galaaz 2.0.0 → 2.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (86) hide show
  1. checksums.yaml +4 -4
  2. data/CHANGELOG.md +25 -5
  3. data/README.md +119 -94
  4. data/Rakefile +17 -10
  5. data/bin/galaaz-jruby +3 -6
  6. data/bin/galaaz-ruby +16 -0
  7. data/bin/galaaz_ruby_env.inc.sh +36 -0
  8. data/bin/gbookdown +2 -3
  9. data/bin/gknit +2 -3
  10. data/bin/gstudio +4 -4
  11. data/bin/run_all_rspec +6 -5
  12. data/bin/run_example +10 -7
  13. data/bin/run_old_rspec +6 -5
  14. data/bin/run_rspec +9 -8
  15. data/bin/run_slow_rspec +6 -5
  16. data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-gfm/midwest_rb.png +0 -0
  17. data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-gfm/scatter_plot_rb.png +0 -0
  18. data/blogs/gknit/gknit_files/figure-gfm/bubble-1.png +0 -0
  19. data/blogs/gknit/gknit_files/figure-gfm/diverging_bar.png +0 -0
  20. data/blogs/manual/manual.Rmd +22 -19
  21. data/blogs/manual/manual.md +119 -94
  22. data/blogs/ruby_plot/ruby_plot_files/figure-gfm/dose_len.png +0 -0
  23. data/blogs/ruby_plot/ruby_plot_files/figure-gfm/facet_by_delivery.png +0 -0
  24. data/blogs/ruby_plot/ruby_plot_files/figure-gfm/facet_by_dose.png +0 -0
  25. data/blogs/ruby_plot/ruby_plot_files/figure-gfm/facets_by_delivery_color.png +0 -0
  26. data/blogs/ruby_plot/ruby_plot_files/figure-gfm/facets_by_delivery_color2.png +0 -0
  27. data/blogs/ruby_plot/ruby_plot_files/figure-gfm/facets_with_decorations.png +0 -0
  28. data/blogs/ruby_plot/ruby_plot_files/figure-gfm/facets_with_jitter.png +0 -0
  29. data/blogs/ruby_plot/ruby_plot_files/figure-gfm/facets_with_points.png +0 -0
  30. data/blogs/ruby_plot/ruby_plot_files/figure-gfm/final_box_plot.png +0 -0
  31. data/blogs/ruby_plot/ruby_plot_files/figure-gfm/final_violin_plot.png +0 -0
  32. data/blogs/ruby_plot/ruby_plot_files/figure-gfm/violin_with_jitter.png +0 -0
  33. data/blogs/test/test.md +10 -0
  34. data/examples/50Plots_MasterList/ScatterPlot.rb +2 -1
  35. data/examples/50Plots_MasterList/scatter_plot.rb +1 -0
  36. data/examples/bioconductor_deseq2_airway/bench_galaaz_three_same_process.rb +1 -0
  37. data/examples/bioconductor_deseq2_airway/deseq2_airway_galaaz.rb +1 -0
  38. data/examples/bioconductor_deseq2_airway/deseq2_airway_galaaz_optimized.rb +1 -0
  39. data/examples/islr/all.rb +1 -0
  40. data/examples/islr/ch2.spec.rb +1 -0
  41. data/examples/islr/ch3.spec.rb +1 -0
  42. data/examples/islr/ch3_boston.rb +1 -0
  43. data/examples/islr/ch3_multiple_regression.rb +1 -0
  44. data/examples/islr/ch6.spec.rb +1 -0
  45. data/examples/islr/x_y_rnorm.jpg +0 -0
  46. data/examples/misc/ggplot.rb +2 -1
  47. data/examples/misc/moneyball.rb +1 -0
  48. data/examples/misc/subsetting.rb +1 -0
  49. data/examples/multithread_shards_to_r/shards_to_r.rb +1 -0
  50. data/examples/sthda_ggplot/all.rb +1 -0
  51. data/examples/sthda_ggplot/one_variable_continuous/density_gg.rb +1 -0
  52. data/examples/sthda_ggplot/one_variable_continuous/geom_area.rb +1 -0
  53. data/examples/sthda_ggplot/one_variable_continuous/geom_density.rb +1 -0
  54. data/examples/sthda_ggplot/one_variable_continuous/geom_dotplot.rb +1 -0
  55. data/examples/sthda_ggplot/one_variable_continuous/geom_freqpoly.rb +1 -0
  56. data/examples/sthda_ggplot/one_variable_continuous/geom_histogram.rb +1 -0
  57. data/examples/sthda_ggplot/one_variable_continuous/histogram_density.rb +1 -0
  58. data/examples/sthda_ggplot/one_variable_continuous/stat.rb +1 -0
  59. data/examples/sthda_ggplot/one_variable_discrete/bar.rb +1 -0
  60. data/examples/sthda_ggplot/qplots/box_violin_dot.rb +1 -0
  61. data/examples/sthda_ggplot/qplots/scatter_plots.rb +1 -0
  62. data/examples/sthda_ggplot/scatter_gg.rb +1 -0
  63. data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_bin2d.rb +1 -0
  64. data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_density2d.rb +1 -0
  65. data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_hex.rb +1 -0
  66. data/examples/sthda_ggplot/two_variables_cont_cont/geom_point.rb +1 -0
  67. data/examples/sthda_ggplot/two_variables_cont_cont/geom_smooth.rb +1 -0
  68. data/examples/sthda_ggplot/two_variables_cont_cont/misc.rb +1 -0
  69. data/examples/sthda_ggplot/two_variables_cont_function/geom_area.rb +1 -0
  70. data/examples/sthda_ggplot/two_variables_disc_cont/geom_bar.rb +1 -0
  71. data/examples/sthda_ggplot/two_variables_disc_cont/geom_boxplot.rb +1 -0
  72. data/examples/sthda_ggplot/two_variables_disc_cont/geom_dotplot.rb +1 -0
