{ "_id": "6a5fb65114e95619b75d7102", "Package": "ZarrArray", "Title": "Bring Zarr datasets in R as DelayedArray objects", "Description": "The ZarrArray package leverages the Rarr package to bring\nZarr datasets in R as DelayedArray objects. The main class in\nthe package is the ZarrArray class. A ZarrArray object is an\narray-like object that represents a Zarr dataset in R.\nZarrArray objects are DelayedArray derivatives and therefore\nsupport all operations (delayed or block-processed) supported\nby DelayedArray objects.", "biocViews": "Infrastructure, DataRepresentation, DataImport", "URL": "https://bioconductor.org/packages/ZarrArray", "BugReports": "https://github.com/Bioconductor/ZarrArray/issues", "Version": "1.1.3", "License": "Artistic-2.0", "Encoding": "UTF-8", "Authors@R": "c(\nperson(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\",\ncomment=c(ORCID=\"0009-0002-8272-4522\")),\nperson(\"Mike\", \"Smith\", role=\"aut\",\ncomment=c(ORCID=\"0000-0002-7800-3848\")),\nperson(\"Hugo\", \"Gruson\", role=\"aut\",\nemail=\"hugo.gruson@embl.de\",\ncomment=c(ORCID=\"0000-0002-4094-1476\")),\nperson(\"Artür\", \"Manukyan\", role=\"aut\",\nemail=\"artur-man@hotmail.com\",\ncomment=c(ORCID=\"0000-0002-0441-9517\")),\nperson(\"Levi\", \"Waldron\", role=\"fnd\",\nemail=\"levi.waldron@sph.cuny.edu\",\ncomment=c(ORCID=\"0000-0003-2725-0694\")))", "VignetteBuilder": "knitr", "Collate": "utils.R options.R ZarrArraySeed-class.R ZarrArray-class.R\nwriteZarrArray-auto-args.R writeZarrArray.R\nZarrSparseMatrixSeed-class.R ZarrSparseMatrix-class.R zzz.R", "Config/pak/sysreqs": "libblosc-dev libxml2-dev libzstd-dev libssl-dev\nzlib1g-dev", "Repository": "https://huber-group-embl.r-universe.dev", "Date/Publication": "2026-07-21 17:05:11 UTC", "RemoteUrl": "https://github.com/Bioconductor/ZarrArray", "RemoteRef": "HEAD", "RemoteSha": "092c417853c7cd2a8a171142e92c46a49b3a58c7", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-21 18:06:31 UTC", "User": "root" }, "Author": "Hervé Pagès [aut, cre] (ORCID: ),\nMike Smith [aut] (ORCID: ),\nHugo Gruson [aut] (ORCID: ),\nArtür Manukyan [aut] (ORCID: ),\nLevi Waldron [fnd] (ORCID: )", "Maintainer": "Hervé Pagès ", "_user": "huber-group-embl", "_type": "src", "_file": "ZarrArray_1.1.3.tar.gz", "_fileid": "https://r2.ropensci.org/2792259ba1154a2702d8f24dabede8a5b37220f71cdf8c13edd84c043f89cd96", "_filesize": 175378, "_sha256": "2792259ba1154a2702d8f24dabede8a5b37220f71cdf8c13edd84c043f89cd96", "_expires": "2026-10-29T18:11:27.000Z", "_created": "2026-07-21T18:06:31.000Z", "_published": "2026-07-21T18:11:28.772Z", "_jobs": [ { "job": 88719840336, "time": 211, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8505322499" }, { "job": 88719840296, "time": 238, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8505334260" }, { "job": 88719840352, "time": 137, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8505288281" }, { "job": 88719840349, "time": 149, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8505293489" }, { "job": 88718852205, "time": 244, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8505221917" }, { "job": 88719840326, "time": 138, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8505288336" }, { "job": 88719840331, "time": 211, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "8505322387" }, { "job": 88719840532, "time": 180, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8505309042" }, { "job": 88719840272, "time": 196, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8505315463" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/huber-group-embl/actions/runs/29855522911", "_status": "success", "_upstream": "https://github.com/Bioconductor/ZarrArray", "_commit": { "id": "092c417853c7cd2a8a171142e92c46a49b3a58c7", "author": "Hugo