===============================
BiocCheckGitClone('BiocHail')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: BiocHail
─ PackageVersion: 0.99.14
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2947/b91dde0c24377a9ba63dfbf44329c8c90a7a09dc/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/b91dde0c24377a9ba63dfbf44329c8c90a7a09dc/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 ‘0.99.14’
* 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 ... [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 ... [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 ... WARNING
filter:
function(x, filter, method, sides, circular, init, ..., hl,
placeholder, drop_placeholder)
filter.hail.table.Table:
function(x, filter, hl, placeholder, drop_placeholder, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [7s/7s] NOTE
filter.hail.table.Table: no visible global function definition for ‘is’
Undefined global functions or variables:
is
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
Undocumented arguments in documentation object 'as.data.frame'
‘x’ ‘row.names’ ‘optional’ ‘...’
Undocumented arguments in documentation object 'as.data.frame.default'
‘x’ ‘row.names’ ‘optional’ ‘...’
Undocumented arguments in documentation object 'colnames'
‘x’ ‘do.NULL’ ‘prefix’
Undocumented arguments in documentation object 'colnames.default'
‘...’
Undocumented arguments in documentation object 'colnames.hail.table.Table'
‘...’
Undocumented arguments in documentation object 'filter'
‘x’ ‘filter’ ‘method’ ‘sides’ ‘circular’ ‘init’ ‘...’ ‘hl’
‘placeholder’ ‘drop_placeholder’
Undocumented arguments in documentation object 'filter.default'
‘...’
Undocumented arguments in documentation object 'filter.hail.table.Table'
‘...’
Undocumented arguments in documentation object 'rownames'
‘x’ ‘do.NULL’ ‘prefix’
Undocumented arguments in documentation object 'rownames.default'
‘...’
Undocumented arguments in documentation object 'rownames.hail.table.Table'
‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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, 3 WARNINGs, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2947/b91dde0c24377a9ba63dfbf44329c8c90a7a09dc/BiocHail.Rcheck/00check.log’
for details.
===============================
BiocCheck('BiocHail_0.99.14.tar.gz')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: BiocHail
─ PackageVersion: 0.99.14
─ sourceDir: /tmp/RtmpcCNf7D/file34b34a719f6204/BiocHail
─ installDir: /tmp/RtmpcCNf7D/file34b34a3a082d8e
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2947/b91dde0c24377a9ba63dfbf44329c8c90a7a09dc/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. 6% 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; 214 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 ──
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
PREFIX=/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/0
Unpacking payload ...
0%| | 0/35 [00:00<?, ?it/s]
Extracting : brotlipy-0.7.0-py38h9ed2024_1003.conda: 0%| | 0/35 [00:00<?, ?it/s]
Extracting : brotlipy-0.7.0-py38h9ed2024_1003.conda: 3%|▎ | 1/35 [00:00<00:29, 1.16it/s]
Extracting : ca-certificates-2022.3.29-hecd8cb5_1.conda: 3%|▎ | 1/35 [00:01<00:29, 1.16it/s]
