Comments (4)
- # Java
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew cask install java; fi
- # Java 8
- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -qq oracle-java8-installer; fi
- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install oracle-java8-set-default; fi
from beastier.
- # Java
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew cask install java; fi
- # Java 8
- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -qq oracle-java8-installer; fi
- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install oracle-java8-set-default; fi
from beastier.
Got error:
> test_check("beastier")
── 1. Error: use, fast (@test-are_beast2_input_lines.R#5) ─────────────────────
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Users/travis/R/Library/rJava/libs/rJava.so':
dlopen(/Users/travis/R/Library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server/libjvm.dylib
Referenced from: /Users/travis/R/Library/rJava/libs/rJava.so
Reason: image not found
1: testthat::expect_true(beastier::are_beast2_input_lines(readLines(beastier::get_beastier_path("anthus_2_4.xml")))) at testthat/test-are_beast2_input_lines.R:5
2: quasi_label(enquo(object), label)
3: eval_bare(get_expr(quo), get_env(quo))
4: beastier::are_beast2_input_lines(readLines(beastier::get_beastier_path("anthus_2_4.xml")))
5: are_beast2_input_lines_deep(lines = lines, verbose = verbose, beast2_path = beast2_path)
6: is_beast2_input_file(filename = filename, verbose = verbose, beast2_path = beast2_path)
7: beastier::create_beast2_validate_cmd(input_filename = filename, beast2_path = beast2_path)
8: create_beast2_validate_cmd_jar(input_filename = input_filename, beast2_jar_path = beast2_path)
9: get_default_java_path()
10: rJava::.jinit
11: getExportedValue(pkg, name)
12: asNamespace(ns)
13: getNamespace(ns)
14: tryCatch(loadNamespace(name), error = function(e) stop(e))
15: tryCatchList(expr, classes, parentenv, handlers)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: value[[3L]](cond)
Thanks to https://github.com/snowflakedb/dplyr-snowflakedb/wiki/Configuring-R-rJava-RJDBC-on-Mac-OS-X, I added:
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then R --quiet -e 'install.packages("rJava", type="source", repos="http://cran.us.r-project.org")'; fi
from beastier.
Done!
from beastier.
Related Issues (20)
- Deprecate BEAST2 options for output filenames HOT 1
- Prevent BEAST2 freeze when overwriting a log file with overwrite set to false
- is_beast2_input_file should suppress warnings
- Add 'save_nexus_as_fasta' function
- BEAST2 run must check if alignment.trees exists? HOT 3
- How to call tree operator HOT 2
- Cannot find bin path HOT 1
- Prettyprint beast2_options HOT 1
- Better error message when calling 'get_beast2_example_filename' without BEAST2 installed
- Fix: CRAN package beastier -- policy violation HOT 7
- Fix CRAN feedback on v2.4.4 HOT 1
- Increase BEAS2 stack size HOT 1
- How to use Beagle HOT 2
- Test failure on Windows release HOT 7
- Cannot create treelog file 'NA' HOT 5
- Speed up `run_beast2` calculation HOT 1
- Fix new CRAN warnings HOT 3
- Get Codecov to 100% again
- Error: length(treelog_line) not equal to 1. HOT 5
- use of dependency archived on CRAN: assertive HOT 3
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from beastier.