Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/BiocHail

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo1	Linux (Ubuntu 22.04.1 LTS)/x86_64	OK	OK	skipped	OK
merida1	macOS 10.14.6 Mojave/x86_64	ERROR	skipped	skipped	skipped

nebbiolo1 Summary

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Package: BiocHail

Version: 0.99.16

RVersion: 4.3

BiocVersion: 3.17

BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocHail

BuildTime: 7 minutes 25.59 seconds

CheckCommand: BiocCheckGitClone('BiocHail') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2947/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2947/7740ce3407fc8ef44e076cbac9546b51217b2bc8/BiocHail.install-out.txt BiocHail_0.99.16.tar.gz && BiocCheck('BiocHail_0.99.16.tar.gz', `new-package`=TRUE)

CheckTime: 3 minutes 15.48 seconds

BuildBinCommand:

BuildBinTime:

PackageFileSize: 2836.08 KiB

BuildID:: BiocHail_20230327014430

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: BiocHail. Starting Build package. Starting Check package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* preparing ‘BiocHail’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘BiocHail_0.99.16.tar.gz’

nebbiolo1 CHECK output

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===============================

 BiocCheckGitClone('BiocHail')

===============================

─ BiocCheckVersion: 1.35.15
─ BiocVersion: 3.17
─ Package: BiocHail
─ PackageVersion: 0.99.16
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2947/7740ce3407fc8ef44e076cbac9546b51217b2bc8/BiocHail
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2947/7740ce3407fc8ef44e076cbac9546b51217b2bc8/BiocHail.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* this is package ‘BiocHail’ version ‘0.99.16’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiocHail’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [10s/10s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [95s/108s] OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
get_ukbb_sumstat_10kloci_mt    36.136 13.696  50.130
as.data.frame.hail.table.Table 10.094 17.201  21.347
filter                          0.243  0.037   5.712
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [31s/17s]
 [32s/18s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE

Status: 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2947/7740ce3407fc8ef44e076cbac9546b51217b2bc8/BiocHail.Rcheck/00check.log’
for details.






===============================

 BiocCheck('BiocHail_0.99.16.tar.gz')

===============================

─ BiocCheckVersion: 1.35.15
─ BiocVersion: 3.17
─ Package: BiocHail
─ PackageVersion: 0.99.16
─ sourceDir: /tmp/RtmpsDTJIH/file21a47d36260ef1/BiocHail
─ installDir: /tmp/RtmpsDTJIH/file21a47d38800e11
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2947/7740ce3407fc8ef44e076cbac9546b51217b2bc8/BiocHail.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
    * NOTE: Update R version dependency from 4.2 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of BiocHail...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 8% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 127 lines (6%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 201 lines
      (10%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 12 NOTES

See the BiocHail.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

nebbiolo1 BUILD BIN output

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merida1 Summary

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Package: BiocHail

Version: 0.99.16

RVersion: 4.3

BiocVersion: 3.17

BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BiocHail

BuildTime: 8 minutes 27.35 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: BiocHail_20230327014430

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: BiocHail. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1.

merida1 BUILD SRC output

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===============================

 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/1.11.3/BiocHail/0.99.16/bsklenv

  added / updated specs:
    - python=3.8.13


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    readline-8.2               |       h9e318b2_1         250 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         250 KB

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-3.1.0-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-8.2-h9e318b2_1
  setuptools         conda-forge/noarch::setuptools-67.6.0-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-0.40.0-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/1.11.3/BiocHail/0.99.16/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/1.11.3/BiocHail/0.99.16/bsklenv

  added / updated specs:
    - pandas=1.3.5
    - python=3.8.13


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    pytz-2023.2                |     pyhd8ed1ab_0         182 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         182 KB

The following NEW packages will be INSTALLED:

  bottleneck         conda-forge/osx-64::bottleneck-1.3.7-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-5.0.0-11_3_0_h97931a8_31
  libgfortran5       conda-forge/osx-64::libgfortran5-12.2.0-he409387_31
  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-16.0.0-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-2023.2-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



