add r-bpcells #55118
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add r-bpcells #55118
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The osx-64 build stops after: whether I use Conda or vendored > testthat::test_package('BPCells', stop_on_failure=FALSE)
*** caught segfault ***
address 0x62696c2f2e2e2f2e, cause 'memory not mapped'
Traceback:
1: write_packed_fragments_hdf5_cpp(it, path, group, buffer_size, chunk_size, overwrite, gzip_level)
2: write_fragments_hdf5(f2, file.path(dir, "overwrite.h5"), "frags")
3: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
4: withCallingHandlers({ code NULL}, error = function(cnd) { if (can_entrace(cnd)) { cnd <- cnd_entrace(cnd) } return_from(env, cnd)})
5: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)), ...)
6: quasi_capture(enquo(object), label, capture_error, entrace = TRUE)
7: expect_error({ write_fragments_hdf5(f2, file.path(dir, "overwrite.h5"), "frags")})
8: eval(code, test_env)
9: eval(code, test_env)
10: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
16: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
18: test_code(desc, code, env = parent.frame(), reporter = reporter)
19: test_that("H5 overwrite works", { dir <- withr::local_tempdir() frags1 <- tibble::tibble(chr = c("chr1", "chr1", "chr2", "chr3", "chr3"), start = c(10, 20, 30, 40, 50), end = start + 5, cell_id = 1:5) frags2 <- tibble::tibble(chr = c("chr1", "chr1", "chr2", "chr3", "chr4"), start = 10 + c(10, 20, 30, 40, 50), end = start + 5, cell_id = 1:5) f1 <- as(frags1, "IterableFragments") f2 <- as(frags2, "IterableFragments") write_fragments_hdf5(f1, file.path(dir, "overwrite.h5"), "frags") expect_error({ write_fragments_hdf5(f2, file.path(dir, "overwrite.h5"), "frags") }) expect_identical(as.data.frame(f1), open_fragments_hdf5(file.path(dir, "overwrite.h5"), "frags") %>% as.data.frame()) rlang::reset_message_verbosity("hdf5_overwrite") expect_message(write_fragments_hdf5(f2, file.path(dir, "overwrite.h5"), "frags", overwrite = TRUE), "dataset does not free old storage") expect_identical(as.data.frame(f2), open_fragments_hdf5(file.path(dir, "overwrite.h5"), "frags") %>% as.data.frame()) expect_identical(as.data.frame(select_cells(f2, c(1, 3, 5))), open_fragments_hdf5(file.path(dir, "overwrite.h5"), "frags") %>% select_cells(c(1, 3, 5)) %>% write_fragments_hdf5(file.path(dir, "overwrite.h5"), "frags", overwrite = TRUE) %>% as.data.frame())})
20: eval(code, test_env)
21: eval(code, test_env)
22: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
28: tryCatchList(expr, classes, parentenv, handlers)
29: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
30: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
31: source_file(path, env = env(env), desc = desc, error_call = error_call)
32: FUN(X[[i]], ...)
33: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
38: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
39: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
40: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
41: test_dir(test_path, package = package, reporter = reporter, ..., load_package = "installed")
42: testthat::test_package("BPCells", stop_on_failure = FALSE)
An irrecoverable exception occurred. R is aborting now ...For now I will abandon the osx-64 build, and accept the failing testthat tests. |
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@BiocondaBot please fetch artifacts |
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No more failing unit tests in Linux thanks to bnprks/BPCells#231. For now let's move forward without osx-64. @BiocondaBot please add label |
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@BiocondaBot please add label |
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@martin-g @jdblischak either of you available for a review? Thanks in advance! |
jdblischak
approved these changes
Apr 14, 2025
diekhans
pushed a commit
to diekhans/bioconda-recipes
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Apr 17, 2025
* add r-bpcells * adjust deps * libs * libs * license name * libs * patch libhwy config * full patch * fix patch * raw test again * macs2 test * use vendor libhwy on osx * skip non-linux * comment unit test failures * add granges conversion patch * test against macs3
mencian
added a commit
that referenced
this pull request
Apr 18, 2025
* Update mirtop to 0.4.30 (#55192) * Update bioframe to 0.8.0 (#55196) * Update palantir to 1.4.0 (#55195) * Update sopa to 2.0.4 (#55194) * Update cgecore to 2.0.1 (#55185) * Update trgt to 2.0.0 (#55193) * Update muat to version 0.1.9 (#55190) Co-authored-by: primasan <primasan@ad.helsinki.fi> * Update Clair3 to v1.1.0 (#55188) * Update polap to 0.4.3.7.5 (#55182) * Update polap to v0.3.7.3 build1 * Update polap to v0.4.3.7 build1 * Update polap to v0.4.3.7 build1 * Update polap to v0.4.3.7 without blast package * Update polap to v0.4.3.7 build1 without dflye * Update polap to v0.4.3.7.1 * Update polap to v0.4.3.7 build1 * Update polap to v0.4.3.7 build1 * Update polap build1 * Update polap build1 * Update polap build1 * Update polap to v0.4.3.7 build1 * Update meta.yaml * Update