From cd264f3a57753e8430e08f1c795148d983c8c3fb Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Sat, 15 Jul 2023 10:31:20 +0200 Subject: [PATCH] [ci run] bulk --- build-fail-blacklist | 4 + .../r-leidenbase/build_failure.linux-64.yaml | 104 ------------------ .../build_failure.linux-64.yaml | 104 ------------------ recipes/r-oncopharmadb/meta.yaml | 2 +- 4 files changed, 5 insertions(+), 209 deletions(-) delete mode 100644 recipes/r-leidenbase/build_failure.linux-64.yaml delete mode 100644 recipes/r-oncopharmadb/build_failure.linux-64.yaml diff --git a/build-fail-blacklist b/build-fail-blacklist index c304bd0bbc170..a95157903f213 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1,4 +1,8 @@ # speed up bulk +recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene +recipes/bioconductor-gseabase +recipes/bioconductor-bumphunter +recipes/bioconductor-biovizbase recipes/bioconductor-ensembldb recipes/bioconductor-variantannotation recipes/bioconductor-genefilter diff --git a/recipes/r-leidenbase/build_failure.linux-64.yaml b/recipes/r-leidenbase/build_failure.linux-64.yaml deleted file mode 100644 index bd17db407f085..0000000000000 --- a/recipes/r-leidenbase/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: eefde0af44b2c806c777a1963b4f54e110995b6ed4eb714c5e8588ec07af4847 # The commit at which this recipe failed to build. -skiplist: false # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.6MB/s 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 4.9MB/s 0.0s - [?25hMamba failed to solve: - - r-base 4.3.* - - r-igraph >=1.3.4 - - libstdcxx-ng >=12 - - glpk 5.0.* - - gmp 6.* - - libxml2 2.10.* - - libblas 3.9.* *netlib - - libgcc-ng >=12 - - liblapack 3.9.* *netlib - - libgfortran5 >=12.3.0 - - libgfortran-ng - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package r-igraph-1.3.4-r40hb34fc8a_0 requires r-base >=4.0,<4.1.0a0, but none of the providers can be installed - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - r-base 4.3.* - - r-igraph >=1.3.4 - - libstdcxx-ng >=12 - - glpk 5.0.* - - gmp 6.* - - libxml2 2.10.* - - libblas 3.9.* *netlib - - libgcc-ng >=12 - - liblapack 3.9.* *netlib - - libgfortran5 >=12.3.0 - - libgfortran-ng - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package r-igraph-1.3.4-r40hb34fc8a_0 requires r-base >=4.0,<4.1.0a0, but none of the providers can be installed - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base[version='>=4.0,<4.1.0a0']"), MatchSpec("r-igraph==1.3.4=r40hb34fc8a_0")} -# Last 100 lines of the build log. diff --git a/recipes/r-oncopharmadb/build_failure.linux-64.yaml b/recipes/r-oncopharmadb/build_failure.linux-64.yaml deleted file mode 100644 index be20dc5993f11..0000000000000 --- a/recipes/r-oncopharmadb/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 8b2820f66fb6e65acc889d123967336380aed494441b9542e2203030bf603210 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - r-fastmap: 1.1.1-r43ha503ecb_1 conda-forge - r-fontawesome: 0.5.1-r43hc72bb7e_1 conda-forge - r-fs: 1.6.2-r43ha503ecb_1 conda-forge - r-gargle: 1.5.1-r43h785f33e_0 conda-forge - r-generics: 0.1.3-r43hc72bb7e_2 conda-forge - r-glue: 1.6.2-r43h57805ef_2 conda-forge - r-googledrive: 2.1.1-r43hc72bb7e_1 conda-forge - r-highr: 0.10-r43hc72bb7e_1 conda-forge - r-htmltools: 0.5.5-r43ha503ecb_1 conda-forge - r-htmlwidgets: 1.6.2-r43hc72bb7e_1 conda-forge - r-httr: 1.4.6-r43hc72bb7e_1 conda-forge - r-jquerylib: 0.1.4-r43hc72bb7e_2 conda-forge - r-jsonlite: 1.8.7-r43h57805ef_0 conda-forge - r-knitr: 1.43-r43hc72bb7e_1 conda-forge - r-later: 1.3.1-r43ha503ecb_1 conda-forge - r-lazyeval: 0.2.2-r43h57805ef_4 conda-forge - r-lgr: 0.4.4-r43hc72bb7e_2 conda-forge - r-lifecycle: 1.0.3-r43hc72bb7e_2 