Extracting : ca-certificates-2022.3.29-hecd8cb5_1.conda: 6%|▌ | 2/35 [00:01<00:16, 2.06it/s]
Extracting : certifi-2021.10.8-py38hecd8cb5_2.conda: 6%|▌ | 2/35 [00:01<00:16, 2.06it/s]
Extracting : cffi-1.15.0-py38hc55c11b_1.conda: 9%|▊ | 3/35 [00:02<00:15, 2.06it/s]
Extracting : cffi-1.15.0-py38hc55c11b_1.conda: 11%|█▏ | 4/35 [00:02<00:21, 1.43it/s]
Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda: 11%|█▏ | 4/35 [00:02<00:21, 1.43it/s]
Extracting : colorama-0.4.4-pyhd3eb1b0_0.conda: 14%|█▍ | 5/35 [00:02<00:21, 1.43it/s]
Extracting : conda-4.12.0-py38hecd8cb5_0.conda: 17%|█▋ | 6/35 [00:08<00:20, 1.43it/s]
Extracting : conda-4.12.0-py38hecd8cb5_0.conda: 20%|██ | 7/35 [00:08<00:37, 1.35s/it]
Extracting : conda-content-trust-0.1.1-pyhd3eb1b0_0.conda: 20%|██ | 7/35 [00:08<00:37, 1.35s/it]
Extracting : conda-package-handling-1.8.1-py38hca72f7f_0.conda: 23%|██▎ | 8/35 [00:08<00:36, 1.35s/it]
Extracting : cryptography-36.0.0-py38hf6deb26_0.conda: 26%|██▌ | 9/35 [00:08<00:35, 1.35s/it]
Extracting : idna-3.3-pyhd3eb1b0_0.conda: 29%|██▊ | 10/35 [00:08<00:33, 1.35s/it]
Extracting : libcxx-12.0.0-h2f01273_0.conda: 31%|███▏ | 11/35 [00:08<00:32, 1.35s/it]
Extracting : libffi-3.3-hb1e8313_2.conda: 34%|███▍ | 12/35 [00:08<00:31, 1.35s/it]
Extracting : ncurses-6.3-hca72f7f_2.conda: 37%|███▋ | 13/35 [00:08<00:29, 1.35s/it]
Extracting : openssl-1.1.1n-hca72f7f_0.conda: 40%|████ | 14/35 [00:08<00:28, 1.35s/it]
Extracting : pip-21.2.4-py38hecd8cb5_0.conda: 43%|████▎ | 15/35 [00:08<00:27, 1.35s/it]
Extracting : pycosat-0.6.3-py38h1de35cc_1.conda: 46%|████▌ | 16/35 [00:08<00:25, 1.35s/it]
Extracting : pycparser-2.21-pyhd3eb1b0_0.conda: 49%|████▊ | 17/35 [00:08<00:24, 1.35s/it]
Extracting : pyopenssl-22.0.0-pyhd3eb1b0_0.conda: 51%|█████▏ | 18/35 [00:08<00:23, 1.35s/it]
Extracting : pysocks-1.7.1-py38_1.conda: 54%|█████▍ | 19/35 [00:08<00:21, 1.35s/it]
Extracting : python-3.8.13-hdfd78df_0.conda: 57%|█████▋ | 20/35 [00:08<00:20, 1.35s/it]
Extracting : python.app-3-py38hca72f7f_0.conda: 60%|██████ | 21/35 [00:08<00:18, 1.35s/it]
Extracting : readline-8.1.2-hca72f7f_1.conda: 63%|██████▎ | 22/35 [00:08<00:17, 1.35s/it]
Extracting : requests-2.27.1-pyhd3eb1b0_0.conda: 66%|██████▌ | 23/35 [00:08<00:16, 1.35s/it]
Extracting : ruamel_yaml-0.15.100-py38h9ed2024_0.conda: 69%|██████▊ | 24/35 [00:08<00:14, 1.35s/it]
Extracting : setuptools-61.2.0-py38hecd8cb5_0.conda: 71%|███████▏ | 25/35 [00:08<00:13, 1.35s/it]
Extracting : six-1.16.0-pyhd3eb1b0_1.conda: 74%|███████▍ | 26/35 [00:08<00:12, 1.35s/it]
Extracting : sqlite-3.38.2-h707629a_0.conda: 77%|███████▋ | 27/35 [00:08<00:10, 1.35s/it]
Extracting : tk-8.6.11-h7bc2e8c_0.conda: 80%|████████ | 28/35 [00:08<00:09, 1.35s/it]
Extracting : tqdm-4.63.0-pyhd3eb1b0_0.conda: 83%|████████▎ | 29/35 [00:08<00:08, 1.35s/it]
Extracting : urllib3-1.26.8-pyhd3eb1b0_0.conda: 86%|████████▌ | 30/35 [00:08<00:06, 1.35s/it]
Extracting : wheel-0.37.1-pyhd3eb1b0_0.conda: 89%|████████▊ | 31/35 [00:08<00:05, 1.35s/it]
Extracting : xz-5.2.5-h1de35cc_0.conda: 91%|█████████▏| 32/35 [00:08<00:04, 1.35s/it]
Extracting : yaml-0.2.5-haf1e3a3_0.conda: 94%|█████████▍| 33/35 [00:08<00:02, 1.35s/it]
Extracting : zlib-1.2.12-h4dc903c_1.conda: 97%|█████████▋| 34/35 [00:08<00:01, 1.35s/it]
