tservice-plugins
/
quartet-rnaseq-report
ウォッチ 1
スター 0
フォーク 0
コード 課題 0 プルリクエスト 0 リリース 5 Wiki アクティビティ
ソースを参照

Fix dependencies.

tags/v0.1.1
YJC 3年前
親
557aeacf35
コミット
d5bb973165
5個のファイルの変更、1219行の追加、84行の削除
分割表示
差分オプション
統計情報を表示 Patchファイルをダウンロード Diffファイルをダウンロード
  1. +0
    -9
      resources/quartet_rnaseq_report.yaml
  2. +858
    -0
      resources/renv.lock
  3. +2
    -0
      resources/renv/.gitignore
  4. +359
    -55
      resources/renv/activate.R
  5. +0
    -20
      resources/renv/renv.lock

+ 0
- 9
resources/quartet_rnaseq_report.yaml ファイルの表示

@@ -1,9 +0,0 @@
run_modules:
- rnaseq_data_generation_information
- rnaseq_performance_assessment
- rnaseq_raw_qc
- rnaseq_post_alignment_qc
- rnaseq_quantification_qc
- rnaseq_supplementary

skip_generalstats: true

+ 858
- 0
resources/renv.lock ファイルの表示

@@ -0,0 +1,858 @@
{
"R": {
"Version": "3.6.3",
"Repositories": [
{
"Name": "CRAN",
"URL": "https://cloud.r-project.org"
}
]
},
"Bioconductor": {
"Version": "3.10"
},
"Packages": {
"BH": {
"Package": "BH",
"Version": "1.72.0-3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "8f9ce74c6417d61f0782cbae5fd2b7b0"
},
"BiocManager": {
"Package": "BiocManager",
"Version": "1.30.12",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "462dbb15753eb52fb62e28507f382d2d"
},
"BiocVersion": {
"Package": "BiocVersion",
"Version": "3.10.1",
"Source": "Bioconductor",
"Hash": "b69e4e634db423b8e6c58103d579ec95"
},
"DT": {
"Package": "DT",
"Version": "0.15",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "85738c69035e67ec4b484a5e02640ef6"
},
"KernSmooth": {
"Package": "KernSmooth",
"Version": "2.23-16",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "997471f25a7ed6c782f0090ce52cc63a"
},
"MASS": {
"Package": "MASS",
"Version": "7.3-52",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "095c8b0dd20f5d9c2a75cf72fdd74dab"
},
"Matrix": {
"Package": "Matrix",
"Version": "1.2-18",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "08588806cba69f04797dab50627428ed"
},
"R6": {
"Package": "R6",
"Version": "2.4.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "292b54f8f4b94669b08f94e5acce6be2"
},
"RColorBrewer": {
"Package": "RColorBrewer",
"Version": "1.1-2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e031418365a7f7a766181ab5a41a5716"
},
"Rcpp": {
"Package": "Rcpp",
"Version": "0.12.18",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "75ffd49f2ce7309ffd72ca94b491ccf4"
},
"askpass": {
"Package": "askpass",
"Version": "1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e8a22846fff485f0be3770c2da758713"
},
"assertthat": {
"Package": "assertthat",
"Version": "0.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "7b2aa2be4bd0497000a5a399f07da3f1"
},
"backports": {
"Package": "backports",
"Version": "1.1.9",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b29e2d989dfb2e71ca3fd7d5bb1c0d58"
},
"base64enc": {
"Package": "base64enc",
"Version": "0.1-3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "543776ae6848fde2f48ff3816d0628bc"
},
"boot": {
"Package": "boot",
"Version": "1.3-24",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "72557d88b5f42f01221dfa436de99301"
},
"brew": {
"Package": "brew",
"Version": "1.0-6",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "92a5f887f9ae3035ac7afde22ba73ee9"
},
"callr": {
"Package": "callr",
"Version": "3.4.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "643163a00cb536454c624883a10ae0bc"
},
"class": {
"Package": "class",
"Version": "7.3-15",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "4fba6a022803b6c3f30fd023be3fa818"
},
"cli": {
"Package": "cli",
"Version": "2.0.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ff0becff7bfdfe3f75d29aff8f3172dd"
},
"clipr": {
"Package": "clipr",
"Version": "0.7.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "08cf4045c149a0f0eaf405324c7495bd"
},
"cluster": {
"Package": "cluster",
"Version": "2.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "db63a44aab5aadcb6bf2f129751d129a"
},
"codetools": {
"Package": "codetools",
"Version": "0.2-16",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "89cf4b8207269ccf82fbeb6473fd662b"
},
"colorspace": {
"Package": "colorspace",
"Version": "1.4-1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6b436e95723d1f0e861224dd9b094dfb"
},
"commonmark": {
"Package": "commonmark",
"Version": "1.7",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0f22be39ec1d141fd03683c06f3a6e67"
},
"covr": {
"Package": "covr",
"Version": "3.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "cbc6df1ef6ee576f844f973c1fc04ab4"
