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
merida1	macOS 10.14.6 Mojave/x86_64	ERROR	skipped	skipped	skipped
nebbiolo1	/	OK	ERROR	skipped	OK

merida1 Summary

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Package: BiocHail

Version: 0.99.8

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: 7 minutes 28.00 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: BiocHail_20230303163653

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: 1. 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... done

## Package Plan ##

  environment location: /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.8/bsklenv

  added / updated specs:
    - python=3.8.13


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2022.12.7-h033912b_0
  libcxx             conda-forge/osx-64::libcxx-15.0.7-h71dddab_0
  libffi             conda-forge/osx-64::libffi-3.3-h046ec9c_2
  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-1.1.1t-hfd90126_0
  pip                conda-forge/noarch::pip-23.0.1-pyhd8ed1ab_0
  python             pkgs/main/osx-64::python-3.8.13-hdfd78df_1
  readline           conda-forge/osx-64::readline-8.1.2-h3899abd_0
  setuptools         conda-forge/noarch::setuptools-67.4.0-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-0.38.4-pyhd8ed1ab_0
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0
  zlib               conda-forge/osx-64::zlib-1.2.13-hfd90126_4


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/0.99.8/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

The following packages will be SUPERSEDED by a higher-priority channel:

  openssl            conda-forge::openssl-1.1.1t-hfd90126_0 --> pkgs/main::openssl-1.1.1t-hca72f7f_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... done

## Package Plan ##

  environment location: /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.8/bsklenv

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


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bottleneck-1.3.6           |   py38hbd87e4b_0         124 KB  conda-forge
    numexpr-2.8.3              |   py38hec72209_1         129 KB  conda-forge
    numpy-1.24.2               |   py38h5a2dcdf_0         6.0 MB  conda-forge
    pandas-1.3.5               |   py38h743cdd8_0         9.1 MB
    ------------------------------------------------------------
                                           Total:        15.3 MB

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
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-10_4_0_h97931a8_28
  libgfortran5       conda-forge/osx-64::libgfortran5-11.3.0-h082f757_28
  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-3.8-2_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
  openssl              pkgs/main::openssl-1.1.1t-hca72f7f_0 --> conda-forge::openssl-1.1.1t-hfd90126_0



Downloading and Extracting Packages

numexpr-2.8.3        | 129 KB    |            |   0% 
numexpr-2.8.3        | 129 KB    | ########## | 100% 
numexpr-2.8.3        | 129 KB    | ########## | 100% 

numpy-1.24.2         | 6.0 MB    |            |   0% 
numpy-1.24.2         | 6.0 MB    | ########## | 100% 
numpy-1.24.2         | 6.0 MB    | ########## | 100% 

pandas-1.3.5         | 9.1 MB    |            |   0% 
pandas-1.3.5         | 9.1 MB    | #####4     |  55% 
pandas-1.3.5         | 9.1 MB    | ########## | 100% 