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/1.11.3/0
added / updated specs:
- brotlipy==0.7.0=py38h9ed2024_1003
- ca-certificates==2022.3.29=hecd8cb5_1
- certifi==2021.10.8=py38hecd8cb5_2
- cffi==1.15.0=py38hc55c11b_1
- charset-normalizer==2.0.4=pyhd3eb1b0_0
- colorama==0.4.4=pyhd3eb1b0_0
- conda-content-trust==0.1.1=pyhd3eb1b0_0
- conda-package-handling==1.8.1=py38hca72f7f_0
- conda==4.12.0=py38hecd8cb5_0
- cryptography==36.0.0=py38hf6deb26_0
- idna==3.3=pyhd3eb1b0_0
- libcxx==12.0.0=h2f01273_0
- libffi==3.3=hb1e8313_2
- ncurses==6.3=hca72f7f_2
- openssl==1.1.1n=hca72f7f_0
- pip==21.2.4=py38hecd8cb5_0
- pycosat==0.6.3=py38h1de35cc_1
- pycparser==2.21=pyhd3eb1b0_0
- pyopenssl==22.0.0=pyhd3eb1b0_0
- pysocks==1.7.1=py38_1
- python.app==3=py38hca72f7f_0
- python==3.8.13=hdfd78df_0
- readline==8.1.2=hca72f7f_1
- requests==2.27.1=pyhd3eb1b0_0
- ruamel_yaml==0.15.100=py38h9ed2024_0
- setuptools==61.2.0=py38hecd8cb5_0
- six==1.16.0=pyhd3eb1b0_1
- sqlite==3.38.2=h707629a_0
- tk==8.6.11=h7bc2e8c_0
- tqdm==4.63.0=pyhd3eb1b0_0
- urllib3==1.26.8=pyhd3eb1b0_0
- wheel==0.37.1=pyhd3eb1b0_0
- xz==5.2.5=h1de35cc_0
- yaml==0.2.5=haf1e3a3_0
- zlib==1.2.12=h4dc903c_1
The following NEW packages will be INSTALLED:
brotlipy pkgs/main/osx-64::brotlipy-0.7.0-py38h9ed2024_1003
ca-certificates pkgs/main/osx-64::ca-certificates-2022.3.29-hecd8cb5_1
certifi pkgs/main/osx-64::certifi-2021.10.8-py38hecd8cb5_2
cffi pkgs/main/osx-64::cffi-1.15.0-py38hc55c11b_1
charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
colorama pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
conda pkgs/main/osx-64::conda-4.12.0-py38hecd8cb5_0
conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.8.1-py38hca72f7f_0
cryptography pkgs/main/osx-64::cryptography-36.0.0-py38hf6deb26_0
idna pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
libcxx pkgs/main/osx-64::libcxx-12.0.0-h2f01273_0
libffi pkgs/main/osx-64::libffi-3.3-hb1e8313_2
ncurses pkgs/main/osx-64::ncurses-6.3-hca72f7f_2
openssl pkgs/main/osx-64::openssl-1.1.1n-hca72f7f_0
pip pkgs/main/osx-64::pip-21.2.4-py38hecd8cb5_0
pycosat pkgs/main/osx-64::pycosat-0.6.3-py38h1de35cc_1
pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
pyopenssl pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
pysocks pkgs/main/osx-64::pysocks-1.7.1-py38_1
python pkgs/main/osx-64::python-3.8.13-hdfd78df_0
python.app pkgs/main/osx-64::python.app-3-py38hca72f7f_0
readline pkgs/main/osx-64::readline-8.1.2-hca72f7f_1
requests pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
ruamel_yaml pkgs/main/osx-64::ruamel_yaml-0.15.100-py38h9ed2024_0
setuptools pkgs/main/osx-64::setuptools-61.2.0-py38hecd8cb5_0
six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
sqlite pkgs/main/osx-64::sqlite-3.38.2-h707629a_0
tk pkgs/main/osx-64::tk-8.6.11-h7bc2e8c_0
tqdm pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0
urllib3 pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
xz pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
yaml pkgs/main/osx-64::yaml-0.2.5-haf1e3a3_0
zlib pkgs/main/osx-64::zlib-1.2.12-h4dc903c_1
Preparing transaction: ...working... done
Executing transaction: ...working...
done
installation finished.