polap to v0.4.3.7 build1 without cflye * Update polap to v0.4.7.3 not yet * Update polap to v0.4.3.7 * Update polap to v0.4.3.7 build2 * Update polap to v0.4.3.7.2 * Update polap to v0.4.3.7.2 * Update polap to v0.4.3.7.2 * Update polap to v0.4.3.7.3 * Update polap to v0.4.3.7.3 try3 * Update polap to v0.4.3.7.3 try4 * Update polap to v0.4.3.7.3 * Update polap to v0.4.3.7.4 * Update polap to 0.4.3.7.5 --------- Co-authored-by: Sang Chul Choi <sangchulchoi@sungshin.ac.kr> * add statsmodels (#55179) * Update meta.yaml (#55181) * Update phabox to 2.1.11 (#55160) * Update piranha-polio to 1.5.1 (#55158) * Update recipe rsat-core, was blacklisted (#55152) * Updated version of RSAT * Updated conda recipe * updated to 2025-03-26 * add version.txt * removed rsat-core from blacklist * updated documentation and citation * commented out 2 perl deps * modified from Fabian's * removed host section and commented out deps * added missing \ * copy also folder share * added r-base to build: * passes test, complains perl: warning: Setting locale failed * passes tests with bioconda-utils build --docker --mulled-test --packages rsat-core * added LC_ALL * imports perl-postscript-simple, see #55114 * release of 2025.04.04 * rebuild after recipes/rsat-core/meta.yaml * build number reset to 0 after PR lint failure --------- Co-authored-by: Fabián Robledo <fabianry97@gmail.com> * Add v2.1.0 (#55167) * Update GRAMPA recipe (#55163) * update grampa recipe to add tests script * adding missing requirement for tests (unzip) * update link command * making a copy instead of a link since there seems to be a problem with that now * Update s4pred (#55169) * s4pred build version bump to retry creating container * download model weights, move to same folder as python scripts, make bash wrappers in bin folder, update test command run with actual script execution * renamed to run_model to match the python script, changed build number to 1 * added wget to host * Update treesimulator to 0.2.8 (#55037) * Update treesimulator to 0.2.5 * Update treesimulator to 0.2.6 * Update treesimulator to 0.2.7 * Update meta.yaml * Update meta.yaml * Update treesimulator to 0.2.8 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update isescan to 1.7.3 (#55197) * Update clair3-illumina to 1.1.0 (#55198) * Add cawlign recipe (#55168) * initial cawlign recipe * fix cawlign build number * fix cawlign build issues * Add MPRAlib (#55159) * initialization of MPRAlib * typo fix * ? * Add rdrpcatch (#55124) * Add rdrpcatch * fixed requests dependency * fixed run_exports * More clear deps * clean up recipe --------- Co-authored-by: dtriskar <dkarapliafis@gmail.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * install_mimi_1.0.0 (#55161) * install_rotate_1.0 * install_mimi_1.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * Update reduce to 4.15 (#55186) * Update reduce to 4.15 * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update last to 1639 (#55199) * Update resfinder to 4.7.0 (#55177) * Update resfinder to 4.7.0 * Update meta.yaml * revert to git --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * add ovrlpy recipe (#55183) Co-authored-by: niklasmueboe <niklasmueboe@github.com> * Update ncbitax2lin to 2.4.1 (#55201) * Update ncbitax2lin to 2.4.1 * add run_exports --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update kma to 1.5.0 (#55200) * Add mypmfs_py package (#55171) * mypmfs_py package * Update meta.yaml * Update meta.yaml * Update meta.yaml license-family * Update meta.yaml py versions fix * Update meta.yaml pin_compatible * Update meta.yaml lowercase name * Update meta.yaml update requirements * Update meta.yaml dependencies fix * Update meta.yaml c++ dependency and license file fix * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update rdrpcatch to 0.0.3 (#55202) * Update mity to 1.2.0 (#55176) * Update mity to 1.2.0 * clean up recipe --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Add recipe for GCI (#54829) * init gci * lint fixes * author recommendations * update url * Update meta.yaml * Delete recipes/gci/build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update genin2 to 2.1.2 (#54932) * Update genin2 to 2.0.3 * Update genin2 to 2.1.0 * Update genin2 to 2.1.1 * Update genin2 to 2.1.2 * add requests --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update pymummer to 0.12.0 (#54811) * Update pymummer to 0.12.0 * Update meta.yaml * Update temp_dir_path.patch * Delete recipes/pymummer/temp_dir_path.patch * remove patch --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update fairy to 0.5.8 (#54554) * Update fairy to 0.5.8 * Update meta.yaml * Update build.sh * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update biskit to 3.0.1 (#54543) * Update biskit to 3.0.0 * add run_exports * Update biskit to 3.0.1 * clean up recipe * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Update cnvpytor to 1.3.2 (#54515) * Update cnvpytor to 1.3.2 * Update meta.yaml * Update meta.yaml * fix typo * Update and rename post-link.sh to .post-link.sh * Delete recipes/cnvpytor/.post-link.