conda-forge - r-magrittr: 2.0.3-r43h57805ef_2 conda-forge - r-memoise: 2.0.1-r43hc72bb7e_2 conda-forge - r-mime: 0.12-r43h57805ef_2 conda-forge - r-oncopharmadb: 1.3.7-r43hdfd78af_0 local - r-openssl: 2.0.6-r43hb353fa6_1 conda-forge - r-pillar: 1.9.0-r43hc72bb7e_1 conda-forge - r-pkgconfig: 2.0.3-r43hc72bb7e_3 conda-forge - r-promises: 1.2.0.1-r43ha503ecb_2 conda-forge - r-purrr: 1.0.1-r43h57805ef_1 conda-forge - r-r6: 2.5.1-r43hc72bb7e_2 conda-forge - r-rappdirs: 0.3.3-r43h57805ef_2 conda-forge - r-rcpp: 1.0.11-r43h7df8631_0 conda-forge - r-rlang: 1.1.1-r43ha503ecb_1 conda-forge - r-rmarkdown: 2.23-r43hc72bb7e_0 conda-forge - r-rstudioapi: 0.15.0-r43hc72bb7e_0 conda-forge - r-sass: 0.4.6-r43ha503ecb_1 conda-forge - r-stringi: 1.7.12-r43hc0c3e09_2 conda-forge - r-stringr: 1.5.0-r43h785f33e_1 conda-forge - r-sys: 3.4.2-r43h57805ef_1 conda-forge - r-tibble: 3.2.1-r43h57805ef_2 conda-forge - r-tidyr: 1.3.0-r43ha503ecb_1 conda-forge - r-tidyselect: 1.2.0-r43hc72bb7e_1 conda-forge - r-tinytex: 0.45-r43hc72bb7e_1 conda-forge - r-utf8: 1.2.3-r43h57805ef_1 conda-forge - r-uuid: 1.1_0-r43h57805ef_2 conda-forge - r-vctrs: 0.6.3-r43ha503ecb_0 conda-forge - r-withr: 2.5.0-r43hc72bb7e_2 conda-forge - r-xfun: 0.39-r43ha503ecb_1 conda-forge - r-yaml: 2.3.7-r43h57805ef_1 conda-forge - readline: 8.2-h8228510_1 conda-forge - sed: 4.8-he412f7d_0 conda-forge - sysroot_linux-64: 2.12-he073ed8_16 conda-forge - tk: 8.6.12-h27826a3_0 conda-forge - tktable: 2.10-hb7b940f_3 conda-forge - xorg-kbproto: 1.0.7-h7f98852_1002 conda-forge - xorg-libice: 1.0.10-h7f98852_0 conda-forge - xorg-libsm: 1.2.3-hd9c2040_1000 conda-forge - xorg-libx11: 1.8.6-h8ee46fc_0 conda-forge - xorg-libxau: 1.0.11-hd590300_0 conda-forge - xorg-libxdmcp: 1.1.3-h7f98852_0 conda-forge - xorg-libxext: 1.3.4-h0b41bf4_2 conda-forge - xorg-libxrender: 0.9.11-hd590300_0 conda-forge - xorg-libxt: 1.3.0-hd590300_0 conda-forge - xorg-renderproto: 0.11.1-h7f98852_1002 conda-forge - xorg-xextproto: 7.3.0-h0b41bf4_1003 conda-forge - xorg-xproto: 7.0.31-h7f98852_1007 conda-forge - xz: 5.2.6-h166bdaf_0 conda-forge - zlib: 1.2.13-hd590300_5 conda-forge - zstd: 1.5.2-hfc55251_7 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - export PREFIX=/opt/conda/conda-bld/r-oncopharmadb_1689373395606/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - export SRC_DIR=/opt/conda/conda-bld/r-oncopharmadb_1689373395606/test_tmp - /opt/conda/conda-bld/r-oncopharmadb_1689373395606/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/R -e 'library('\''oncoPharmaDB'\'')' - - R version 4.3.1 (2023-06-16) -- "Beagle Scouts" - Copyright (C) 2023 The R Foundation for Statistical Computing - Platform: x86_64-conda-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. - - 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. - - During startup - Warning message: - Setting LC_TIME failed, using "C" - > library('oncoPharmaDB') - Error in library("oncoPharmaDB") : - there is no package called oncoPharmaDB - Execution halted - Tests failed for r-oncopharmadb-1.3.7-r43hdfd78af_0.tar.bz2 - moving package to /opt/conda/conda-bld/broken - WARNING:conda_build.build:Tests failed for r-oncopharmadb-1.3.7-r43hdfd78af_0.tar.bz2 - moving package to /opt/conda/conda-bld/broken - TESTS FAILED: r-oncopharmadb-1.3.7-r43hdfd78af_0.tar.bz2 -# Last 100 lines of the build log. diff --git a/recipes/r-oncopharmadb/meta.yaml b/recipes/r-oncopharmadb/meta.yaml index aa0c23c6c4c7e..2ecb3ad90f13f 100644 --- a/recipes/r-oncopharmadb/meta.yaml +++ b/recipes/r-oncopharmadb/meta.yaml @@ -39,7 +39,7 @@ requirements: test: commands: - - $R -e "library('oncoPharmaDB')" + - $R -e "library('pharmOncoX')" about: home: https://github.com/sigven/oncoPharmaDB