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/0.99.14/bsklenv
added / updated specs:
- python=3.8.13
The following packages will be downloaded:
package | build
---------------------------|-----------------
bzip2-1.0.8 | h0d85af4_4 155 KB conda-forge
ca-certificates-2022.12.7 | h033912b_0 142 KB conda-forge
libffi-3.4.2 | h0d85af4_5 50 KB conda-forge
libsqlite-3.40.0 | ha978bb4_0 873 KB conda-forge
libzlib-1.2.13 | hfd90126_4 64 KB conda-forge
ncurses-6.3 | h96cf925_1 915 KB conda-forge
openssl-3.1.0 | hfd90126_0 2.2 MB conda-forge
pip-23.0.1 | pyhd8ed1ab_0 1.3 MB conda-forge
python-3.8.13 |h66c20e1_0_cpython 12.8 MB conda-forge
readline-8.1.2 | h3899abd_0 266 KB conda-forge
setuptools-67.6.0 | pyhd8ed1ab_0 566 KB conda-forge
sqlite-3.40.0 | h9ae0607_0 885 KB conda-forge
tk-8.6.12 | h5dbffcc_0 3.4 MB conda-forge
wheel-0.40.0 | pyhd8ed1ab_0 54 KB conda-forge
xz-5.2.6 | h775f41a_0 233 KB conda-forge
------------------------------------------------------------
Total: 23.8 MB
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/0.99.14/bsklenv
added / updated specs:
- python=3.8.13
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2023.01.10 | hecd8cb5_0 121 KB
------------------------------------------------------------
Total: 121 KB
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hecd8cb5_0
Downloading and Extracting Packages
ca-certificates-2023 | 121 KB | | 0%
ca-certificates-2023 | 121 KB | ########## | 100%
ca-certificates-2023 | 121 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 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/0.99.14/bsklenv
added / updated specs:
- pandas=1.3.5
- python=3.8.13
The following packages will be downloaded:
package | build
---------------------------|-----------------
bottleneck-1.3.7 | py38hbd87e4b_0 124 KB conda-forge
libblas-3.9.0 |16_osx64_openblas 13 KB conda-forge
libcblas-3.9.0 |16_osx64_openblas 13 KB conda-forge
libcxx-15.0.7 | h71dddab_0 1.1 MB conda-forge
libgfortran-5.0.0 |11_3_0_h97931a8_31 156 KB conda-forge
libgfortran5-12.2.0 | he409387_31 1.5 MB conda-forge
liblapack-3.9.0 |16_osx64_openblas 13 KB conda-forge
libopenblas-0.3.21 |openmp_h429af6e_3 9.6 MB conda-forge
llvm-openmp-15.0.7 | h61d9ccf_0 287 KB conda-forge
numexpr-2.8.3 | py38hec72209_1 129 KB conda-forge
numpy-1.24.2 | py38h5a2dcdf_0 6.0 MB conda-forge
packaging-23.0 | pyhd8ed1ab_0 40 KB conda-forge
pandas-1.3.5 | py38h743cdd8_0 9.1 MB
python-dateutil-2.8.2 | pyhd8ed1ab_0 240 KB conda-forge
python_abi-3.8 | 3_cp38 6 KB conda-forge
pytz-2022.7.1 | pyhd8ed1ab_0 182 KB conda-forge
six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge
------------------------------------------------------------
Total: 28.5 MB
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-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
Downloading and Extracting Packages
libcblas-3.9.0 | 13 KB | | 0%
libcblas-3.9.0 | 13 KB | ########## | 100%
libcblas-3.9.0 | 13 KB | ########## | 100%
pandas-1.3.5 | 9.1 MB | | 0%
pandas-1.3.5 | 9.1 MB | ##2 | 22%
pandas-1.3.5 | 9.1 MB | #######9 | 79%
pandas-1.3.5 | 9.1 MB | ########## | 100%
libcxx-15.0.7 | 1.1 MB | | 0%
libcxx-15.0.7 | 1.1 MB | ########## | 100%
libcxx-15.0.7 | 1.1 MB | ########## | 100%
pytz-2022.7.1 | 182 KB | | 0%
pytz-2022.7.1 | 182 KB | ########## | 100%
pytz-2022.7.1 | 182 KB | ########## | 100%
packaging-23.0 | 40 KB | | 0%
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packaging-23.0 | 40 KB | ########## | 100%
libblas-3.9.0 | 13 KB | | 0%
libblas-3.9.0 | 13 KB | ########## | 100%
liblapack-3.9.0 | 13 KB | | 0%
liblapack-3.9.0 | 13 KB | ########## | 100%
python_abi-3.8 | 6 KB | | 0%
python_abi-3.8 | 6 KB | ########## | 100%
python_abi-3.8 | 6 KB | ########## | 100%
libgfortran5-12.2.0 | 1.5 MB | | 0%
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libgfortran5-12.2.0 | 1.5 MB | ########## | 100%
llvm-openmp-15.0.7 | 287 KB | | 0%
llvm-openmp-15.0.7 | 287 KB | ########## | 100%
llvm-openmp-15.0.7 | 287 KB | ########## | 100%
python-dateutil-2.8. | 240 KB | | 0%
python-dateutil-2.8. | 240 KB | ########## | 100%
python-dateutil-2.8. | 240 KB | ########## | 100%
numpy-1.24.2 | 6.0 MB | | 0%
numpy-1.24.2 | 6.0 MB | ######3 | 64%
numpy-1.24.2 | 6.0 MB | ########## | 100%
libgfortran-5.0.0 | 156 KB | | 0%
libgfortran-5.0.0 | 156 KB | ########## | 100%
libgfortran-5.0.0 | 156 KB | ########## | 100%
six-1.16.0 | 14 KB | | 0%
six-1.16.0 | 14 KB | ########## | 100%
numexpr-2.8.3 | 129 KB | | 0%
numexpr-2.8.3 | 129 KB | ########## | 100%
bottleneck-1.3.7 | 124 KB | | 0%
bottleneck-1.3.7 | 124 KB | ########## | 100%