  73. data/examples/sthda_ggplot/two_variables_disc_cont/geom_jitter.rb +1 -0
  74. data/examples/sthda_ggplot/two_variables_disc_cont/geom_line.rb +1 -0
  75. data/examples/sthda_ggplot/two_variables_disc_cont/geom_violin.rb +1 -0
  76. data/examples/sthda_ggplot/two_variables_disc_disc/geom_jitter.rb +1 -0
  77. data/examples/sthda_ggplot/two_variables_error/geom_crossbar.rb +1 -0
  78. data/lib/R_interface/rvector.rb +15 -0
  79. data/lib/galaaz_ruby.rb +34 -0
  80. data/lib/new_bridge/envelope.rb +2 -2
  81. data/specs/gknit_include_engine_spec.rb +2 -2
  82. data/specs/gknit_install_timeout_report_spec.rb +2 -2
  83. data/specs/gknit_internal_error_report_spec.rb +2 -2
  84. data/specs/gknit_vector_map_output_spec.rb +2 -2
  85. data/version.rb +1 -1
  86. metadata +39 -13
metadata CHANGED
@@ -1,13 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: galaaz
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  version: !ruby/object:Gem::Version
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- version: 2.0.0
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+ version: 2.1.0
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  platform: ruby
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  authors:
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  - Rodrigo Botafogo
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+ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2026-08-17 00:00:00.000000000 Z
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+ date: 2026-09-03 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: msgpack
@@ -66,27 +67,31 @@ dependencies:
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  - !ruby/object:Gem::Version
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  version: 6.1.2.1
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  description: |
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- Galaaz brings the full R ecosystem to Ruby developers. Galaaz 2.0 runs Ruby on JRuby and
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- talks to standard GNU Rthe same R you use with CRAN and Bioconductor—in a separate
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- process. A bridge handles requests, results, and typing so you can drive R from Ruby
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- (for example calling R functions, loading packages, and working with R objects) without
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- giving up multithreaded JRuby for application code.
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+ Galaaz is R-on-Rails: R scientists keep GNU R (CRAN / Bioconductor) for statistics and
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+ graphics, and use Ruby—often Railsto put that work on the web (HTTP, auth, jobs, HTML)
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+ without rewriting analyses in another stack. Ruby developers also get full access to R
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+ libraries through the same bridge.
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+
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+ Galaaz 2.0 talks to standard GNU R in a separate process. A bridge handles requests,
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+ results, and typing so you can drive R from Ruby (calling R functions, loading packages,
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+ and working with R objects). **JRuby** and **CRuby** are both supported for the same
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+ NewBridge protocol (tested with JRuby 10.1.1.0 + Java 21, and CRuby 3.3).
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  Like RinRuby, rpy2, or reticulate, Galaaz is a cross-language bridge; unlike embedding a
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  second interpreter in one VM, using GNU R means compiled R packages and Bioconductor work
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  as usual. Large tables can optionally flow through Apache Arrow on the R side when you use
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  the helpers described in the project documentation.
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- You need both JRuby and a working GNU R installation in PATH for the bridge to run.
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+ You need JRuby or CRuby and a working GNU R installation in PATH for the bridge to run.
