===============================
R CMD BUILD
===============================
* 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
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv
added / updated specs:
- python=3.8.13
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
ca-certificates conda-forge/osx-64::ca-certificates-2022.12.7-h033912b_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.40.0-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-3.0.8-hfd90126_0
pip conda-forge/noarch::pip-23.0.1-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.8.13-h66c20e1_0_cpython
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/noarch::setuptools-67.5.1-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.40.0-h9ae0607_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
wheel conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv
added / updated specs:
- python=3.8.13
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hecd8cb5_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv
added / updated specs:
- pandas=1.3.5
- python=3.8.13
The following NEW packages will be INSTALLED:
bottleneck conda-forge/osx-64::bottleneck-1.3.6-py38hbd87e4b_0
libblas conda-forge/osx-64::libblas-3.9.0-16_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-16_osx64_openblas
libcxx conda-forge/osx-64::libcxx-15.0.7-h71dddab_0
libgfortran conda-forge/osx-64::libgfortran-5.0.0-12_2_0_h97931a8_30
libgfortran5 conda-forge/osx-64::libgfortran5-12.2.0-he409387_30
liblapack conda-forge/osx-64::liblapack-3.9.0-16_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.21-openmp_h429af6e_3
llvm-openmp conda-forge/osx-64::llvm-openmp-15.0.7-h61d9ccf_0
numexpr conda-forge/osx-64::numexpr-2.8.3-py38hec72209_1
numpy conda-forge/osx-64::numpy-1.24.2-py38h5a2dcdf_0
packaging conda-forge/noarch::packaging-23.0-pyhd8ed1ab_0
pandas pkgs/main/osx-64::pandas-1.3.5-py38h743cdd8_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/osx-64::python_abi-3.8-3_cp38
pytz conda-forge/noarch::pytz-2022.7.1-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2023.01.10~ --> conda-forge::ca-certificates-2022.12.7-h033912b_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting hail==0.2.108
Using cached hail-0.2.108-py3-none-any.whl (108.1 MB)
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Using cached aiohttp-3.8.4-cp38-cp38-macosx_10_9_x86_64.whl (359 kB)
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Collecting Jinja2==3.0.3
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Requirement already satisfied: numpy<2 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages (from hail==0.2.108) (1.24.2)
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Collecting rich==12.6.0
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Using cached janus-1.0.0-py3-none-any.whl (6.9 kB)
Requirement already satisfied: pandas<1.5.0,>=1.3.0 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages (from hail==0.2.108) (1.3.5)
Collecting avro<1.12,>=1.10
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Collecting google-cloud-storage>=1.25.*
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Collecting dill<0.4,>=0.3.1.1
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Collecting google-auth==2.14.1
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Collecting requests<3,>=2.25.1
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Collecting nest-asyncio<2,>=1.5.4
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Collecting ukbb-common
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Collecting PyYAML>=3.10
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Requirement already satisfied: python-dateutil>=2.1 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages (from bokeh==1.4.0->hail==0.2.108) (2.8.2)
Collecting pillow>=4.0
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Requirement already satisfied: packaging>=16.8 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages (from bokeh==1.4.0->hail==0.2.108) (23.0)
Requirement already satisfied: six>=1.5.2 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages (from bokeh==1.4.0->hail==0.2.108) (1.16.0)
Collecting rsa<5,>=3.1.4
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Collecting cachetools<6.0,>=2.0.0
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Collecting commonmark<0.10.0,>=0.9.0
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Collecting pygments<3.0.0,>=2.6.0
Using cached Pygments-2.14.0-py3-none-any.whl (1.1 MB)
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Collecting aiosignal>=1.1.2
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Collecting google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5
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Requirement already satisfied: setuptools in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages (from hurry.filesize<1,>=0.9->hail==0.2.108) (67.5.1)
Requirement already satisfied: pytz>=2017.3 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages (from pandas<1.5.0,>=1.3.0->hail==0.2.108) (2022.7.1)
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Collecting pycparser