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update survindel2 to 1.1.4 (#54542) * Update survindel2 to 1.1.4 * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update pastrami to 1.0.0 (#54438) * Update pastrami to 1.0.0 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update pybwa to 2.0.1 (#55205) * Update mpralib to 0.6.1 (#55214) * Add r-pio (#55213) * add r-pio * end line * Update r-acidgenomes to 0.7.5 (#55216) * Update zol to 1.5.10 (#55231) * Update ToolDistillator from 0.9.1 to 0.9.2 (#55217) * Update meta.yaml for ToolDistillator 0.9.2 * add setuptools * Update virulencefinder version (#55212) * Update virulencefinder version * RM old code from build.sh * Add pip install to build.sh * Add pdm-backend to meta.yaml * Update nextclade to 3.13.0 (#55240) Co-authored-by: nextstrain-bot <nextstrainbot@nextstrain.org> * Add `wget` to fusioncatcher dependencies (#55242) * Add `wget` to fusioncatcher dependencies * bump build number * Add run_exports * grampa recipe: add build script and update tests script (#55246) * Update kbo-cli to v0.2.1. (#55227) * Update kbo-cli to v0.2.1. * Update url and sha256sum * Update dependencies ganon v2.1.1 (#55248) * fastqtk: add linux-aarch64 (#55209) * fastqtk: add linux-aarch64 * spacing change , to re-start CI * ➕ Update dependencies for vuegen v0.3.2 (#55210) * ➕ Update dependencies for vuegen v0.3.2 * ⬇️ Decreaser build number * ⬆️ Increase build number * ⬆️ Increaser build number bc of circleci error * epa-ng: add linux-aarch64 (#55238) * epa-ng: add linux-aarch64 * add patches to enable aarch64 * New patches - to be applied at build time * use cmake < 4 - this package cannae handle it * - patch the origin of the x86_64 specific genesis code. * progress towards sorting out cxxflags * limit patch to the origin of the arch specific bit * set CXXFLAGS to CMake * pass cxxflags in quotes * no need to double-run make * Add cmake patch * remove cxxflags setting - it's not using them * add patch for CMakeLists.txt * FIX incorrect source for r-scbio (#55229) * FIX incorrect source code After amitfrish/scBio#21: scBio release 0.1.4 has not up-to-date archive assets, resulting in arguments for function CPM() not present in the conda package when they should be present. * Update meta.yaml after failed PR to bioconda-recipes max_pin="x.x.x" was chosen as per https://bioconda.github.io/contributor/linting.html#missing-run-exports and inspection of scBio repo (https://github.com/amitfrish/scBio), breaking change can be introduced even in patch release * Update aliceasm (#55237) * add aliceasm * run_exports in aliceasm recipe * build number * correct linting * added omp for osx * added omp for osx * Update recipes/aliceasm/meta.yaml * added bcalm dependancy * moved to version 0.6.33 * debugged dependencies * solved bug bcalm --help retruns 1 * correct dep * update aliceasm * empty --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update plink2 to 2.0.0-a.6.9 (#55220) * update plink2 to 2.0.0-a.6.9 * reset build number * fix version number to remove hyphen * Update rdrpcatch to 0.0.4 (#55233) * Update captus to 1.3.3 (#55232) * Update hictk to 2.1.1 (#55230) * Updated build for ARM (#55218) * Update ont-modkit to 0.4.4 (#55206) * Update mimeo to 1.2.1 (#55207) * Update libcifpp to 8.0.0 (#55208) * Update resfinder to 4.7.2 (#55211) * Update resfinder to 4.7.1 * Update resfinder to 4.7.2 * Update tower-cli to 0.11.2 (#55243) * Update snakemake-executor-plugin-slurm to 1.2.0 (#55219) * Update tiddit to 3.9.3 (#55221) * Update pyjess to 0.5.0 (#55222) * Update fasten to 0.8.7 (#55228) * Update kaptive to 3.1.0 (#55234) * Update pybiolib to 1.2.701 (#55235) * Update architeuthis to 0.4.0 (#55236) * Update picrust2 to 2.6.2 (#55239) * Update ppanggolin to 2.2.2 (#55249) * Update sawfish to 1.0.0 (#55250) * Update severus to 1.5 (#55251) * Add amulety recipe (#55258) * Add epicore recipe (#54954) * add recipe for epicore package * add run_exports * update meta.yaml * remove outdated meta.yaml * move meta.yaml * update script command * update version * update sha256 --------- Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> * Update augur to 29.1.0 (#55256) * Add cvanmf recipe (#55262) * Update strobealign to 0.16.0 (#55270) * Update lexicmap to 0.7.0 (#55271) * Update nanomotif to 0.6.0 (#55264) * Update screadcounts to 1.4.1 (#55275) * Update screadcounts to 1.4.1 * Update meta.yaml --------- Co-authored-by: Nathan Edwards <edwardsnj@users.noreply.github.com> * Update giatools to 0.4.0 (#55281) * Add eider recipe (#55279) * Update oarfish to 0.8.0 (#55289) * Update screadcounts to 1.4.2 (#55290) * Update whatshap to 2.6 (#55280) * Update r-acidbase to 0.7.4 (#55303) * Update latch to 2.59.0 (#55286) * Update argnorm to 0.8.0 (#55306) * Update quantms-rescoring to 0.0.8 (#55312) * Update r-acidsinglecell to 0.4.4 (#55304) * Update metafun to 0.3.0 (#55310) * Update metafun to 0.3.0 * Update metafun to 0.3.0 * reduce: Update build script to add `-DHET_DICTIONARY` and `-DHET_DICTOLD` flags (#55300) * reduce: Update build script to add `-DHET_DICTIONARY` and `-DHET_DICTOLD` flags * reduce: Add comment referencing issue for `-DHET_DICTIONARY` and `-DHET_DICTOLD` flags * Update to v4.5 (#55299) * Update to v4.5 * Update meta.yaml v4.5 * Install mimi 1.0.0 (#55288) * install_rotate_1.0 * install_mimi_1.