Downloading and Extracting Packages

pytz-2023.2          | 182 KB    |            |   0% 
pytz-2023.2          | 182 KB    | ########## | 100% 
pytz-2023.2          | 182 KB    | ########## | 100% 
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)
Collecting ukbb_pan_ancestry==0.0.2
  Using cached ukbb_pan_ancestry-0.0.2-py3-none-any.whl (13 kB)
Collecting google-cloud-storage>=1.25.*
  Using cached google_cloud_storage-2.7.0-py2.py3-none-any.whl (110 kB)
Collecting python-json-logger<3,>=2.0.2
  Using cached python_json_logger-2.0.7-py3-none-any.whl (8.1 kB)
Collecting PyJWT
  Using cached PyJWT-2.6.0-py3-none-any.whl (20 kB)
Collecting hurry.filesize<1,>=0.9
  Using cached hurry.filesize-0.9-py3-none-any.whl
Collecting Jinja2==3.0.3
  Using cached Jinja2-3.0.3-py3-none-any.whl (133 kB)
Collecting requests<3,>=2.25.1
  Using cached requests-2.28.2-py3-none-any.whl (62 kB)
Collecting janus<1.1,>=0.6
  Using cached janus-1.0.0-py3-none-any.whl (6.9 kB)
Collecting uvloop<1,>=0.16.0
  Using cached uvloop-0.17.0-cp38-cp38-macosx_10_9_x86_64.whl (1.5 MB)
Collecting google-auth==2.14.1
  Using cached google_auth-2.14.1-py2.py3-none-any.whl (175 kB)
Collecting boto3<2.0,>=1.17
  Downloading boto3-1.26.99-py3-none-any.whl (135 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 135.5/135.5 kB 5.0 MB/s eta 0:00:00
Collecting botocore<2.0,>=1.20
  Downloading botocore-1.29.99-py3-none-any.whl (10.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.5/10.5 MB 45.9 MB/s eta 0:00:00
Collecting pyspark<3.2.0,>=3.1.1
  Using cached pyspark-3.1.3-py2.py3-none-any.whl
Collecting tabulate<1,>=0.8.9
  Using cached tabulate-0.9.0-py3-none-any.whl (35 kB)
Collecting azure-storage-blob<13,>=12.11.0
  Using cached azure_storage_blob-12.15.0-py3-none-any.whl (387 kB)
Collecting protobuf==3.20.2
  Using cached protobuf-3.20.2-cp38-cp38-macosx_10_9_x86_64.whl (982 kB)
Collecting aiohttp<4,>=3.8.1
  Using cached aiohttp-3.8.4-cp38-cp38-macosx_10_9_x86_64.whl (359 kB)
Collecting sortedcontainers<3,>=2.4.0
  Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB)
Collecting avro<1.12,>=1.10
  Using cached avro-1.11.1-py2.py3-none-any.whl
Collecting plotly<5.11,>=5.5.0
  Using cached plotly-5.10.0-py2.py3-none-any.whl (15.2 MB)
Collecting bokeh==1.4.0
  Using cached bokeh-1.4.0-py3-none-any.whl
Collecting orjson<4,>=3.6.4
  Downloading orjson-3.8.8-cp38-cp38-macosx_10_9_x86_64.macosx_11_0_arm64.macosx_10_9_universal2.whl (490 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 490.6/490.6 kB 18.5 MB/s eta 0:00:00
Requirement already satisfied: pandas<1.5.0,>=1.3.0 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/BiocHail/0.99.16/bsklenv/lib/python3.8/site-packages (from hail==0.2.108) (1.3.5)
Collecting humanize<2,>=1.0.0
  Using cached humanize-1.1.0-py3-none-any.whl (52 kB)
Collecting Deprecated<1.3,>=1.2.10
  Using cached Deprecated-1.2.13-py2.py3-none-any.whl (9.6 kB)
Collecting dill<0.4,>=0.3.1.1
  Using cached dill-0.3.6-py3-none-any.whl (110 kB)
Collecting decorator<5
  Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting nest-asyncio<2,>=1.5.4
  Using cached nest_asyncio-1.5.6-py3-none-any.whl (5.2 kB)
Collecting frozenlist<2,>=1.3.1
  Using cached frozenlist-1.3.3-cp38-cp38-macosx_10_9_x86_64.whl (36 kB)
Collecting parsimonious<0.9
  Using cached parsimonious-0.8.1-py3-none-any.whl
Collecting asyncinit<0.3,>=0.2.4
  Using cached asyncinit-0.2.4-py3-none-any.whl (2.8 kB)
Collecting azure-identity<2,>=1.6.0
  Using cached azure_identity-1.12.0-py3-none-any.whl (135 kB)
Requirement already satisfied: numpy<2 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/BiocHail/0.99.16/bsklenv/lib/python3.8/site-packages (from hail==0.2.108) (1.24.2)
Collecting rich==12.6.0
  Using cached rich-12.6.0-py3-none-any.whl (237 kB)
Collecting aiohttp-session<2.13,>=2.7
  Using cached aiohttp_session-2.12.0-py3-none-any.whl (12 kB)
Collecting scipy<1.10,>1.2
  Using cached scipy-1.9.3-cp38-cp38-macosx_10_9_x86_64.whl (34.2 MB)
Collecting ukbb-common
  Using cached ukbb_common-0.1.2-py3-none-any.whl (33 kB)
Collecting PyYAML>=3.10
  Using cached PyYAML-6.0-cp38-cp38-macosx_10_9_x86_64.whl (192 kB)
Requirement already satisfied: python-dateutil>=2.1 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/BiocHail/0.99.16/bsklenv/lib/python3.8/site-packages (from bokeh==1.4.0->hail==0.2.108) (2.8.2)
Requirement already satisfied: six>=1.5.2 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/BiocHail/0.99.16/bsklenv/lib/python3.8/site-packages (from bokeh==1.4.0->hail==0.2.108) (1.16.0)
Collecting tornado>=4.3
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Collecting google-resumable-media>=2.3.2
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Collecting tenacity>=6.2.0
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Collecting pycparser
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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 boto3-1.26.99 botocore-1.29.99 cachetools-5.3.0 certifi-2022.12.7 cffi-1.15.1 charset-normalizer-3.1.0 commonmark-0.9.1 cryptography-40.0.1 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-1.59.0 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-3.8.8 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 urllib3-1.26.15 uvloop-0.17.0 wrapt-1.15.0 yarl-1.8.2
2023-03-26 21:52:33.608 WARN  NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
Initializing Hail with default parameters...
2023-03-26 21:52:35.313 WARN  SparkContext:69 - Another SparkContext is being constructed (or threw an exception in its constructor). This may indicate an error, since only one SparkContext should be running in this JVM (see SPARK-2243). The other SparkContext was created at:
org.apache.spark.SparkContext.<init>(SparkContext.scala:85)
is.hail.backend.spark.SparkBackend$.configureAndCreateSparkContext(SparkBackend.scala:148)
is.hail.backend.spark.SparkBackend$.apply(SparkBackend.scala:230)
is.hail.backend.spark.SparkBackend.apply(SparkBackend.scala)
java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
java.base/java.lang.reflect.Method.invoke(Method.java:577)
py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
py4j.Gateway.invoke(Gateway.java:282)
py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
py4j.commands.CallCommand.execute(CallCommand.java:79)
py4j.GatewayConnection.run(GatewayConnection.java:238)
java.base/java.lang.Thread.run(Thread.java:833)
Quitting from lines 57-61 (gwas_tut.Rmd) 
Error: processing vignette 'gwas_tut.Rmd' failed with diagnostics:
py4j.protocol.Py4JJavaError: An error occurred while calling z:is.hail.backend.spark.SparkBackend.apply.
<... omitted ...>ke(ReflectionEngine.java:357)
	at py4j.Gateway.invoke(Gateway.java:282)
	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
	at py4j.commands.CallCommand.execute(CallCommand.java:79)
	at py4j.GatewayConnection.run(GatewayConnection.java:238)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.ExceptionInInitializerError: Exception java.lang.IllegalAccessError: class org.apache.spark.storage.StorageUtils$ (in unnamed module @0x6671dc81) cannot access class sun.nio.ch.DirectBuffer (in module java.base) because module java.base does not export sun.nio.ch to unnamed module @0x6671dc81 [in thread "Thread-3"]
	at org.apache.spark.storage.StorageUtils$.<init>(StorageUtils.scala:213)
	at org.apache.spark.storage.StorageUtils$.<clinit>(StorageUtils.scala)
	... 19 more