},
"cowplot": {
"Package": "cowplot",
"Version": "1.0.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "82bae0172ae9d4c4f88a440ad01f73bb"
},
"crayon": {
"Package": "crayon",
"Version": "1.3.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0d57bc8e27b7ba9e45dba825ebc0de6b"
},
"crosstalk": {
"Package": "crosstalk",
"Version": "1.1.0.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ae55f5d7c02f0ab43c58dd050694f2b4"
},
"curl": {
"Package": "curl",
"Version": "4.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "2b7d10581cc730804e9ed178c8374bd6"
},
"data.table": {
"Package": "data.table",
"Version": "1.13.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "06d5863292e2e8ffbb063ce34e77bb2a"
},
"desc": {
"Package": "desc",
"Version": "1.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6c8fe8fa26a23b79949375d372c7b395"
},
"devtools": {
"Package": "devtools",
"Version": "2.3.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "271df6a328617c64149283e98b1cd8da"
},
"digest": {
"Package": "digest",
"Version": "0.6.15",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "706759233d88683f590d78ab6c82360a"
},
"dplyr": {
"Package": "dplyr",
"Version": "1.0.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "d0509913b27ea898189ee664b6030dc2"
},
"edgeR": {
"Package": "edgeR",
"Version": "3.28.1",
"Source": "Bioconductor",
"Hash": "89c7b7cf2495fd8a434f6d0b40ec5060"
},
"ellipsis": {
"Package": "ellipsis",
"Version": "0.3.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "fd2844b3a43ae2d27e70ece2df1b4e2a"
},
"evaluate": {
"Package": "evaluate",
"Version": "0.14",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ec8ca05cffcc70569eaaad8469d2a3a7"
},
"exp2qcdt": {
"Package": "exp2qcdt",
"Version": "0.2.2",
"Source": "GitHub",
"RemoteType": "github",
"RemoteHost": "api.github.com",
"RemoteRepo": "exp2qcdt",
"RemoteUsername": "clinico-omics",
"RemoteRef": "HEAD",
"RemoteSha": "319a5eba8f9b5b5e3355ac8045f573a400627583",
"Hash": "31f1244a56a68cfb8184738fd9210523"
},
"fansi": {
"Package": "fansi",
"Version": "0.4.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "7fce217eaaf8016e72065e85c73027b5"
},
"farver": {
"Package": "farver",
"Version": "2.0.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "dad6793a5a1f73c8e91f1a1e3e834b05"
},
"foreign": {
"Package": "foreign",
"Version": "0.8-75",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9a7efaa7320b9f327a904d1e615b0b46"
},
"fs": {
"Package": "fs",
"Version": "1.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "44594a07a42e5f91fac9f93fda6d0109"
},
"gdata": {
"Package": "gdata",
"Version": "2.18.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "465ccb84427f5fe2c54f8620666db131"
},
"generics": {
"Package": "generics",
"Version": "0.0.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b8cff1d1391fd1ad8b65877f4c7f2e53"
},
"ggplot2": {
"Package": "ggplot2",
"Version": "3.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "4ded8b439797f7b1693bd3d238d0106b"
},
"ggthemes": {
"Package": "ggthemes",
"Version": "4.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "dfa67ccc3fb199f102a34d557ec1ff45"
},
"gh": {
"Package": "gh",
"Version": "1.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "89ea5998938d1ad55f035c8a86f96b74"
},
"git2r": {
"Package": "git2r",
"Version": "0.27.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "531a82d1beed1f545beb25f4f5945bf7"
},
"glue": {
"Package": "glue",
"Version": "1.4.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f43e0d5e85ccb0a4045670c0607ee504"
},
"gmodels": {
"Package": "gmodels",
"Version": "2.18.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "beb8ca96406a2828f25e49ab17001c39"
},
"gtable": {
"Package": "gtable",
"Version": "0.3.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ac5c6baf7822ce8732b343f14c072c4d"
},
"gtools": {
"Package": "gtools",
"Version": "3.8.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0a749b4458d19a54acae93c64e3e7c85"
},
"highr": {
"Package": "highr",
"Version": "0.8",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "4dc5bb88961e347a0f4d8aad597cbfac"
},
"htmltools": {
"Package": "htmltools",
"Version": "0.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "7d651b7131794fe007b1ad6f21aaa401"
},
"htmlwidgets": {
"Package": "htmlwidgets",
"Version": "1.5.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "41bace23583fbc25089edae324de2dc3"
},
"httr": {
"Package": "httr",
"Version": "1.4.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "a525aba14184fec243f9eaec62fbed43"