bottleneck-1.3.6     | 124 KB    |            |   0% 
bottleneck-1.3.6     | 124 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
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Collecting pyspark<3.2.0,>=3.1.1
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Collecting requests<3,>=2.25.1
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Collecting Jinja2==3.0.3
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Collecting plotly<5.11,>=5.5.0
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Collecting hurry.filesize<1,>=0.9
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Collecting azure-core<2.0.0,>=1.11.0
  Downloading azure_core-1.26.3-py3-none-any.whl (174 kB)
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Collecting cryptography>=2.5
  Downloading cryptography-39.0.2-cp36-abi3-macosx_10_12_x86_64.whl (2.9 MB)
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Collecting isodate>=0.6.1
  Downloading isodate-0.6.1-py2.py3-none-any.whl (41 kB)
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Collecting jmespath<2.0.0,>=0.7.1
  Downloading jmespath-1.0.1-py3-none-any.whl (20 kB)
Collecting s3transfer<0.7.0,>=0.6.0
  Downloading s3transfer-0.6.0-py3-none-any.whl (79 kB)
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Collecting urllib3<1.27,>=1.25.4
  Using cached urllib3-1.26.14-py2.py3-none-any.whl (140 kB)
Collecting wrapt<2,>=1.10
  Downloading wrapt-1.15.0-cp38-cp38-macosx_10_9_x86_64.whl (35 kB)
Collecting google-resumable-media>=2.3.2
  Downloading google_resumable_media-2.4.1-py2.py3-none-any.whl (77 kB)
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Collecting google-cloud-core<3.0dev,>=2.3.0
  Downloading google_cloud_core-2.3.2-py2.py3-none-any.whl (29 kB)
Collecting google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.5
  Downloading google_api_core-2.11.0-py3-none-any.whl (120 kB)
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Requirement already satisfied: setuptools in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.8/bsklenv/lib/python3.8/site-packages (from hurry.filesize<1,>=0.9->hail==0.2.108) (67.4.0)
Requirement already satisfied: pytz>=2017.3 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/BiocHail/0.99.8/bsklenv/lib/python3.8/site-packages (from pandas<1.5.0,>=1.3.0->hail==0.2.108) (2022.7.1)
Collecting tenacity>=6.2.0
  Downloading tenacity-8.2.2-py3-none-any.whl (24 kB)
Collecting py4j==0.10.9
  Downloading py4j-0.10.9-py2.py3-none-any.whl (198 kB)
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Collecting idna<4,>=2.5
  Using cached idna-3.4-py3-none-any.whl (61 kB)
Collecting certifi>=2017.4.17
  Using cached certifi-2022.12.7-py3-none-any.whl (155 kB)
Collecting cffi>=1.12
  Downloading cffi-1.15.1-cp38-cp38-macosx_10_9_x86_64.whl (178 kB)
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Collecting googleapis-common-protos<2.0dev,>=1.56.2
  Downloading googleapis_common_protos-1.58.0-py2.py3-none-any.whl (223 kB)
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Collecting google-crc32c<2.0dev,>=1.0
  Downloading google_crc32c-1.5.0-cp38-cp38-macosx_10_9_x86_64.whl (30 kB)
Collecting portalocker<3,>=1.0
  Downloading portalocker-2.7.0-py2.py3-none-any.whl (15 kB)
Collecting pyasn1<0.5.0,>=0.4.6
  Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB)
Collecting pycparser
  Using cached pycparser-2.21-py2.py3-none-any.whl (118 kB)
Building wheels for collected packages: bokeh, avro, hurry.filesize, parsimonious, pyspark
  Building wheel for bokeh (setup.py): started
  Building wheel for bokeh (setup.py): finished with status 'done'
  Created wheel for bokeh: filename=bokeh-1.4.0-py3-none-any.whl size=23689194 sha256=f623a1acfdf9b0b0a5575483802a34b7d69ea60df93ed82bd59097ae72421ae5
  Stored in directory: /Users/pkgbuild/Library/Caches/pip/wheels/4a/79/96/e953cfb5c24da5e5e03eb1ecb280ca88dce65661fb4d38c7b5
  Building wheel for avro (pyproject.toml): started
  Building wheel for avro (pyproject.toml): finished with status 'done'
  Created wheel for avro: filename=avro-1.11.1-py2.py3-none-any.whl size=116717 sha256=a199204537a6b987d819acf61fdb46f59e3b0cc1008c9ef0622ec347ce74839b
  Stored in directory: /Users/pkgbuild/Library/Caches/pip/wheels/27/d5/22/e3641b9a6a2669624c1d515f942bf8187f03c5c2151e13a76e
  Building wheel for hurry.filesize (setup.py): started
  Building wheel for hurry.filesize (setup.py): finished with status 'done'
  Created wheel for hurry.filesize: filename=hurry.filesize-0.9-py3-none-any.whl size=4116 sha256=23b9114d0ecb829ced660e6bd879bca7e0ba4fd3b6599ded4af2b3b764e38336
  Stored in directory: /Users/pkgbuild/Library/Caches/pip/wheels/15/4b/2b/e1eaf7375b72542a9a3f3c3fa66b7098cc9e8048fe345deace
  Building wheel for parsimonious (setup.py): started
  Building wheel for parsimonious (setup.py): finished with status 'done'
  Created wheel for parsimonious: filename=parsimonious-0.8.1-py3-none-any.whl size=42707 sha256=fd55e7587024ff3b78da39cbdd9ad861ae01a078c2cc259cdfd054838f473cfb
  Stored in directory: /Users/pkgbuild/Library/Caches/pip/wheels/d8/af/19/fb896f509a437aca2dcf62583e84d7fb2cd5b628c1564a609c
  Building wheel for pyspark (setup.py): started
  Building wheel for pyspark (setup.py): finished with status 'done'
  Created wheel for pyspark: filename=pyspark-3.1.3-py2.py3-none-any.whl size=214463470 sha256=89c9a19424efccad1946391888e390fb548fe1cd8fb64fe45d5b43e573253269
  Stored in directory: /Users/pkgbuild/Library/Caches/pip/wheels/d1/b2/3a/d019c9382e6429910cef8ef0aae6a1970bfbbba13562590d70
Successfully built bokeh avro hurry.filesize parsimonious pyspark
Installing collected packages: sortedcontainers, pyasn1, py4j, commonmark, charset-normalizer, 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, 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 boto3-1.26.83 botocore-1.29.83 cachetools-5.3.0 certifi-2022.12.7 cffi-1.15.1 charset-normalizer-3.0.1 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/0.99.8/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/0.99.8/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/0.99.8/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/0.99.8/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/0.99.8/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/0.99.8/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/0.99.8/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/0.99.8/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/0.99.8/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/0.99.8/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/0.99.8/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/0.99.8/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