Using cached pycparser-2.21-py2.py3-none-any.whl (118 kB)
Installing collected packages: sortedcontainers, pyasn1, py4j, commonmark, wrapt, uvloop, urllib3, typing-extensions, tornado, tenacity, tabulate, scipy, rsa, PyYAML, python-json-logger, pyspark, PyJWT, pygments, pycparser, pyasn1-modules, protobuf, portalocker, pillow, parsimonious, orjson, nest-asyncio, multidict, MarkupSafe, jmespath, isodate, idna, hurry.filesize, humanize, google-crc32c, frozenlist, dill, decorator, charset-normalizer, certifi, cachetools, avro, attrs, asyncinit, async-timeout, yarl, rich, requests, plotly, Jinja2, janus, googleapis-common-protos, google-resumable-media, google-auth, Deprecated, cffi, botocore, aiosignal, s3transfer, google-api-core, cryptography, bokeh, azure-core, aiohttp, google-cloud-core, boto3, azure-storage-blob, aiohttp-session, msal, google-cloud-storage, msal-extensions, azure-identity, hail, ukbb-common, ukbb_pan_ancestry
Successfully installed Deprecated-1.2.13 Jinja2-3.0.3 MarkupSafe-2.1.2 PyJWT-2.6.0 PyYAML-6.0 aiohttp-3.8.4 aiohttp-session-2.12.0 aiosignal-1.3.1 async-timeout-4.0.2 asyncinit-0.2.4 attrs-22.2.0 avro-1.11.1 azure-core-1.26.3 azure-identity-1.12.0 azure-storage-blob-12.15.0 bokeh-1.4.0 boto3-1.26.86 botocore-1.29.86 cachetools-5.3.0 certifi-2022.12.7 cffi-1.15.1 charset-normalizer-3.1.0 commonmark-0.9.1 cryptography-39.0.2 decorator-4.4.2 dill-0.3.6 frozenlist-1.3.3 google-api-core-2.11.0 google-auth-2.14.1 google-cloud-core-2.3.2 google-cloud-storage-2.7.0 google-crc32c-1.5.0 google-resumable-media-2.4.1 googleapis-common-protos-1.58.0 hail-0.2.108 humanize-1.1.0 hurry.filesize-0.9 idna-3.4 isodate-0.6.1 janus-1.0.0 jmespath-1.0.1 msal-1.21.0 msal-extensions-1.0.0 multidict-6.0.4 nest-asyncio-1.5.6 orjson-3.8.7 parsimonious-0.8.1 pillow-9.4.0 plotly-5.10.0 portalocker-2.7.0 protobuf-3.20.2 py4j-0.10.9 pyasn1-0.4.8 pyasn1-modules-0.2.8 pycparser-2.21 pygments-2.14.0 pyspark-3.1.3 python-json-logger-2.0.7 requests-2.28.2 rich-12.6.0 rsa-4.9 s3transfer-0.6.0 scipy-1.9.3 sortedcontainers-2.4.0 tabulate-0.9.0 tenacity-8.2.2 tornado-6.2 typing-extensions-4.5.0 ukbb-common-0.1.2 ukbb_pan_ancestry-0.0.2 urllib3-1.26.14 uvloop-0.17.0 wrapt-1.15.0 yarl-1.8.2
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages/pyspark/bin/spark-class: line 71: /usr/local/jdk-14.0.1.jdk/Contents/Home/bin/java: No such file or directory
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages/pyspark/bin/spark-class: line 96: CMD: bad array subscript
head: illegal line count -- -1
Initializing Hail with default parameters...
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages/pyspark/bin/spark-class: line 71: /usr/local/jdk-14.0.1.jdk/Contents/Home/bin/java: No such file or directory
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages/pyspark/bin/spark-class: line 96: CMD: bad array subscript
head: illegal line count -- -1
Quitting from lines 57-61 (gwas_tut.Rmd)
Error: processing vignette 'gwas_tut.Rmd' failed with diagnostics:
Exception: Java gateway process exited before sending its port number
--- failed re-building ‘gwas_tut.Rmd’
--- re-building ‘large_t2t.Rmd’ using rmarkdown
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages/pyspark/bin/spark-class: line 71: /usr/local/jdk-14.0.1.jdk/Contents/Home/bin/java: No such file or directory
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages/pyspark/bin/spark-class: line 96: CMD: bad array subscript
head: illegal line count -- -1
Initializing Hail with default parameters...
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages/pyspark/bin/spark-class: line 71: /usr/local/jdk-14.0.1.jdk/Contents/Home/bin/java: No such file or directory
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages/pyspark/bin/spark-class: line 96: CMD: bad array subscript
head: illegal line count -- -1
Quitting from lines 65-75 (large_t2t.Rmd)
Error: processing vignette 'large_t2t.Rmd' failed with diagnostics:
Exception: Java gateway process exited before sending its port number
--- failed re-building ‘large_t2t.Rmd’
--- re-building ‘ukbb.Rmd’ using rmarkdown
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages/pyspark/bin/spark-class: line 71: /usr/local/jdk-14.0.1.jdk/Contents/Home/bin/java: No such file or directory
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages/pyspark/bin/spark-class: line 96: CMD: bad array subscript
head: illegal line count -- -1
Initializing Hail with default parameters...
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages/pyspark/bin/spark-class: line 71: /usr/local/jdk-14.0.1.jdk/Contents/Home/bin/java: No such file or directory
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.11/bsklenv/lib/python3.8/site-packages/pyspark/bin/spark-class: line 96: CMD: bad array subscript
head: illegal line count -- -1
Quitting from lines 38-42 (ukbb.Rmd)
Error: processing vignette 'ukbb.Rmd' failed with diagnostics:
Exception: Java gateway process exited before sending its port number
--- failed re-building ‘ukbb.Rmd’
SUMMARY: processing the following files failed:
‘gwas_tut.Rmd’ ‘large_t2t.Rmd’ ‘ukbb.Rmd’
Error: Vignette re-building failed.
Execution halted