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * install_mimi_1.0.0 * Update meta.yaml * setuptools is needed after all * install_mimi_1.0.1 * install_mimi_1.0.1 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update bindash to 2.4 (#55292) * Update bindash to 2.4 * Update bindash to 2.4 * Update plothic to 1.0.0 (#55307) * Update ampliconsuite to 1.3.6 (#55298) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update Sentieon recipe to 202503 (#55295) * Update carveme to 1.6.3 (#55265) * Update captus to 1.3.4 (#55259) * Update bedops to 2.4.42 (#55254) * Update recipe for dysgu (#55263) * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Add tmscoring (#55261) * add yaml * python <3.12 * make it noarch * Update perl-math-bigint to 2.005003 (#55316) * Update reframed to 1.5.4 (#55266) * Update reframed to 1.5.4 * add setuptools --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update snakemake-executor-plugin-slurm to 1.2.1 (#55285) * Update snakemake to 9.1.10 (#55276) * Update picard to 3.4.0 (#55314) * Update picard-slim to 3.4.0 (#55313) * Update scanpy-cli to 0.2.0 (#55305) * Update scanpy-cli to 0.1.7 * Update scanpy-cli to 0.1.8 * Update scanpy-cli to 0.2.0 * Update oakvar to 2.12.12 (#55297) * Update solvebio to 2.30.1 (#55282) * Update drep to 3.6.1 (#55294) * Update drep to 3.6.1 * add setuptools * add networkx --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update shiba2sashimi to 0.1.4 (#55319) * Update kmercamel to 2.1.1 (#55317) * Update kmercamel to 2.1.1 * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update cenote-taker3 to 3.4.0 (#55273) * Update cenote-taker3 to 3.4.0 * pin pyhmmer to >=0.11.0 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update igv to 2.19.3 (#55296) * Update igv to 2.19.3 * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update srnaMapper to new version (#55241) * Update srnaMapper to new version * Explicitely add BWA * Reset build number to 0 * Correct lib path * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Updating build of arborator (#55278) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add mimick recipe (#55284) * add mimick recipe * fix the folder error * rm skip * fix biopython bound * fix all bounds :( * rm aarch64 b/c of incompatibility with pywgsim * pin python to >=3.10 according to pyproject.toml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Removed wfa2 external dependency in linux (#55277) * Removed wfa2 external dependency in linux * Update build.sh * Fix ARM build * trigger GitHub actions * trigger GitHub actions * Update build.sh * clean up recipe * Update build.sh * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update r-geneexpressionfromgeo to 1.2 (#55267) * Update r-geneexpressionfromgeo to 1.2 * add run_exports * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update floria to 0.0.2 (#55255) * Update floria to 0.0.2 * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * eskrim does not work with python 3.13 (#55269) * eskrim does not work with python 3.13 * clean up recipe --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update perl-test-file to 1.995 (#55321) * Update odgi to 0.9.1 (#55252) * Update odgi to 0.9.1 * Fix cmake command to include policy version for build consistency * Fix cmake command by removing redundant policy version specification * Fix cmake command by moving policy version specification to the correct position * Update meta.yaml * Update build.sh --------- Co-authored-by: AndreaGuarracino <andreaguarracino@outlook.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update searchgui to 4.3.14 (#55322) * Update fusionreport to 4.0.0 (#55215) * update fusionreport * apply linitng * apply linting * clean up recipe * fix typo * fix source URL --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update smoothxg to 0.8.1 (#55253) * Update smoothxg to 0.8.1 * Add CMAKE_POLICY_VERSION_MINIMUM to cmake commands in build.sh * Remove redundant CMake policy version specification in build command * Fix cmake command formatting in build.sh * Update meta.yaml * Update build.sh * Update build.sh * fix typo * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml --------- Co-authored-by: AndreaGuarracino <andreaguarracino@outlook.