From 07eafdc74ecd8a10240cbe7407d6eea4450631a7 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Sun, 19 Feb 2023 11:36:29 -0500 Subject: [PATCH 1/8] update r-lib actions --- .github/workflows/pythonapp.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 25c2ddfe..7da56125 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -50,8 +50,8 @@ jobs: run: | python -m pmlb.profiling - - uses: r-lib/actions/setup-r@v1 - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-r@v2 + - uses: r-lib/actions/setup-pandoc@v2 - name: Install R packages run: Rscript -e 'install.packages(c("rmarkdown", "plotly", "dplyr", "htmlwidgets", "htmltools", "jsonlite", "readr", "DT", "remotes", "pmlbr"))' From d546a7331009dd2ca8ba08e4f1c9e58dd63502a7 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Sun, 19 Feb 2023 16:38:09 +0000 Subject: [PATCH 2/8] update dataset files Created by https://github.com/EpistasisLab/pmlb/actions/runs/4217169359\nfrom 07eafdc on 2023-02-19 --- .lfs-assets-id | 4 ++-- pmlb/all_summary_stats.tsv | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.lfs-assets-id b/.lfs-assets-id index 6345493b..2de5d5ba 100644 --- a/.lfs-assets-id +++ b/.lfs-assets-id @@ -106,7 +106,6 @@ 4757ff95609abb91a98577cf6023c804ba2b0b749a9dfcc48597ac49d4bf72a0 479f25b491115302fb2adaaa80f2670ab812154007d68ec5c566a45f6210d04d 47c92e5d64f038751dc26c7c33b3ecb24d031b1c4ce304b7aad4097b3dd0bd31 -491d45db3eb8ce30a838207b4f3eca02267c8a603c56358b7ff8babde9c40c0f 49e69e07ba6bd94a37550fbee5eed107bb26dd18a88d68d5b567722df17adee7 4a2bfb8dd7b1b617c1d7ffe8ae85a3dade9178e5d5dd6aa049189843321e1ff3 4a3c14c493429b459a6f760532828083d836b6de9c930d3d0befaa4353753f65 @@ -126,6 +125,7 @@ 52ac257854fadc38544098fc62402fee94e38a4688bf1c44fe34ee6cffd4784e 5327418df12a934f7089642b55abf1abd2e9ba286dea775b2862e4cc890e4da8 54388a6fba767cc75f6fd07a0e20339fe9fa3eb4ce9fca3e621f26b00b426d74 +546c047502ad902c099a627f831f338bc77e824d2e7cadcc2733bd3d6a0a949e 5489616c6233c73567bbf7188ed54ef3e1f31653a3582eafc682f4a9f8e74bdf 5515c0467bd2a945027c09b73fdec8469d07feb6b0742242dfcc6a2bfc0dcc22 5576935381b138bee157c44f39b203aa2e77860a32003494044771c582add97b @@ -148,6 +148,7 @@ 5eb60cdd947ecb4ea476ba854299dbe18d522df3ed684fb8f60657fdd4132910 5ebd813b1e30817354b31d0f51e4ad3a31dea6fa2f1eb85680112bea6ec63e9b 5f123396e5bd9bf37facd88266cee4b5d8df358a5d99a91c5e0ae131d66dde06 +5fa6a6badd6b4e35fa5320bf27d06248fa01b7732380950c0057d6cf72c73739 5fe909e08a622224135a2dcfd409bbe10abab4919f917a07b771c3fb00580852 60c909d5dd423662965b602d5beca52eb74340346ec59a4bf41c2a2084461520 610a94a55c4ffbd15e1c33063b48ee19f4e1501fe941358417e4add861f6b2c9 @@ -393,7 +394,6 @@ f14fd01559b154384ecd57147159be294e4dbc29a1a0f037d65405b1a66fd056 f2d1272e53c40b007c9cac300adbfe84e26c9220b505088b09200de8131f6d8e f385f7aca664516023d5cab78b92223e0c025b3b155e7aa5358cee097ac7f1fb f3a0b514802c80c42d42dfcc9eb260278a46e09293a9cb9d59420548e30a5a25 -f3ade821f9a0caebdd8b244319e66932c4b453ade027f42f86ed8ea1a50251ba f5b2d99fd5cedd50730dea186dab5f2cec9ab6afdf3f533b2fe3c56653136182 f5c6631a9716b8c50951dbf0eb66c2f00d299c115fee72a0c23aff5a7f59fd57 f64bb4a6d214a59a50b70b0f3270e334725b6cc010443a484cc751b595a46fe9 diff --git a/pmlb/all_summary_stats.tsv b/pmlb/all_summary_stats.tsv