-any.whl (13.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.4/13.4 MB 15.1 MB/s eta 0:00:00 Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Using cached Deprecated-1.2.18-py2.py3-none-any.whl (10.0 kB) Using cached dill-0.3.9-py3-none-any.whl (119 kB) Using cached frozenlist-1.5.0-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (283 kB) Using cached google_auth-2.38.0-py2.py3-none-any.whl (210 kB) Using cached google_auth_oauthlib-0.8.0-py2.py3-none-any.whl (19 kB) Using cached humanize-4.12.1-py3-none-any.whl (127 kB) Using cached janus-1.0.0-py3-none-any.whl (6.9 kB) Using 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Using cached uvloop-0.21.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB) Using cached ukbb_common-0.1.2-py3-none-any.whl (33 kB) Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB) Using cached aiosignal-1.3.2-py2.py3-none-any.whl (7.6 kB) Using cached attrs-25.3.0-py3-none-any.whl (63 kB) Using cached azure_common-1.1.28-py2.py3-none-any.whl (14 kB) Using cached azure_core-1.32.0-py3-none-any.whl (198 kB) Using cached azure_mgmt_core-1.5.0-py3-none-any.whl (30 kB) Using cached cachetools-5.5.2-py3-none-any.whl (10 kB) Using cached certifi-2025.1.31-py3-none-any.whl (166 kB) Using cached charset_normalizer-3.4.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (145 kB) Using cached click-8.1.8-py3-none-any.whl (98 kB) Using cached commonmark-0.9.1-py2.py3-none-any.whl (51 kB) Using cached contourpy-1.3.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (323 kB) Using cached cryptography-44.0.2-cp39-abi3-manylinux_2_34_x86_64.whl (4.2 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Using cached requests_oauthlib-2.0.0-py2.py3-none-any.whl (24 kB) Using cached rsa-4.9-py3-none-any.whl (34 kB) Using cached s3transfer-0.11.4-py3-none-any.whl (84 kB) Using cached shellingham-1.5.4-py2.py3-none-any.whl (9.8 kB) Using cached tenacity-9.0.0-py3-none-any.whl (28 kB) Using cached tornado-6.4.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (437 kB) Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB) Using cached urllib3-2.3.0-py3-none-any.whl (128 kB) Using cached wrapt-1.17.2-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (89 kB) Using cached xyzservices-2025.1.0-py3-none-any.whl (88 kB) Using cached yarl-1.18.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (336 kB) Using cached cffi-1.17.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (479 kB) Using cached MarkupSafe-3.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB) Using cached oauthlib-3.2.2-py3-none-any.whl (151 kB) Using cached pyasn1-0.6.1-py3-none-any.whl (83 kB) Using cached PyJWT-2.10.1-py3-none-any.whl (22 kB) Using cached pycparser-2.22-py3-none-any.whl (117 kB) Installing collected packages: sortedcontainers, py4j, commonmark, azure-common, xyzservices, wrapt, uvloop, urllib3, typing-extensions, tornado, tenacity, tabulate, shellingham, regex, pyyaml, python-json-logger, pyspark, PyJWT, pygments, pycparser, pyasn1, protobuf, propcache, pillow, packaging, orjson, oauthlib, numpy, nest-asyncio, multidict, MarkupSafe, jproperties, jmespath, isodate, idna, humanize, frozenlist, dill, decorator, click, charset-normalizer, certifi, cachetools, avro, attrs, aiohappyeyeballs, yarl, scipy, rsa, rich, requests, pyasn1-modules, plotly, parsimonious, Jinja2, janus, Deprecated, contourpy, cffi, botocore, aiosignal, typer, s3transfer, requests-oauthlib, pycares, google-auth, cryptography, bokeh, azure-core, aiohttp, msrest, google-auth-oauthlib, boto3, azure-storage-blob, azure-mgmt-core, aiodns, msal, azure-mgmt-storage, msal-extensions, azure-identity, hail, ukbb-common, ukbb_pan_ancestry Attempting uninstall: numpy Found existing installation: numpy 2.2.4 Uninstalling numpy-2.2.4: Successfully uninstalled numpy-2.2.4 Successfully installed Deprecated-1.2.18 Jinja2-3.1.6 MarkupSafe-3.0.2 PyJWT-2.10.1 aiodns-2.0.0 aiohappyeyeballs-2.6.1 aiohttp-3.11.14 aiosignal-1.3.2 attrs-25.3.0 avro-1.11.3 azure-common-1.1.28 azure-core-1.32.0 azure-identity-1.21.0 azure-mgmt-core-1.5.0 azure-mgmt-storage-20.1.0 azure-storage-blob-12.25.0 bokeh-3.3.4 boto3-1.37.18 botocore-1.37.18 cachetools-5.5.2 certifi-2025.1.31 cffi-1.17.1 charset-normalizer-3.4.1 click-8.1.8 commonmark-0.9.1 contourpy-1.3.1 cryptography-44.0.2 decorator-4.4.2 dill-0.3.9 frozenlist-1.5.0 google-auth-2.38.0 google-auth-oauthlib-0.8.0 hail-0.2.133 humanize-4.12.1 idna-3.10 isodate-0.7.2 janus-1.0.0 jmespath-1.0.1 jproperties-2.1.2 msal-1.32.0 msal-extensions-1.3.1 msrest-0.7.1 multidict-6.2.0 nest-asyncio-1.6.0 numpy-1.26.4 oauthlib-3.2.2 orjson-3.10.15 packaging-24.2 parsimonious-0.10.0 pillow-11.1.0 plotly-5.24.1 propcache-0.3.0 protobuf-3.20.2 py4j-0.10.9.7 pyasn1-0.6.1 pyasn1-modules-0.4.1 pycares-4.5.0 pycparser-2.22 pygments-2.19.1 pyspark-3.5.5 python-json-logger-2.0.7 pyyaml-6.0.2 regex-2024.11.6 requests-2.32.3 requests-oauthlib-2.0.0 rich-12.6.0 rsa-4.9 s3transfer-0.11.4 scipy-1.11.4 shellingham-1.5.4 sortedcontainers-2.4.0 tabulate-0.9.0 tenacity-9.0.0 tornado-6.4.2 typer-0.15.2 typing-extensions-4.12.2 ukbb-common-0.1.2 ukbb_pan_ancestry-0.0.2 urllib3-2.3.0 uvloop-0.21.0 wrapt-1.17.2 xyzservices-2025.1.0 yarl-1.18.3 Quitting from large_t2t.Rmd:68-79 [do17] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `.activate_fallback()`: ! ImportError: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: version `OPENSSL_3.3.0' not found (required by /home/biocbuild/.cache/R/basilisk/1.19.3/BiocHail/1.7.1/bsklenv/lib/python3.12/lib-dynload/_ssl.cpython-312-x86_64-linux-gnu.so) Run `reticulate::py_last_error()` for details. --- Backtrace: ▆ 1. └─BiocHail::hail_init() 2. └─basilisk::basiliskStart(bsklenv, testload = "hail") 3. └─basilisk:::.activate_fallback(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'large_t2t.Rmd' failed with diagnostics: ImportError: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: version `OPENSSL_3.3.0' not found (required by /home/biocbuild/.cache/R/basilisk/1.19.3/BiocHail/1.7.1/bsklenv/lib/python3.12/lib-dynload/_ssl.cpython-312-x86_64-linux-gnu.so) Run `reticulate::py_last_error()` for details. --- 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