},
"ini": {
"Package": "ini",
"Version": "0.3.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6154ec2223172bce8162d4153cda21f7"
},
"isoband": {
"Package": "isoband",
"Version": "0.2.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6e58bd3d6b3dd82a944cd6f05ade228f"
},
"jsonlite": {
"Package": "jsonlite",
"Version": "1.7.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "2657f20b9a74c996c602e74ebe540b06"
},
"knitr": {
"Package": "knitr",
"Version": "1.29",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e5f4c41c17df8cdf7b0df12117c0d99a"
},
"labeling": {
"Package": "labeling",
"Version": "0.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "73832978c1de350df58108c745ed0e3e"
},
"later": {
"Package": "later",
"Version": "1.1.0.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "d0a62b247165aabf397fded504660d8a"
},
"lattice": {
"Package": "lattice",
"Version": "0.20-38",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "848f8c593fd1050371042d18d152e3d7"
},
"lazyeval": {
"Package": "lazyeval",
"Version": "0.2.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "d908914ae53b04d4c0c0fd72ecc35370"
},
"lifecycle": {
"Package": "lifecycle",
"Version": "0.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "361811f31f71f8a617a9a68bf63f1f42"
},
"limma": {
"Package": "limma",
"Version": "3.42.2",
"Source": "Bioconductor",
"Hash": "d56e7c663eb11536c78fe2f25d9fa544"
},
"locfit": {
"Package": "locfit",
"Version": "1.5-9.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "760b5b542e8435237d1b3c253bfe18e7"
},
"magrittr": {
"Package": "magrittr",
"Version": "1.5",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "1bb58822a20301cee84a41678e25d9b7"
},
"markdown": {
"Package": "markdown",
"Version": "1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "61e4a10781dd00d7d81dd06ca9b94e95"
},
"memoise": {
"Package": "memoise",
"Version": "1.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "58baa74e4603fcfb9a94401c58c8f9b1"
},
"mgcv": {
"Package": "mgcv",
"Version": "1.8-31",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "4bb7e0c4f3557583e1e8d3c9ffb8ba5c"
},
"mime": {
"Package": "mime",
"Version": "0.9",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e87a35ec73b157552814869f45a63aa3"
},
"munsell": {
"Package": "munsell",
"Version": "0.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6dfe8bf774944bd5595785e3229d8771"
},
"nlme": {
"Package": "nlme",
"Version": "3.1-144",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e80d41932d3cc235ccbbbb9732ae162e"
},
"nnet": {
"Package": "nnet",
"Version": "7.3-12",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "68287aec1f476c41d16ce1ace445800c"
},
"openssl": {
"Package": "openssl",
"Version": "1.4.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b3209c62052922b6c629544d94c8fa8a"
},
"pillar": {
"Package": "pillar",
"Version": "1.4.6",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "bdf26e55ccb7df3e49a490150277f002"
},
"pkgbuild": {
"Package": "pkgbuild",
"Version": "1.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "404684bc4e3685007f9720adf13b06c1"
},
"pkgconfig": {
"Package": "pkgconfig",
"Version": "2.0.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b8a063ca3694e651ac46f71b4bf0e090"
},
"pkgload": {
"Package": "pkgload",
"Version": "1.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b6b150cd4709e0c0c9b5d51ac4376282"
},
"plyr": {
"Package": "plyr",
"Version": "1.8.6",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ec0e5ab4e5f851f6ef32cd1d1984957f"
},
"praise": {
"Package": "praise",
"Version": "1.0.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "a555924add98c99d2f411e37e7d25e9f"
},
"prettyunits": {
"Package": "prettyunits",
"Version": "1.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "95ef9167b75dde9d2ccc3c7528393e7e"
},
"processx": {
"Package": "processx",
"Version": "3.4.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "03446ed0b8129916f73676726cb3c48f"
},
"promises": {
"Package": "promises",
"Version": "1.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "a8730dcbdd19f9047774909f0ec214a4"
},
"ps": {
"Package": "ps",
"Version": "1.3.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "a54a7dfd68124abb2225dbfa9a85c457"
},
"purrr": {
"Package": "purrr",
"Version": "0.3.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "97def703420c8ab10d8f0e6c72101e02"
},
"rcmdcheck": {
"Package": "rcmdcheck",
"Version": "1.3.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ed95895886dab6d2a584da45503555da"