index 4ecdc19e..072e383d 100644 --- a/pmlb/all_summary_stats.tsv +++ b/pmlb/all_summary_stats.tsv @@ -154,7 +154,7 @@ australian 690 14 4 3 7 categorical 2.0 0.0121319050619617 classification auto 202 25 3 6 16 categorical 5.0 0.0453754533869228 classification backache 180 32 22 4 6 categorical 2.0 0.521604938271605 classification balance_scale 625 4 0 4 0 categorical 3.0 0.14622976 classification -banana 5300 2 0 0 2 continuous 2.0 0.0106907796368814 regression +banana 5300 2 0 0 2 binary 2.0 0.0106907796368815 classification biomed 209 8 0 1 7 categorical 2.0 0.079691399006433 classification breast 699 10 0 8 2 categorical 2.0 0.0963751609186227 classification breast_cancer 286 9 2 6 1 categorical 2.0 0.1645068218494792 classification @@ -402,7 +402,7 @@ tae 151 5 2 0 3 categorical 3.0 0.0003070040787684 classification texture 5500 40 0 0 40 categorical 11.0 0.0 classification threeOf9 512 9 9 0 0 categorical 2.0 0.00494384765625 classification tic_tac_toe 958 9 0 9 0 categorical 2.0 0.0941810748732789 classification -titanic 2201 3 0 0 3 continuous 2.0 0.1252664674125861 regression +titanic 2207 8 1 3 4 binary 2.0 0.126512852276882 classification tokyo1 959 44 0 2 42 categorical 2.0 0.0775149209345414 classification twonorm 7400 20 0 0 20 categorical 2.0 6.57414170927761e-07 classification vehicle 846 18 0 0 18 categorical 4.0 0.0004266124179609 classification From 094e95963b77d338cf13cd4ddd396f96164e1251 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Sun, 19 Feb 2023 12:27:34 -0500 Subject: [PATCH 3/8] more symlinks --- .github/workflows/pythonapp.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 7da56125..6fb87ef6 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -69,6 +69,7 @@ jobs: conda install -c conda-forge libstdcxx-ng sudo rm /usr/lib/x86_64-linux-gnu/libstdc++.so.6 sudo ln -s /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /usr/lib/x86_64-linux-gnu/libstdc++.so.6 + sudo ln -s /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /opt/R/4.2.2/lib/R/bin/exec/R/libstdc++.so.6 - name: Build site run: | From 954fcce5c12175cc6eee4d569e7ff90b1533b3f7 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Sun, 19 Feb 2023 13:23:17 -0500 Subject: [PATCH 4/8] cp /opt/R/4.2.2/lib/R/bin/exec/R/ --- .github/workflows/pythonapp.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 6fb87ef6..c5f76b84 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -69,7 +69,7 @@ jobs: conda install -c conda-forge libstdcxx-ng sudo rm /usr/lib/x86_64-linux-gnu/libstdc++.so.6 sudo ln -s /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /usr/lib/x86_64-linux-gnu/libstdc++.so.6 - sudo ln -s /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /opt/R/4.2.2/lib/R/bin/exec/R/libstdc++.so.6 + sudo cp /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /opt/R/4.2.2/lib/R/bin/exec/R/ - name: Build site run: | From 336b10a5f0e349f77678f6a725923bc962f6807d Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Sun, 19 Feb 2023 13:55:02 -0500 Subject: [PATCH 5/8] reticulate --- .github/workflows/pythonapp.