===============================
BiocCheckGitClone('BiocHail')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: BiocHail
─ PackageVersion: 0.99.15
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2947/f7ad123ba674d50a35fb42d6d3f06b45faed05c4/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/f7ad123ba674d50a35fb42d6d3f06b45faed05c4/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 ‘0.99.15’
* 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 ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
* checking loading without being on the library search path ... [0s/0s] WARNING
Error: package or namespace load failed for ‘BiocHail’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘BiocFileCache’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... [15s/16s] 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 ... NOTE
S3 methods shown with full name in documentation object 'as.data.frame.default':
‘as.data.frame.default’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [0s/0s] ERROR
Running examples in ‘BiocHail-Ex.R’ failed
The error occurred in:
R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> pkgname <- "BiocHail"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> base::assign(".ExTimings", "BiocHail-Ex.timings", pos = 'CheckExEnv')
> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
> base::assign(".format_ptime",
+ function(x) {
+ if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
+ if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
+ options(OutDec = '.')
+ format(x[1L:3L], digits = 7L)
+ },
+ pos = 'CheckExEnv')
>
> ### * </HEADER>
> library('BiocHail')
Error: package or namespace load failed for ‘BiocHail’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘BiocFileCache’
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’ [0s/0s]
[0s/0s] ERROR
Running the tests in ‘tests/test.R’ failed.
Complete output:
> library(testthat)
Error in library(testthat) : there is no package called 'testthat'
Execution halted
* 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: 2 ERRORs, 1 WARNING, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2947/f7ad123ba674d50a35fb42d6d3f06b45faed05c4/BiocHail.Rcheck/00check.log’
for details.
===============================
BiocCheck('BiocHail_0.99.15.tar.gz')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: BiocHail
─ PackageVersion: 0.99.15
─ sourceDir: /tmp/RtmpfFhFcX/file12a21165bcbf67/BiocHail
─ installDir: /tmp/RtmpfFhFcX/file12a211763c0e85
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2947/f7ad123ba674d50a35fb42d6d3f06b45faed05c4/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...
* WARNING: Non-empty \value sections found in man pages.
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 7% 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; 124 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; 204 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 ──
1 ERRORS | 1 WARNINGS | 11 NOTES
See the BiocHail.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
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/0.99.15/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-3.1.0-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-8.1.2-h3899abd_0
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/0.99.15/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/0.99.15/bsklenv
added / updated specs:
- pandas=1.3.5
- python=3.8.13
The following packages will be downloaded:
package | build
---------------------------|-----------------
llvm-openmp-16.0.0 | h61d9ccf_0 290 KB conda-forge
------------------------------------------------------------
Total: 290 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-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
Downloading and Extracting Packages
llvm-openmp-16.0.0 | 290 KB | | 0%
llvm-openmp-16.0.0 | 290 KB | 5 | 6%
llvm-openmp-16.0.0 | 290 KB | ########## | 100%
llvm-openmp-16.0.0 | 290 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)
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Requirement already satisfied: numpy<2 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/BiocHail/0.99.15/bsklenv/lib/python3.8/site-packages (from hail==0.2.108) (1.24.2)
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Collecting msal-extensions<2.0.0,>=0.3.0
Using cached msal_extensions-1.0.0-py2.py3-none-any.whl (19 kB)
Collecting cryptography>=2.5
Using cached cryptography-39.0.2-cp36-abi3-macosx_10_12_x86_64.whl (2.9 MB)
Collecting msal<2.0.0,>=1.12.0
Using cached msal-1.21.0-py2.py3-none-any.whl (89 kB)
Collecting azure-core<2.0.0,>=1.11.0
Using cached azure_core-1.26.3-py3-none-any.whl (174 kB)
Collecting isodate>=0.6.1
Using cached isodate-0.6.1-py2.py3-none-any.whl (41 kB)
Collecting s3transfer<0.7.0,>=0.6.0
Using cached s3transfer-0.6.0-py3-none-any.whl (79 kB)
Collecting jmespath<2.0.0,>=0.7.1
Using cached jmespath-1.0.1-py3-none-any.whl (20 kB)
Collecting urllib3<1.27,>=1.25.4
Using cached urllib3-1.26.15-py2.py3-none-any.whl (140 kB)
Collecting wrapt<2,>=1.10
Using cached wrapt-1.15.0-cp38-cp38-macosx_10_9_x86_64.whl (35 kB)
Collecting google-resumable-media>=2.3.2
Using cached google_resumable_media-2.4.1-py2.py3-none-any.whl (77 kB)
Collecting google-cloud-core<3.0dev,>=2.3.0
Using cached 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
Using cached google_api_core-2.11.0-py3-none-any.whl (120 kB)
Requirement already satisfied: setuptools in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/BiocHail/0.99.15/bsklenv/lib/python3.8/site-packages (from hurry.filesize<1,>=0.9->hail==0.2.108) (67.6.0)
Requirement already satisfied: pytz>=2017.3 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/BiocHail/0.99.15/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
Using cached tenacity-8.2.2-py3-none-any.whl (24 kB)
Collecting py4j==0.10.9
Using cached py4j-0.10.9-py2.py3-none-any.whl (198 kB)
Collecting certifi>=2017.4.17
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Collecting idna<4,>=2.5
Using cached idna-3.4-py3-none-any.whl (61 kB)
Collecting cffi>=1.12
Using cached cffi-1.15.1-cp38-cp38-macosx_10_9_x86_64.whl (178 kB)
Collecting googleapis-common-protos<2.0dev,>=1.56.2
Using cached googleapis_common_protos-1.58.0-py2.py3-none-any.whl (223 kB)
Collecting google-crc32c<2.0dev,>=1.0
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Collecting portalocker<3,>=1.0
Using cached 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)
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 boto3-1.26.94 botocore-1.29.94 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 urllib3-1.26.15 uvloop-0.17.0 wrapt-1.15.0 yarl-1.8.2
/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/BiocHail/0.99.15/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/1.11.3/BiocHail/0.99.15/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/1.11.3/BiocHail/0.99.15/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/1.11.3/BiocHail/0.99.15/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/1.11.3/BiocHail/0.99.15/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/1.11.3/BiocHail/0.99.15/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/1.11.3/BiocHail/0.99.15/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/1.11.3/BiocHail/0.99.15/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/1.11.3/BiocHail/0.99.15/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/1.11.3/BiocHail/0.99.15/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/1.11.3/BiocHail/0.99.15/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/1.11.3/BiocHail/0.99.15/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