{ "_id": "6a197cb4acfb0bcc41df6723", "Package": "basilisk", "Version": "1.24.0", "Date": "2025-05-19", "Title": "Freezing Python Dependencies Inside Bioconductor Packages", "Authors@R": "c(person(\"Aaron\", \"Lun\", role=c(\"aut\", \"cre\", \"cph\"),\nemail=\"infinite.monkeys.with.keyboards@gmail.com\"),\nperson(\"Vince\", \"Carey\", role=\"ctb\"))", "biocViews": "Infrastructure", "Description": "Installs a self-contained conda instance that is managed\nby the R/Bioconductor installation machinery. This aims to\nprovide a consistent Python environment that can be used\nreliably by Bioconductor packages. Functions are also provided\nto enable smooth interoperability of multiple Python\nenvironments in a single R session.", "License": "GPL-3", "RoxygenNote": "7.3.2", "StagedInstall": "false", "VignetteBuilder": "knitr", "BugReports": "https://github.com/LTLA/basilisk/issues", "Encoding": "UTF-8", "Config/pak/sysreqs": "libpng-dev python3", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:51:49 UTC", "RemoteUrl": "https://github.com/bioc/basilisk", "RemoteRef": "RELEASE_3_23", "RemoteSha": "e0f57932e79e0a3099126ebba1221bd07cde4c30", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 09:10:39 UTC", "User": "root" }, "Author": "Aaron Lun [aut, cre, cph],\nVince Carey [ctb]", "Maintainer": "Aaron Lun ", "MD5sum": "1f58676a42c8999c345ddf6206f56c3a", "_user": "bioc-release", "_type": "src", "_file": "basilisk_1.24.0.tar.gz", "_fileid": "62cad5959056b0e5e7161dd1ff78c595933e6924431258173d4225f4e64fef8e", "_filesize": 200771, "_sha256": "62cad5959056b0e5e7161dd1ff78c595933e6924431258173d4225f4e64fef8e", "_created": "2026-05-29T09:10:39.000Z", "_published": "2026-05-29T11:47:00.129Z", "_jobs": [ { "job": 78471860257, "time": 150, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7287230631" }, { "job": 78471860221, "time": 2215, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7287863352" }, { "job": 78471860135, "time": 2546, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7287962142" }, { "job": 78471860176, "time": 775, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7289858528" }, { "job": 78471860210, "time": 926, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7289900272" }, { "job": 78469288377, "time": 1028, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7287184948" }, { "job": 78471860143, "time": 115, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7287219766" }, { "job": 78471860177, "time": 619, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7287375448" }, { "job": 78471860191, "time": 667, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7287390840" }, { "job": 78471860243, "time": 722, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7287408740" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627947955", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/basilisk", "_commit": { "id": "e0f57932e79e0a3099126ebba1221bd07cde4c30", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380709 }, "_maintainer": { "name": "Aaron Lun", "email": "infinite.monkeys.with.keyboards@gmail.com", "login": "ltla", "twitter": "@realAaronLun", "description": "(ノಠ益ಠ)ノ彡┻━┻\n", "uuid": 8166669 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "reticulate", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "dir.expiry", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "callr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 42, "_updates": [ { "week": "2025-35", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "infrastructure", "bioconductor-package" ], "_stars": 29, "_contributors": [ { "user": "ltla", "count": 468, "uuid": 8166669 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "vjcitn", "count": 6, "uuid": 4624066 }, { "user": "hpages", "count": 3, "uuid": 8810451 }, { "user": "mbstadler", "count": 2, "uuid": 13657342 }, { "user": "csoneson", "count": 1, "uuid": 5628952 }, { "user": "jfortin1", "count": 1, "uuid": 2328424 }, { "user": "martin-g", "count": 1, "uuid": 232002 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 6297, "source": "https://www.bioconductor.org/packages/stats/bioc/basilisk" }, "_devurl": "https://github.com/ltla/basilisk", "_searchresults": 127, "_rbuild": "4.6.0", "_assets": [ "extra/basilisk.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ltla/basilisk", "_realowner": "bioc", "_cranurl": false, "_exports": [ "BasiliskEnvironment", "basiliskRun", "basiliskStart", "basiliskStop", "clearExternalDir", "configureBasiliskEnv", "createLocalBasiliskEnv", "defaultPythonVersion", "destroyOldVersions", "getBasiliskCheckVersions", "getBasiliskFork", "getBasiliskShared", "getExternalDir", "getPythonBinary", "getSystemDir", "isLinux", "isLinuxAarch64", "isMacOSX", "isMacOSXArm", "isWindows", "listPackages", "listPythonVersion", "lockExternalDir", "obtainEnvironmentPath", "PyPiLink", "setBasiliskCheckVersions", "setBasiliskFork", "setBasiliskShared", "setupBasiliskEnv", "unlockExternalDir", "useBasiliskEnv", "useSystemDir" ], "_help": [ { "page": "BasiliskEnvironment-class", "title": "The BasiliskEnvironment class", "topics": [ "BasiliskEnvironment", "BasiliskEnvironment-class" ] }, { "page": "basiliskStart", "title": "Start and stop 'basilisk'-related processes", "topics": [ "basiliskRun", "basiliskStart", "basiliskStop" ] }, { "page": "clearExternalDir", "title": "Clear