bottleneck-1.3.7 | 124 KB | ########## | 100%
libopenblas-0.3.21 | 9.6 MB | | 0%
libopenblas-0.3.21 | 9.6 MB | ###9 | 39%
libopenblas-0.3.21 | 9.6 MB | ########3 | 84%
libopenblas-0.3.21 | 9.6 MB | ########## | 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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Downloading boto3-1.26.94-py3-none-any.whl (135 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 135.1/135.1 kB 2.8 MB/s eta 0:00:00
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Using cached asyncinit-0.2.4-py3-none-any.whl (2.8 kB)
Collecting rich==12.6.0
Using cached rich-12.6.0-py3-none-any.whl (237 kB)
Collecting requests<3,>=2.25.1
Using cached requests-2.28.2-py3-none-any.whl (62 kB)
Collecting orjson<4,>=3.6.4
Using cached orjson-3.8.7-cp38-cp38-macosx_10_9_x86_64.macosx_11_0_arm64.macosx_10_9_universal2.whl (489 kB)
Collecting plotly<5.11,>=5.5.0
Using cached plotly-5.10.0-py2.py3-none-any.whl (15.2 MB)
Collecting botocore<2.0,>=1.20
Downloading botocore-1.29.94-py3-none-any.whl (10.5 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.5/10.5 MB 11.1 MB/s eta 0:00:00
Collecting Deprecated<1.3,>=1.2.10
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Using cached azure_identity-1.12.0-py3-none-any.whl (135 kB)
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Using cached aiohttp_session-2.12.0-py3-none-any.whl (12 kB)
Collecting python-json-logger<3,>=2.0.2
Using cached python_json_logger-2.0.7-py3-none-any.whl (8.1 kB)
Requirement already satisfied: numpy<2 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/BiocHail/0.99.14/bsklenv/lib/python3.8/site-packages (from hail==0.2.108) (1.24.2)
Collecting uvloop<1,>=0.16.0
Using cached uvloop-0.17.0-cp38-cp38-macosx_10_9_x86_64.whl (1.5 MB)
Collecting azure-storage-blob<13,>=12.11.0
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Collecting pyspark<3.2.0,>=3.1.1
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Collecting hurry.filesize<1,>=0.9
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Collecting Jinja2==3.0.3
Using cached Jinja2-3.0.3-py3-none-any.whl (133 kB)
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/0.99.14/bsklenv/lib/python3.8/site-packages (from hail==0.2.108) (1.3.5)
Collecting parsimonious<0.9
Using cached parsimonious-0.8.1-py3-none-any.whl
Collecting bokeh==1.4.0
Using cached bokeh-1.4.0-py3-none-any.whl
Collecting PyJWT
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Collecting tabulate<1,>=0.8.9
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Collecting scipy<1.10,>1.2
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Collecting PyYAML>=3.10
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Collecting pillow>=4.0
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Requirement already satisfied: six>=1.5.2 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/BiocHail/0.99.14/bsklenv/lib/python3.8/site-packages (from bokeh==1.4.0->hail==0.2.108) (1.16.0)
Requirement already satisfied: python-dateutil>=2.1 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/BiocHail/0.99.14/bsklenv/lib/python3.8/site-packages (from bokeh==1.4.0->hail==0.2.108) (2.8.2)
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Collecting attrs>=17.3.0
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Collecting msal<2.0.0,>=1.12.0
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Collecting cryptography>=2.5
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Collecting urllib3<1.27,>=1.25.4
Downloading urllib3-1.26.15-py2.py3-none-any.whl (140 kB)
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Requirement already satisfied: pytz>=2017.3 in /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.3/BiocHail/0.99.14/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 boto3-1.26.94 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/0.99.14/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/0.99.14/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/0.99.14/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/0.99.14/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/0.99.14/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/0.99.14/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/0.99.14/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/0.99.14/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/0.99.14/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/0.99.14/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/0.99.14/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/0.99.14/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