merida1 CHECK output

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merida1 BUILD BIN output

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nebbiolo1 Summary

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Package: BiocHail

Version: 0.99.8

RVersion:

BiocVersion: 3.17

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

BuildTime: 9 minutes 44.37 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/BiocHail_20230303163653/BiocHail.install-out.txt BiocHail_0.99.8.tar.gz && BiocCheck('BiocHail_0.99.8.tar.gz', `new-package`=TRUE)

CheckTime: 2 minutes 13.35 seconds

BuildBinCommand:

BuildBinTime:

PackageFileSize: 2592.70 KiB

BuildID:: BiocHail_20230303163653

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

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

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_0.99.8.tar.gz’

nebbiolo1 CHECK output

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

 BiocCheckGitClone('BiocHail')

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

─ BiocCheckVersion: 1.35.12
─ BiocVersion: 3.17
─ Package: BiocHail
─ PackageVersion: 0.99.8
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2947/BiocHail_20230303163653/BiocHail
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
    * ERROR: System files found that should not be Git tracked.
      docs/reference/hail-20230218-2105-0.2.108-fc03e9d5dc08.log
      docs/reference/hail-20230218-2107-0.2.108-fc03e9d5dc08.log
* 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 ──
1 ERRORS | 0 WARNINGS | 0 NOTES

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




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

 R CMD CHECK

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

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2947/BiocHail_20230303163653/BiocHail.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* 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 22.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* this is package ‘BiocHail’ version ‘0.99.8’
* 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 ... OK
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [7s/7s] 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 ... WARNING
  Warning: large data file saved inefficiently:
                size ASCII compress
  pcs_191k.rda 125Kb FALSE     none
* checking files in ‘vignettes’ ... OK
* checking examples ... [86s/69s] OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
get_ukbb_sumstat_10kloci_mt 35.467 10.353  46.157
get_1kg                      9.952 24.313  16.884
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [39s/13s]
 [39s/14s] 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 ... [2s/2s] OK
* DONE

Status: 1 WARNING
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2947/BiocHail_20230303163653/BiocHail.Rcheck/00check.log’
for details.






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

 BiocCheck('BiocHail_0.99.8.tar.gz')

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

─ BiocCheckVersion: 1.35.12
─ BiocVersion: 3.17
─ Package: BiocHail
─ PackageVersion: 0.99.8
─ sourceDir: /tmp/RtmpPV8Rkx/file169188467551c9/BiocHail
─ installDir: /tmp/RtmpPV8Rkx/file169188556c9d9c
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2947/BiocHail_20230303163653/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...
    * NOTE: Consider adding these automatically suggested biocViews:
      DataImport
Search 'biocViews' at https://contributions.bioconductor.org
* 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 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. 12% 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; 109 lines (7%) 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; 159 lines
      (11%) 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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