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index c5f76b84..36d2e11a 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -69,11 +69,10 @@ jobs: conda install -c conda-forge libstdcxx-ng sudo rm /usr/lib/x86_64-linux-gnu/libstdc++.so.6 sudo ln -s /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /usr/lib/x86_64-linux-gnu/libstdc++.so.6 - sudo cp /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /opt/R/4.2.2/lib/R/bin/exec/R/ - name: Build site run: | - Rscript -e 'print(reticulate::py_discover_config())' + # Rscript -e 'print(reticulate::py_discover_config())' Rscript -e 'rmarkdown::render_site(input = "docs_sources")' - run: ls -lhR docs/ From 963e2c8709a8686f3d053d60b95b12700c448ac1 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Sun, 19 Feb 2023 15:02:33 -0500 Subject: [PATCH 6/8] mkdir otp/R --- .github/workflows/pythonapp.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 36d2e11a..805e0b83 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -69,6 +69,8 @@ jobs: conda install -c conda-forge libstdcxx-ng sudo rm /usr/lib/x86_64-linux-gnu/libstdc++.so.6 sudo ln -s /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /usr/lib/x86_64-linux-gnu/libstdc++.so.6 + mkdir -p /opt/R/4.2.2/lib/R/bin/exec/R + sudo cp /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /opt/R/4.2.2/lib/R/bin/exec/R/ - name: Build site run: | From 0c0cd1b3ffcd94f00cb0a6bfdb5c561627c25704 Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Sun, 19 Feb 2023 15:26:53 -0500 Subject: [PATCH 7/8] find libstdc++ --- .github/workflows/pythonapp.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 805e0b83..3f7a613b 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -67,10 +67,11 @@ jobs: - name: Install gcc run: | conda install -c conda-forge libstdcxx-ng + find / -name "libstdc++.so*" sudo rm /usr/lib/x86_64-linux-gnu/libstdc++.so.6 sudo ln -s /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /usr/lib/x86_64-linux-gnu/libstdc++.so.6 - mkdir -p /opt/R/4.2.2/lib/R/bin/exec/R - sudo cp /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /opt/R/4.2.2/lib/R/bin/exec/R/ + # mkdir -p /opt/R/4.2.2/lib/R/bin/exec/R + # sudo cp /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /opt/R/4.2.2/lib/R/bin/exec/R/ - name: Build site run: | From faa29a38d84700d0e435e51765e59fdecd01707c Mon Sep 17 00:00:00 2001 From: lelaboratoire Date: Sun, 19 Feb 2023 15:53:47 -0500 Subject: [PATCH 8/8] remove gcc installation --- .github/workflows/pythonapp.yml | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 3f7a613b..84337428 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -64,18 +64,9 @@ jobs: reticulate::py_discover_config() shell: Rscript {0} - - name: Install gcc - run: | - conda install -c conda-forge libstdcxx-ng - find / -name "libstdc++.so*" - sudo rm /usr/lib/x86_64-linux-gnu/libstdc++.so.6 - sudo ln -s /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /usr/lib/x86_64-linux-gnu/libstdc++.so.6 - # mkdir -p /opt/R/4.2.2/lib/R/bin/exec/R - # sudo cp /home/runner/.local/share/r-miniconda/pkgs/libstdcxx-ng-12.1.0-ha89aaad_16/lib/libstdc++.so.6.0.30 /opt/R/4.2.2/lib/R/bin/exec/R/ - - name: Build site run: | - # Rscript -e 'print(reticulate::py_discover_config())' + Rscript -e 'print(reticulate::py_discover_config())' Rscript -e 'rmarkdown::render_site(input = "docs_sources")' - run: ls -lhR docs/