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update captus to 1.3.6 (#55320) * Update captus to 1.3.5 * add entry_points * Update build.sh * Update meta.yaml * Delete recipes/captus/build.sh * Update meta.yaml * Update captus to 1.3.6 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update aviary to 0.12.0 (#55323) * Update aviary to 0.12.0 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update mypmfs_py to 0.1.8 (#55225) * Update mypmfs_py to 0.1.8 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * xtandem: add arm64 build (#55324) * tandemx: add arm64 build * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Add dmox (#54435) * Create meta.yaml This is the framework for the conda recipe for dmox. Once a release is tagged, we can submit this PR to bioconda for testing @iago-lito * Update meta.yaml remove the skip option * Update meta.yaml * adjust installation to move binary to PATH * add checksum * add proper parameters as specified by linter * rm host section, add noarch skip * align with current rust compiling recipe guide * add AT symbol to reciple maintainer * rm AT sign * add "v" to url * add cmake * just add cxx compiler * make sure cmake is a dep * just C compiler, not cxx? * Attempt to fix zlib-ng build. * Add cargo to test dependencies. * Move `cargo test` to build stage. * Leave tombstone into test section. * Replace tombstone with `dmox --help`. * Introduce and check third-party licenses. * Add THIRDPARTY.yml to license-file. * Attempt to fix MACOS build. * 🐛 Attempt to debug macos build. * clean up recipe * fix typo * Update build.sh --------- Co-authored-by: Iago Bonnici <iago.bonnici@umontpellier.fr> Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add MACH2 v1.0.1 (#54261) * Add MACH2 v1.0.1 * Add MACH2 v1.0.1 - mentioned gurobi channel * Add MACH2 v1.0.1 - changed gurobipy to gurobi * Add MACH2 v1.0.1 - made gurobi optional in code * Update sawfish to 1.0.1 (#55326) * Update gapmm2 to 25.4.13 (#55328) * Add qcatch 0.1.2 to bioconda (#55074) * Add qcatch 0.1.2 to bioconda * clean up recipe * add requests --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update cogent3 to 2025.3.22a4 (#54902) * Update cogent3 to 2025.3.22a3 * Update cogent3 to 2025.3.22a4 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update captus to 1.3.7 (#55330) * Update teloscope to 0.1.0 (#55329) * Update teloscope to 0.1.0 * Update meta.yaml * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update gsearch v0.2.6 (#55325) * Update gsearch v0.2.6 * Update gsearch v0.2.6 * Update gsearch v0.2.6 * Update gsearch v0.2.6 * Update gsearch v0.2.6 * Rebuild gmap (#55331) * Update carveme to 1.6.4 (#55332) * Rebuild libcifpp (#55334) * Update checkqc to 4.0.6 (#55335) * Update checkqc to 4.0.6 * Add jsonschema * Update checkqc to 4.0.6 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update PPanGGOLiN (#55260) * update ppanggolin recipe * add space between tool and version * add space between tool and version again * Update ltr_harvest_parallel (#55283) * change ltr_harvest_parallel repo source * fix duplicate key * osx-arm64 build for bioconductor-rhtslib and bioconductor-rsamtools (#55351) * osx-arm64 build for bioconductor-rhtslib and bioconductor-rsamtools * bump build number * Update methylartist to 1.4.0 (#55344) * Update methylartist to 1.4.0 * add setuptools --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update wfmash to 0.23.0 (#55353) * Update pggb to 0.7.3 (#55345) * Update pggb to 0.7.3 * update versions * Update vg dependency version to 1.63.1 * Update wfmash dependency version to 0.14.0 --------- Co-authored-by: AndreaGuarracino <andreaguarracino@outlook.com> * add osx-arm64, bump build number (#55354) * Update arvados-python-client to 3.1.1 (#55350) * Update ebi-eva-common-pyutils to 0.7.0 (#55338) * Update sniffles to 2.6.2 (#55337) * Update sniffles to 2.6.2 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update ogtfinder to 0.0.2 (#55336) * Update sr2silo to 0.1.1 (#55333) * Update sr2silo to 0.1.0 * add poetry-dynamic-versioning * Update meta.yaml * Update sr2silo to 0.1.1 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * osx-arm64 for bioconductor-sparsearray and bioconductor-s4arrays (#55356) * Update latch to 2.59.1 (#55360) * Update qcatch to 0.2.3 (#55359) * Update snakemake to 9.1.11 (#55341) * Update fast2q to 2.7.8 (#55348) * Update fast2q to 2.7.8 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add DeepDETAILS (#55349) * Update captus to 1.3.8 (#55362) * Update drep to 3.6.2 (#55352) * Update drep to 3.6.2 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * hictkpy: bump to v1.2.0 (#55339) * Simplify recipe * Bump hictkpy * Bugfix * Update URL * Remove Python version constraints from `vambcore` (#55272) * Remove Python version constraints from `vambcore` * Remove cross-compilation * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update snakemake to 9.2.0 (#55361) * Add TWILIGHT v0.1.1 (#55203) * add twilight * add space between package and version * add pin * modify package name * Update meta.yaml * Update build.sh --------- Co-authored-by: y3tseng <y3tseng@AD.UCSD.EDU@raptor.ucsd.edu> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add recipe for bbmapy (#55204) * Add recipe for bbmapy - a low dependency bbmap python wrapper * fix recipe for bbmapy * fix recipe after removing pytools from bbmapy * updating bbmapy version * move ensure_java to test on run, not build * fix wrong function name * add beefy Xmx to test commands * change ensure java function * change ensure java to use conda_prefix (again?) * fix tests - ensure_java moved * clean up recipe * revert license_file --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update cleanifier to 0.2.1 (#54925) * Update cleanifier to 0.2.1 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update