the external installation directory", "topics": [ "clearExternalDir" ] }, { "page": "configureBasiliskEnv", "title": "Configure client environments", "topics": [ "configureBasiliskEnv" ] }, { "page": "createLocalBasiliskEnv", "title": "Manually create a local virtual environment manually", "topics": [ "createLocalBasiliskEnv" ] }, { "page": "destroyOldVersions", "title": "Destroy old versions?", "topics": [ "destroyOldVersions" ] }, { "page": "basiliskOptions", "title": "Options for 'basilisk'", "topics": [ "getBasiliskCheckVersions", "getBasiliskFork", "getBasiliskShared", "setBasiliskCheckVersions", "setBasiliskFork", "setBasiliskShared" ] }, { "page": "getExternalDir", "title": "External directory for virtual environments", "topics": [ "getExternalDir" ] }, { "page": "getBinaries", "title": "Get Python binary paths", "topics": [ "getPythonBinary" ] }, { "page": "getSystemDir", "title": "Get the system installation directory", "topics": [ "getSystemDir" ] }, { "page": "platform", "title": "Find the operating system or architecture.", "topics": [ "isLinux", "isLinuxAarch64", "isMacOSX", "isMacOSXArm", "isWindows" ] }, { "page": "listPackages", "title": "List packages", "topics": [ "listPackages", "listPythonVersion" ] }, { "page": "lockExternalDir", "title": "Lock external directory", "topics": [ "lockExternalDir", "unlockExternalDir" ] }, { "page": "obtainEnvironmentPath", "title": "Obtain the environment path", "topics": [ "obtainEnvironmentPath" ] }, { "page": "PyPiLink", "title": "Link to PyPi", "topics": [ "PyPiLink" ] }, { "page": "setupBasiliskEnv", "title": "Set up 'basilisk'-managed environments", "topics": [ "defaultPythonVersion", "setupBasiliskEnv" ] }, { "page": "useBasiliskEnv", "title": "Use 'basilisk' environments", "topics": [ "useBasiliskEnv" ] }, { "page": "useSystemDir", "title": "Use the R system directory?", "topics": [ "useSystemDir" ] } ], "_readme": "https://github.com/bioc/basilisk/raw/RELEASE_3_23/README.md", "_rundeps": [ "dir.expiry", "filelock", "here", "jsonlite", "lattice", "Matrix", "png", "rappdirs", "Rcpp", "RcppTOML", "reticulate", "rlang", "rprojroot", "withr" ], "_vignettes": [ { "source": "motivation.Rmd", "filename": "motivation.html", "title": "Freezing Python versions inside Bioconductor packages", "author": "Aaron Lun", "engine": "knitr::rmarkdown", "headings": [ "Overview", "For package developers", "Setting up the package", "Specifying Python environments", "Defining BasiliskEnvironment objects", "Populating environments on installation", "Using the environments", "Basics", "Function constraints", "Persisting variables across calls", "For end users", "Troubleshooting known issues", "Fine-tuning basilisk's behavior", "Using basilisk directly for analyses", "Session information" ], "created": "2019-10-05 10:58:47", "modified": "2025-05-19 20:40:18", "commits": 45 } ], "_score": 10.544887203322164, "_indexed": false, "_nocasepkg": "basilisk", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/basilisk", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.24.0", "date": "2026-05-29T09:13:09.000Z", "distro": "noble", "commit": "e0f57932e79e0a3099126ebba1221bd07cde4c30", "fileid": "40525badf1384b5585bf5c48e83fafd48e293bd1fe63ed48b4ec380be7d7cb38", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627947955" }, { "r": "4.6.0", "os": "linux", "version": "1.24.0", "date": "2026-05-29T09:18:59.000Z", "distro": "noble", "commit": "e0f57932e79e0a3099126ebba1221bd07cde4c30", "fileid": "73364be90b00c29255bc071b81feedad7cc3375a484c79acc3116851ddb368c2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627947955" }, { "r": "4.5.3", "os": "mac", "version": "1.24.0", "date": "2026-05-29T11:32:35.000Z", "commit": "e0f57932e79e0a3099126ebba1221bd07cde4c30", "fileid": "857fb67c3696577f6100bb3d7fb8e59edf348c590f40bb717e576665cd50bc9e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627947955" }, { "r": "4.6.0", "os": "mac", "version": "1.24.0", "date": "2026-05-29T11:32:17.000Z", "commit": "e0f57932e79e0a3099126ebba1221bd07cde4c30", "fileid": "67d5744a08989553c3b31e3f46724d8ab956b15815f00d28fdf174e99e19e898", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627947955" }, { "r": "4.6.0", "os": "wasm", "version": "1.24.0", "date": "2026-05-29T09:12:50.000Z", "commit": "e0f57932e79e0a3099126ebba1221bd07cde4c30", "fileid": "5971974e795e5bba65676fb59d9fada5b037d0cb541a6b1e3fd7e8a1df93ffa8", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627947955" }, { "r": "4.7.0", "os": "win", "version": "1.24.0", "date": "2026-05-29T09:11:52.000Z", "commit": "e0f57932e79e0a3099126ebba1221bd07cde4c30", "fileid": "7fe5557ca22ebc6f5665b85294db5be2bce85bf66bc90bef435277afe2c0d5af", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627947955" }, { "r": "4.5.3", "os": "win", "version": "1.24.0", "date": "2026-05-29T09:11:58.000Z", "commit": "e0f57932e79e0a3099126ebba1221bd07cde4c30", "fileid": "220c64a8608beb0bff57ebc23f240863bdbaf4f943a26c2859debcf7824eb4d6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627947955" }, { "r": "4.6.0", "os": "win", "version": "1.24.0", "date": "2026-05-29T09:12:09.000Z", "commit": "e0f57932e79e0a3099126ebba1221bd07cde4c30", "fileid": "2c05dbc16161fd84bbd1ec57df386372be0ecd0d0ec0d38b3ec22a4e54694553", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627947955" } ] }