Gruson ", "committer": "GitHub ", "message": "Replace inefficient patterns (#10)\n\n* Use startsWith() instead of substr()\n\nmicrobenchmark::microbenchmark(file.path(\"a\", \"b\"), paste0(\"a\", \"/\", \"b\"), times = 1e4)\n#> Unit: nanoseconds\n#> expr min lq mean median uq max neval\n#> file.path(\"a\", \"b\") 574 639 1022.293 677 763 84528 10000\n#> paste0(\"a\", \"/\", \"b\") 848 943 1403.952 1009 1111 170456 10000\n\n* Use !nzchar() instead of == \"\"\n\nmicrobenchmark::microbenchmark(\"test/test/test/test\" == \"\", !nzchar(\"test/test/test/test\"), times = 1e4)\n#> Unit: nanoseconds\n#> expr min lq mean median uq max neval\n#> \"test/test/test/test\" == \"\" 60 68 91.1651 74 79 5723 10000\n#> !nzchar(\"test/test/test/test\") 51 58 80.0586 61 70 9719 10000\n\n* Use file.path() consistently\n\nmicrobenchmark::microbenchmark(paste0(\"group\", \"/data\"), paste0(\"group\", \"/\", \"data\"), file.path(\"group\", \"data\"), times = 1e5)\n#> Unit: nanoseconds\n#> expr min lq mean median uq max neval\n#> paste0(\"group\", \"/data\") 786 874 1026.1339 902 957 2266881 1e+05\n#> paste0(\"group\", \"/\", \"data\") 871 968 1151.3651 1000 1081 1589845 1e+05\n#> file.path(\"group\", \"data\") 590 655 786.3354 678 734 1586759 1e+05\n\n* Use dim() <- NULL instead of as.vector()\n\nx <- sample(1:1e7, 1e7, replace = TRUE)\ndim(x) <- 1e7\n\nbench::mark(\n as.vector(x),\n as.integer(x),\n # We assign to y here for benchmarking purposes. To avoid removing dim for our test object after the first iteration.\n {\n y <- x\n dim(y) <- NULL\n y\n },\n iterations = 1000\n)\n#> # A tibble: 3 × 6\n#> expression min median `\nitr/sec` mem_alloc\n`\ngc/sec`\n#> \n#> 1 as.vector(x) 11.5ms 12.3ms 81.3 38.1MB 25.3\n#> 2 as.integer(x) 11.5ms 12.3ms 81.2 38.1MB 20.3\n#> 3 { y <- x dim(y) <- NULL y } 326ns 359ns 2545301. 0B ", "time": 1784653511 }, "_maintainer": { "name": "Hervé Pagès", "email": "hpages.on.github@gmail.com", "login": "hpages", "linkedin": "in/hervé-pagès-5038527", "description": "", "uuid": 8810451, "orcid": "0009-0002-8272-4522" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "SparseArray", "role": "Depends" }, { "package": "DelayedArray", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Arrays", "role": "Imports" }, { "package": "Rarr", "version": ">= 2.1.9", "role": "Imports" }, { "package": "paws.storage", "role": "Suggests" }, { "package": "HDF5Array", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "anndataR", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioconductor", "_selfowned": false, "_usedby": 5, "_updates": [ { "week": "2026-04", "n": 1 }, { "week": "2026-05", "n": 8 }, { "week": "2026-14", "n": 4 }, { "week": "2026-15", "n": 1 }, { "week": "2026-16", "n": 1 }, { "week": "2026-17", "n": 1 }, { "week": "2026-18", "n": 3 }, { "week": "2026-29", "n": 3 }, { "week": "2026-30", "n": 4 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.1.2", "bioc": "3.24" }, { "branch": "release", "version": "1.0.0", "bioc": "3.23" } ], "_topics": [ "infrastructure", "datarepresentation", "dataimport", "bioconductor-package", "core-package", "u24ca289073" ], "_stars": 5, "_contributors": [ { "user": "hpages", "count": 20, "uuid": 8810451 }, { "user": "bisaloo", "count": 3, "uuid": 10783929 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 }, { "user": "artur-man", "count": 2, "uuid": 39335576 } ], "_userbio": { "uuid": 57364287, "type": "organization", "name": "EMBL Huber Group", "followers": 19, "description": "Repository for joint projects by members and ex-members of the Huber group at EMBL. 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