Vamb to 5.0.3 (#54983) * Update Vamb to 5.0.2 * Add identifiers * Relax version requirements * Update requirements * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update mimick to 1.0.1 (#55370) * Update captus to 1.3.9 (#55364) * Update captus to 1.3.9 * fix install script --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update dbcan to v5.0.3 (#55369) * Add mpboot (#55008) * Add mpboot * fix sha * Try adding minimum cmake version arg * fix make command * fix make * tryagain * Try patching * unix2dos * try again * Fix exe nameTry again * simplify, use zlib>1.3.1 * fix * Try againtry again * fix copy * f * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update muat to version 0.1.10 (#55365) Co-authored-by: primasan <primasan@ad.helsinki.fi> * Add bakrep-cli to BioConda (#54922) * Create meta.yaml * add run_exports to meta.yaml * fix package in run_exports * change subpackage name to bakrep-cli in meta.yaml * add setuptools --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update mysterymaster meta.yaml (#55347) * Add cdskit (#55257) * Add cdskit recipe * Add cdskit recipe (fixed submodule issue) * Trigger build by bumping build number * Fix source URL and sha256 * Fix sha256 for cdskit source tarball * Fix: remove duplicate build script definition * Fix: meta.yaml license * Add Bioconda recipe for cdskit v0.14.1 * Add Bioconda recipe for cdskit 0.14.1 * Fix lint: reset build number and add run_exports * Fix: requirements python version * rmblast: add osx-arm64 (#55363) * rmblast: add osx-arm64 * Clean up rmblast * add zstd * Update build.sh --------- Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add kmer2stats recipe (#55224) * Add kmer2stats recipe * fix typo * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * fix test, did a little mistake * fix test * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update dnachisel to 3.2.15 (#55068) * Update gsmap to 1.73.0 (#53896) * add r-bpcells (#55118) * add r-bpcells * adjust deps * libs * libs * license name * libs * patch libhwy config * full patch * fix patch * raw test again * macs2 test * use vendor libhwy on osx * skip non-linux * comment unit test failures * add granges conversion patch * test against macs3 * Update genmod to 3.10.1 (#55372) * Update pasta (#54563) Co-authored-by: ZerryNi <996002763.com> Co-authored-by: Saim Momin <64724322+SaimMomin12@users.noreply.github.com> * add osx builds for rtracklayer, genomicalignments (#55357) * add osx builds fr rtracklayer, genomicalignments * add osx-arm64 & bump build for r-restfulr * Update wally to 0.7.1 (#55380) * add osx-arm64 for bioconductor-deseq2 (#55382) * add osx-arm64 for bioconductor-deseq2 * reset build number * retry bumping build number * Update quantms-rescoring to 0.0.9 (#55391) * Build raxml-ng for osx-arm64 (#55381) * Build raxml-ng for osx-arm64 * bump build number of course * Set cmake minimum to 3.5 * Update nanomotif to 0.6.1 (#55377) * Update cmat to 3.3.3 (#55383) * Add ervmancer (#55385) * init ervmancer bioconda package for PR * update with run_export * chore: update versions for dependencies, update summary and description of package * chore: fix spacing for python deps * chore: fix spacing for all deps * chore: fix phrasing for description/summary * remove channels block * Update psm-utils to 1.4.1 (#55389) * Update pilea to 0.2.1 (#55393) * Update ms2rescore to 3.1.5 (#55387) * Update biscuit to 1.6.1.20250415 (#55394) * Update buscolite to 25.4.3 (#55371) * Update buscolite to 25.4.3 * add packaging --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update augur to 30.0.0 (#55395) * sfld: add linux-aarch64 (#55392) * paraclu: add linux-aarch64 (#55384) * paraclu: add linux-aarch64 * Update meta.yaml: remove whitespace to trigger build; last build was borked by transient net error * add osx-arm64 * Update gottcha2 to 2.1.9 (#55396) * Add r-floral (#55132) * Add r-floral * r-floral lint fixes * r-floral lint fixes * fix r-floral * Update recipes/r-floral/meta.yaml Co-authored-by: Mervin Fansler <mmfansler@gmail.com> * Apply suggestions from code review Co-authored-by: Mervin Fansler <mmfansler@gmail.com> * Add missing dependencies for r-floral --------- Co-authored-by: Mervin Fansler <mmfansler@gmail.com> * Update r-classdiscovery to 3.4.8 (#55165) * Update r-classdiscovery to 3.4.8 * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update Replidec v0.3.4 (#55375) * replidec_v0.3.4 * add run_export * UPDATE:replidec_v0.3.4 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update ampd-up to 1.0.1 (#55397) * delly: add arm64 build (#55398) * add htslib to the run deps (#55388) * Rebuild postmaster recipe (#55400) * Rebuild postmaster recipe * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update msoma to 0.1.1 (#55404) * cdbtools: bump build to with fresher zlib (#55399) * cdbtools: bump build to wih fresher zlib * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * clean up recipe --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> * Update dna_features_viewer to 3.1.4 (#55017) * Update dna_features_viewer to 3.1.4 * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * update concoct (#54560) * concoct * Update meta.yaml * Update build.sh --------- Co-authored-by: ZerryNi <996002763.