},
"rematch2": {
"Package": "rematch2",
"Version": "2.1.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "76c9e04c712a05848ae7a23d2f170a40"
},
"remotes": {
"Package": "remotes",
"Version": "2.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "430a0908aee75b1fcba0e62857cab0ce"
},
"renv": {
"Package": "renv",
"Version": "0.13.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9f10d9db5b50400c348920c5c603385e"
},
"reshape2": {
"Package": "reshape2",
"Version": "1.4.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "bb5996d0bd962d214a11140d77589917"
},
"rex": {
"Package": "rex",
"Version": "1.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "093584b944440c5cd07a696b3c8e0e4c"
},
"rlang": {
"Package": "rlang",
"Version": "0.4.7",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "c06d2a6887f4b414f8e927afd9ee976a"
},
"roxygen2": {
"Package": "roxygen2",
"Version": "7.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "fcd94e00cc409b25d07ca50f7bf339f5"
},
"rpart": {
"Package": "rpart",
"Version": "4.1-15",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9787c1fcb680e655d062e7611cadf78e"
},
"rprojroot": {
"Package": "rprojroot",
"Version": "1.3-2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f6a407ae5dd21f6f80a6708bbb6eb3ae"
},
"rstudioapi": {
"Package": "rstudioapi",
"Version": "0.11",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "33a5b27a03da82ac4b1d43268f80088a"
},
"rversions": {
"Package": "rversions",
"Version": "2.0.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0ec41191f744d0f5afad8c6f35cc36e4"
},
"scales": {
"Package": "scales",
"Version": "1.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6f76f71042411426ec8df6c54f34e6dd"
},
"sessioninfo": {
"Package": "sessioninfo",
"Version": "1.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "308013098befe37484df72c39cf90d6e"
},
"spatial": {
"Package": "spatial",
"Version": "7.3-11",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f27a078d834614513608da2c08031130"
},
"stringi": {
"Package": "stringi",
"Version": "1.2.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "bca4c3464ae356a8649d907944da78b4"
},
"stringr": {
"Package": "stringr",
"Version": "1.4.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0759e6b6c0957edb1311028a49a35e76"
},
"survival": {
"Package": "survival",
"Version": "3.1-8",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ad25122f95d04988f6f79d69aaadd53d"
},
"sys": {
"Package": "sys",
"Version": "3.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b227d13e29222b4574486cfcbde077fa"
},
"testthat": {
"Package": "testthat",
"Version": "2.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0829b987b8961fb07f3b1b64a2fbc495"
},
"tibble": {
"Package": "tibble",
"Version": "3.0.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "08bd36bd34b20d4f7971d49e81deaab0"
},
"tidyr": {
"Package": "tidyr",
"Version": "0.8.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "95ded1450e6af17d0d3eb4b39233c43d"
},
"tidyselect": {
"Package": "tidyselect",
"Version": "1.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6ea435c354e8448819627cf686f66e0a"
},
"usethis": {
"Package": "usethis",
"Version": "1.6.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e1985f5a9985fea2e338fa7eb99018ca"
},
"utf8": {
"Package": "utf8",
"Version": "1.1.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "4a5081acfb7b81a572e4384a7aaf2af1"
},
"vctrs": {
"Package": "vctrs",
"Version": "0.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "5ba3006888ac62fd5e97b208d00d3317"
},
"viridisLite": {
"Package": "viridisLite",
"Version": "0.3.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ce4f6271baa94776db692f1cb2055bee"
},
"whisker": {
"Package": "whisker",
"Version": "0.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ca970b96d894e90397ed20637a0c1bbe"
},
"withr": {
"Package": "withr",
"Version": "2.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ecd17882a0b4419545691e095b74ee89"
},
"xfun": {
"Package": "xfun",
"Version": "0.16",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b4106139b90981a8bfea9c10bab0baf1"
},
"xml2": {
"Package": "xml2",
"Version": "1.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "d4d71a75dd3ea9eb5fa28cc21f9585e2"
},
"xopen": {
"Package": "xopen",
"Version": "1.0.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6c85f015dee9cc7710ddd20f86881f58"
},
"yaml": {
"Package": "yaml",
"Version": "2.2.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "2826c5d9efb0a88f657c7a679c7106db"
}
}
}