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  Build the native gatekeeper after install with: make -C ext/new_bridge all
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  email: rodrigo.a.botafogo@gmail.com
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  executables:
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  - galaaz
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- - gbookdown
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+ - gstudio
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  - gknit
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- - gknit-draft
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+ - gbookdown
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  - grun
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- - gstudio
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+ - gknit-draft
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  extensions: []
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  extra_rdoc_files: []
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  files:
@@ -97,7 +102,9 @@ files:
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  - bin/galaaz
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  - bin/galaaz-bootstrap
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  - bin/galaaz-jruby
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+ - bin/galaaz-ruby
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  - bin/galaaz_jruby_env.inc.sh
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+ - bin/galaaz_ruby_env.inc.sh
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  - bin/gbookdown
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  - bin/gknit
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  - bin/gknit-draft
@@ -120,6 +127,8 @@ files:
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  - blogs/galaaz_ggplot/galaaz_ggplot.log
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  - blogs/galaaz_ggplot/galaaz_ggplot.md
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  - blogs/galaaz_ggplot/galaaz_ggplot.tex
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+ - blogs/galaaz_ggplot/galaaz_ggplot_files/figure-gfm/midwest_rb.png
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+ - blogs/galaaz_ggplot/galaaz_ggplot_files/figure-gfm/scatter_plot_rb.png
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  - blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/midwest_rb.png
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  - blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/scatter_plot_rb.png
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  - blogs/galaaz_ggplot/galaaz_ggplot_files/figure-markdown_github/midwest_rb.png
@@ -128,6 +137,8 @@ files:
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  - blogs/galaaz_ggplot/midwest_external_png
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  - blogs/gknit/gknit.Rmd
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  - blogs/gknit/gknit.md
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+ - blogs/gknit/gknit_files/figure-gfm/bubble-1.png
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+ - blogs/gknit/gknit_files/figure-gfm/diverging_bar.png
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  - blogs/gknit/gknit_files/figure-html/bubble-1.png
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  - blogs/gknit/gknit_files/figure-html/diverging_bar.png
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  - blogs/gknit/lst.rds
@@ -157,6 +168,17 @@ files:
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  - blogs/ruby_plot/ruby_plot.log
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  - blogs/ruby_plot/ruby_plot.md
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  - blogs/ruby_plot/ruby_plot.tex
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+ - blogs/ruby_plot/ruby_plot_files/figure-gfm/dose_len.png
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+ - blogs/ruby_plot/ruby_plot_files/figure-gfm/facet_by_delivery.png
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+ - blogs/ruby_plot/ruby_plot_files/figure-gfm/facet_by_dose.png
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+ - blogs/ruby_plot/ruby_plot_files/figure-gfm/facets_by_delivery_color.png
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+ - blogs/ruby_plot/ruby_plot_files/figure-gfm/facets_by_delivery_color2.png
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+ - blogs/ruby_plot/ruby_plot_files/figure-gfm/facets_with_decorations.png
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+ - blogs/ruby_plot/ruby_plot_files/figure-gfm/facets_with_jitter.png
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+ - blogs/ruby_plot/ruby_plot_files/figure-gfm/facets_with_points.png
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+ - blogs/ruby_plot/ruby_plot_files/figure-gfm/final_box_plot.png
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+ - blogs/ruby_plot/ruby_plot_files/figure-gfm/final_violin_plot.png
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+ - blogs/ruby_plot/ruby_plot_files/figure-gfm/violin_with_jitter.png
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  - blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.png
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  - blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_delivery.png
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  - blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_dose.png
@@ -180,6 +202,7 @@ files:
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  - blogs/ruby_plot/ruby_plot_files/figure-latex/final_violin_plot.png
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  - blogs/ruby_plot/ruby_plot_files/figure-latex/violin_with_jitter.png
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  - blogs/test/test.Rmd
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+ - blogs/test/test.md
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  - examples/50Plots_MasterList/Images/midwest-scatterplot.PNG
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  - examples/50Plots_MasterList/ScatterPlot.rb
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  - examples/50Plots_MasterList/scatter_plot.rb
@@ -315,6 +338,7 @@ files:
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  - lib/R_interface/rvector.rb
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  - lib/galaaz.rb
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  - lib/galaaz_jruby.rb
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+ - lib/galaaz_ruby.rb
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  - lib/gknit.rb
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  - lib/gknit/diagnostics.rb
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  - lib/gknit/draft.rb
@@ -450,6 +474,7 @@ metadata:
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  documentation_uri: https://rbotafogo.github.io/galaaz/
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  changelog_uri: https://github.com/rbotafogo/galaaz/blob/galaaz2_0/CHANGELOG.md
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  yard.run: yri
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+ post_install_message:
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  rdoc_options: []
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  require_paths:
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  - lib
@@ -464,7 +489,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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- rubygems_version: 4.0.3
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+ rubygems_version: 3.5.22
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+ signing_key:
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  specification_version: 4
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- summary: Tightly coupling Ruby and R
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+ summary: 'R-on-Rails: tightly couple Ruby and GNU R for data science on the web'
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  test_files: []