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update annotsv to 3.4.6 (#54194) * Update annotsv to 3.4.5 * Update annotsv to 3.4.5 * Update annotsv to 3.4.6 * edit tests --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update instanovo to 1.1.1 (#54966) * Update instanovo to 1.1.0 * Update instanovo to 1.1.1 * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update flair to 2.1.2 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update pneumo-typer to v2.0.1#2 (#55406) * Update gcluster to v2.0.7#4 (#55405) * Rebuild lastz recipe (#55410) * Rebuild lastz recipe * Update build.sh * Update caspeak to 1.1.2 (#55411) * Relax Python version requirement to >=3.8 (support Python 3.12) (#55407) * Relax Python version requirement to >=3.8 (support Python 3.12) * Bump build number to 1 for Python 3.12 support * Update sha256 for rebuilt 0.14.2 * Fix sha256 for cdskit 0.14.2 * Fix source URL and sha256 for cdskit v0.14.2 (kfuku52) * Trigger rebuild after upstream fix * Fix source URL and sha256 for cdskit v0.14.2 (kfuku52) * update pigpen_0.0.6 to include r-lme4 and postmaster (#54546) * update pigpen_0.0.6 to include r-lme4 and postmaster * increment build number * postmaster not available for osx * postmaster not available on aarch64 * Update recipes/pigpen/meta.yaml Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com> * Update meta.yaml --------- Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add recipes panaln (#55414) * Create meta.yaml * Create build.sh * Update tower-cli to 0.11.3 (#55416) * Update snakemake to 9.3.0 (#55417) * augustus: add linux-aarch64 (#55413) * augustus: add linux-aarch64 * Create conda_build_config.yaml: pin due to cstdint declaration requirement * aster: add arm64 build (#55415) * aster: add arm64 build * Update build.sh * Update atlas to 2.0.0-rc.10 (#55378) * update to version 10 * for some reason, mkl seems to be needed now * Update fastp to 0.24.1 (#55418) * Update muat to version 0.1.11 (#55420) Co-authored-by: primasan <primasan@ad.helsinki.fi> * Update roadies to 0.1.8 (#53044) * update roadies * updated build files to add correct perl version * fixed package name * updated meta.yaml * fixed mashtree dependencies * added gcc * added c compiler * added gcc to run and host * fix for gcc not working * fix in build file for gcc not working * updated lastz flags * removed conda_build_config file * updated lastz * updated lastz gcc not found error * updated lastz to take current master - temporary fix * updated with new LASTZ release * Update meta.yaml * removed redundant line of code * Update build.sh * Update meta.yaml * add lastz * pin lastz to >=1.04.52 Co-authored-by: M Bernt <m.bernt@ufz.de> * delete extraneous section now that lastz is built with _40 Co-authored-by: M Bernt <m.bernt@ufz.de> * Update build.sh * add aster --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: M Bernt <m.bernt@ufz.de> * Update mehari to 0.35.0 (#53131) * Update mehari to 0.35.0 --------- Co-authored-by: Till Hartmann <till.hartmann@bih-charite.de> Co-authored-by: Till Hartmann <till.hartmann@udo.edu> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update annonars to 0.44.0 (#53114) * Update annonars to 0.44.0 * update recipe meta.yaml --------- Co-authored-by: Till Hartmann <till.hartmann@bih-charite.de> * Update grz-cli to 0.4.0 (#55427) --------- Co-authored-by: Travis Wrightsman <travis@wrightsman.org> * feat: primer3 to support osx-arm64 (#55432) * Update ncbi-stxtyper to 1.0.42 (#55436) * Update r-ukbrapr to 0.3.5 (#55430) * Update captus to 1.4.0 (#55433) * Update roadies to 0.1.10 (#55431) --------- Co-authored-by: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Co-authored-by: Prima Sanjaya <mr.primasanjaya@gmail.com> Co-authored-by: primasan <primasan@ad.helsinki.fi> Co-authored-by: zhenxian <920596906@qq.com> Co-authored-by: Sang Chul Choi <goshng@yahoo.co.kr> Co-authored-by: Sang Chul Choi <sangchulchoi@sungshin.ac.kr> Co-authored-by: Xi Chen <38089207+xinehc@users.noreply.github.com> Co-authored-by: Kez Cleal <42997789+kcleal@users.noreply.github.com> Co-authored-by: eead-csic-compbio <bcontreras@eead.csic.es> Co-authored-by: Fabián Robledo <fabianry97@gmail.com> Co-authored-by: Roberto Rossini <71787608+robomics@users.noreply.github.com> Co-authored-by: Gregg Thomas <gwct@users.noreply.github.