See `reticulate::py_last_error()` for details
--- failed re-building ‘gwas_tut.Rmd’

--- re-building ‘large_t2t.Rmd’ using rmarkdown
2023-03-26 21:52:35.443 WARN  SparkContext:69 - Another SparkContext is being constructed (or threw an exception in its constructor). This may indicate an error, since only one SparkContext should be running in this JVM (see SPARK-2243). The other SparkContext was created at:
org.apache.spark.SparkContext.<init>(SparkContext.scala:85)
is.hail.backend.spark.SparkBackend$.configureAndCreateSparkContext(SparkBackend.scala:148)
is.hail.backend.spark.SparkBackend$.apply(SparkBackend.scala:230)
is.hail.backend.spark.SparkBackend.apply(SparkBackend.scala)
java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
java.base/java.lang.reflect.Method.invoke(Method.java:577)
py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
py4j.Gateway.invoke(Gateway.java:282)
py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
py4j.commands.CallCommand.execute(CallCommand.java:79)
py4j.GatewayConnection.run(GatewayConnection.java:238)
java.base/java.lang.Thread.run(Thread.java:833)
Initializing Hail with default parameters...
2023-03-26 21:52:35.498 WARN  SparkContext:69 - Another SparkContext is being constructed (or threw an exception in its constructor). This may indicate an error, since only one SparkContext should be running in this JVM (see SPARK-2243). The other SparkContext was created at:
org.apache.spark.SparkContext.<init>(SparkContext.scala:85)
is.hail.backend.spark.SparkBackend$.configureAndCreateSparkContext(SparkBackend.scala:148)
is.hail.backend.spark.SparkBackend$.apply(SparkBackend.scala:230)
is.hail.backend.spark.SparkBackend.apply(SparkBackend.scala)
java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
java.base/java.lang.reflect.Method.invoke(Method.java:577)
py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
py4j.Gateway.invoke(Gateway.java:282)
py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
py4j.commands.CallCommand.execute(CallCommand.java:79)
py4j.GatewayConnection.run(GatewayConnection.java:238)
java.base/java.lang.Thread.run(Thread.java:833)
Quitting from lines 65-75 (large_t2t.Rmd) 
Error: processing vignette 'large_t2t.Rmd' failed with diagnostics:
py4j.protocol.Py4JJavaError: An error occurred while calling z:is.hail.backend.spark.SparkBackend.apply.
<... omitted ...>ke(ReflectionEngine.java:357)
	at py4j.Gateway.invoke(Gateway.java:282)
	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
	at py4j.commands.CallCommand.execute(CallCommand.java:79)
	at py4j.GatewayConnection.run(GatewayConnection.java:238)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.ExceptionInInitializerError: Exception java.lang.IllegalAccessError: class org.apache.spark.storage.StorageUtils$ (in unnamed module @0x6671dc81) cannot access class sun.nio.ch.DirectBuffer (in module java.base) because module java.base does not export sun.nio.ch to unnamed module @0x6671dc81 [in thread "Thread-3"]
	at org.apache.spark.storage.StorageUtils$.<init>(StorageUtils.scala:213)
	at org.apache.spark.storage.StorageUtils$.<clinit>(StorageUtils.scala)
	... 19 more

See `reticulate::py_last_error()` for details
--- failed re-building ‘large_t2t.Rmd’

--- re-building ‘ukbb.Rmd’ using rmarkdown
2023-03-26 21:52:35.629 WARN  SparkContext:69 - Another SparkContext is being constructed (or threw an exception in its constructor). This may indicate an error, since only one SparkContext should be running in this JVM (see SPARK-2243). The other SparkContext was created at:
org.apache.spark.SparkContext.<init>(SparkContext.scala:85)
is.hail.backend.spark.SparkBackend$.configureAndCreateSparkContext(SparkBackend.scala:148)
is.hail.backend.spark.SparkBackend$.apply(SparkBackend.scala:230)
is.hail.backend.spark.SparkBackend.apply(SparkBackend.scala)
java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
java.base/java.lang.reflect.Method.invoke(Method.java:577)
py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
py4j.Gateway.invoke(Gateway.java:282)
py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
py4j.commands.CallCommand.execute(CallCommand.java:79)
py4j.GatewayConnection.run(GatewayConnection.java:238)
java.base/java.lang.Thread.run(Thread.java:833)
Initializing Hail with default parameters...
2023-03-26 21:53:52.489 WARN  SparkContext:69 - Another SparkContext is being constructed (or threw an exception in its constructor). This may indicate an error, since only one SparkContext should be running in this JVM (see SPARK-2243). The other SparkContext was created at:
org.apache.spark.SparkContext.<init>(SparkContext.scala:85)
is.hail.backend.spark.SparkBackend$.configureAndCreateSparkContext(SparkBackend.scala:148)
is.hail.backend.spark.SparkBackend$.apply(SparkBackend.scala:230)
is.hail.backend.spark.SparkBackend.apply(SparkBackend.scala)
java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
java.base/java.lang.reflect.Method.invoke(Method.java:577)
py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
py4j.Gateway.invoke(Gateway.java:282)
py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
py4j.commands.CallCommand.execute(CallCommand.java:79)
py4j.GatewayConnection.run(GatewayConnection.java:238)
java.base/java.lang.Thread.run(Thread.java:833)
Quitting from lines 38-42 (ukbb.Rmd) 
Error: processing vignette 'ukbb.Rmd' failed with diagnostics:
py4j.protocol.Py4JJavaError: An error occurred while calling z:is.hail.backend.spark.SparkBackend.apply.
<... omitted ...>ke(ReflectionEngine.java:357)
	at py4j.Gateway.invoke(Gateway.java:282)
	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
	at py4j.commands.CallCommand.execute(CallCommand.java:79)
	at py4j.GatewayConnection.run(GatewayConnection.java:238)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.ExceptionInInitializerError: Exception java.lang.IllegalAccessError: class org.apache.spark.storage.StorageUtils$ (in unnamed module @0x6671dc81) cannot access class sun.nio.ch.DirectBuffer (in module java.base) because module java.base does not export sun.nio.ch to unnamed module @0x6671dc81 [in thread "Thread-3"]
	at org.apache.spark.storage.StorageUtils$.<init>(StorageUtils.scala:213)
	at org.apache.spark.storage.StorageUtils$.<clinit>(StorageUtils.scala)
	... 19 more

See `reticulate::py_last_error()` for details
--- 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

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