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Danielle Callan <53306535+d-callan@users.noreply.github.com> Co-authored-by: Max <visze@users.noreply.github.com> Co-authored-by: dimitris-karapliafis <116268242+dimitris-karapliafis@users.noreply.github.com> Co-authored-by: dtriskar <dkarapliafis@gmail.com> Co-authored-by: Nabil Rahiman <nabil.rahiman@gmail.com> Co-authored-by: niklasmueboe <42138117+niklasmueboe@users.noreply.github.com> Co-authored-by: niklasmueboe <niklasmueboe@github.com> Co-authored-by: alexhold5 <87720137+alexhold5@users.noreply.github.com> Co-authored-by: joshuazhuang7 <joshua.zhuang@yahoo.com> Co-authored-by: Moray Smith <65286772+SwiftSeal@users.noreply.github.com> Co-authored-by: Brandon Hastings <65084955+brandon-hastings@users.noreply.github.com> Co-authored-by: Clea Siguret <37694850+clsiguret@users.noreply.github.com> Co-authored-by: Ryan James Kennedy <67742838+ryanjameskennedy@users.noreply.github.com> Co-authored-by: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Co-authored-by: nextstrain-bot <nextstrainbot@nextstrain.org> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Tommi Mäklin <tommi@maklin.fi> Co-authored-by: pirovc <4673375+pirovc@users.noreply.github.com> Co-authored-by: David Lecomber <david.lecomber@arm.com> Co-authored-by: Sebastián Ayala Ruano <52267585+sayalaruano@users.noreply.github.com> Co-authored-by: SciLiciumTheo <101104633+SciLiciumTheo@users.noreply.github.com> Co-authored-by: RolandFaure <64131971+RolandFaure@users.noreply.github.com> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> Co-authored-by: Hugo Tavares <tavareshugo@users.noreply.github.com> Co-authored-by: Vivaswat Shastry <vivshastry@gmail.com> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Jana Hoffmann <105642758+janaHoffmann1@users.noreply.github.com> Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Co-authored-by: Anthony Duncan <36088426+apduncan@users.noreply.github.com> Co-authored-by: Nathan Edwards <edwardsnj@users.noreply.github.com> Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: UENO, M. <eunosium-1128@live.jp> Co-authored-by: Ryan Doughty <57912116+rdoughty10@users.noreply.github.com> Co-authored-by: Jens Luebeck <jluebeck@ucsd.edu> Co-authored-by: Don Freed <DonFreed@users.noreply.github.com> Co-authored-by: Rubén Chaves <ruben.chaves@irbbarcelona.org> Co-authored-by: mzytnicki <34034101+mzytnicki@users.noreply.github.com> Co-authored-by: Aaron Petkau <aaron.petkau@gmail.com> Co-authored-by: Pavel V. Dimens <19176506+pdimens@users.noreply.github.com> Co-authored-by: Michael Kovaliov <32510658+RedPenguin100@users.noreply.github.com> Co-authored-by: Florian Plaza Oñate <4588656+fplazaonate@users.noreply.github.com> Co-authored-by: AndreaGuarracino <andreaguarracino@outlook.com> Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com> Co-authored-by: Iago Bonnici <iago.bonnici@umontpellier.fr> Co-authored-by: Mrinmoy Saha Roddur <mrinmoy.roddur@gmail.com> Co-authored-by: Yuan Gao <107954058+ygao61@users.noreply.github.com> Co-authored-by: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Co-authored-by: Jean Mainguy <jean.mainguy@outlook.fr> Co-authored-by: Jacques Dainat <jacques.dainat@gmail.com> Co-authored-by: Alicia A. Evans <108547992+aliciaaevans@users.noreply.github.com> Co-authored-by: Apratim Mitra <16709900+mitraak@users.noreply.github.com> Co-authored-by: Li Yao <ly349@cornell.edu> Co-authored-by: Antônio Camargo <apcamargo@users.noreply.github.com> Co-authored-by: y3tseng <146570926+y3tseng@users.noreply.github.com> Co-authored-by: y3tseng <y3tseng@AD.UCSD.EDU@raptor.ucsd.edu> Co-authored-by: UriNeri <41674327+UriNeri@users.noreply.github.com> Co-authored-by: Cornelius Roemer <cornelius.roemer@gmail.com> Co-authored-by: Oliver Schwengers <oliver.schwengers@computational.bio.uni-giessen.de> Co-authored-by: grabherr <manfredgrabherr@gmail.com> Co-authored-by: Asaka Yusuke <48976189+kamome1201@users.noreply.github.com> Co-authored-by: Adam Taranto <adam.p.taranto@gmail.com> Co-authored-by: SantaMcCloud <100047964+SantaMcCloud@users.noreply.github.com> Co-authored-by: Mervin Fansler <mervin.fansler@bric.ku.dk> Co-authored-by: ZerryNi <47553636+ZerryNi@users.noreply.github.com> Co-authored-by: Saim Momin <64724322+SaimMomin12@users.noreply.github.com> Co-authored-by: Bryant Duong <bryantduong@users.noreply.github.com> Co-authored-by: Tyler Funnell <tfunnell@coh.org> Co-authored-by: Mervin Fansler <mmfansler@gmail.com> Co-authored-by: pengSherryYel <32877803+pengSherryYel@users.noreply.github.com> Co-authored-by: Xiangyang1984 <58356520+Xiangyang1984@users.noreply.github.com> Co-authored-by: Matthew Taliaferro <taliaferrojm@gmail.com> Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com> Co-authored-by: Guo3 <jgxygll@163.com> Co-authored-by: David Lecomber <david+dslarm@lecomber.net> Co-authored-by: Andreas Füglistaler <andreas.fueglistaler@protonmail.com> Co-authored-by: Anshu Gupta <114828525+ang037@users.noreply.github.com> Co-authored-by: M Bernt <m.bernt@ufz.de> Co-authored-by: Till Hartmann <till.hartmann@bih-charite.de> Co-authored-by: Till Hartmann <till.hartmann@udo.edu> Co-authored-by: Travis Wrightsman <travis@wrightsman.org> Co-authored-by: Nils Homer <nh13@users.noreply.github.com>
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Adding R package BPCells as
r-bpcells.Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
Please use the following BiocondaBot commands:
Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
Note that the
@BiocondaBot please mergecommand is now depreciated. Please just squash and merge instead.Also, the bot watches for comments from non-members that include
@bioconda/<team>and will automatically re-post them to notify the addressed<team>.