+ 2
- 0
resources/renv/.gitignore ファイルの表示

@@ -1,3 +1,5 @@
library/
local/
lock/
python/
staging/

+ 359
- 55
resources/renv/activate.R ファイルの表示

@@ -2,7 +2,7 @@
local({

# the requested version of renv
version <- "0.12.0"
version <- "0.13.0"

# the project directory
project <- getwd()
@@ -39,16 +39,6 @@ local({
# load bootstrap tools
bootstrap <- function(version, library) {
# read repos (respecting override if set)
repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
if (is.na(repos))
repos <- getOption("repos")
# fix up repos
on.exit(options(repos = repos), add = TRUE)
repos[repos == "@CRAN@"] <- "https://cloud.r-project.org"
options(repos = repos)
# attempt to download renv
tarball <- tryCatch(renv_bootstrap_download(version), error = identity)
if (inherits(tarball, "error"))
@@ -61,6 +51,66 @@ local({
}
renv_bootstrap_tests_running <- function() {
getOption("renv.tests.running", default = FALSE)
}
renv_bootstrap_repos <- function() {
# check for repos override
repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
if (!is.na(repos))
return(repos)
# if we're testing, re-use the test repositories
if (renv_bootstrap_tests_running())
return(getOption("renv.tests.repos"))
# retrieve current repos
repos <- getOption("repos")
# ensure @CRAN@ entries are resolved
repos[repos == "@CRAN@"] <- "https://cloud.r-project.org"
# add in renv.bootstrap.repos if set
default <- c(FALLBACK = "https://cloud.r-project.org")
extra <- getOption("renv.bootstrap.repos", default = default)
repos <- c(repos, extra)
# remove duplicates that might've snuck in
dupes <- duplicated(repos) | duplicated(names(repos))
repos[!dupes]
}
renv_bootstrap_download <- function(version) {
# if the renv version number has 4 components, assume it must
# be retrieved via github
nv <- numeric_version(version)
components <- unclass(nv)[[1]]
methods <- if (length(components) == 4L) {
list(
renv_bootstrap_download_github
)
} else {
list(
renv_bootstrap_download_cran_latest,
renv_bootstrap_download_cran_archive
)
}
for (method in methods) {
path <- tryCatch(method(version), error = identity)
if (is.character(path) && file.exists(path))
return(path)
}
stop("failed to download renv ", version)
}
renv_bootstrap_download_impl <- function(url, destfile) {
mode <- "wb"
@@ -73,7 +123,7 @@ local({
if (fixup)
mode <- "w+b"
download.file(
utils::download.file(
url = url,
destfile = destfile,
mode = mode,
@@ -82,60 +132,92 @@ local({
}
renv_bootstrap_download <- function(version) {
methods <- list(
renv_bootstrap_download_cran_latest,
renv_bootstrap_download_cran_archive,
renv_bootstrap_download_github
)
for (method in methods) {
path <- tryCatch(method(version), error = identity)
if (is.character(path) && file.exists(path))
return(path)
}
renv_bootstrap_download_cran_latest <- function(version) {
stop("failed to download renv ", version)
repos <- renv_bootstrap_download_cran_latest_find(version)
}
message("* Downloading renv ", version, " ... ", appendLF = FALSE)
renv_bootstrap_download_cran_latest <- function(version) {
downloader <- function(type) {
# check for renv on CRAN matching this version
db <- as.data.frame(available.packages(), stringsAsFactors = FALSE)
tryCatch(
utils::download.packages(
pkgs = "renv",
destdir = tempdir(),
repos = repos,
type = type,
quiet = TRUE
),
condition = identity
)
entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
if (nrow(entry) == 0) {
fmt <- "renv %s is not available from your declared package repositories"
stop(sprintf(fmt, version))
}
message("* Downloading renv ", version, " from CRAN ... ", appendLF = FALSE)
info <- tryCatch(
download.packages("renv", destdir = tempdir()),
condition = identity
)
# first, try downloading a binary on Windows + macOS if appropriate
binary <-
!identical(.Platform$pkgType, "source") &&
!identical(getOption("pkgType"), "source") &&
Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
if (binary) {
info <- downloader(type = "binary")
if (!inherits(info, "condition")) {
message("OK (downloaded binary)")
return(info[1, 2])
}
}
# otherwise, try downloading a source tarball
info <- downloader(type = "source")
if (inherits(info, "condition")) {
message("FAILED")
return(FALSE)
}
message("OK")
# report success and return
message("OK (downloaded source)")
info[1, 2]
}
renv_bootstrap_download_cran_latest_find <- function(version) {
all <- renv_bootstrap_repos()
for (repos in all) {
db <- tryCatch(
as.data.frame(
x = utils::available.packages(repos = repos),
stringsAsFactors = FALSE
),
error = identity
)
if (inherits(db, "error"))
next
entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
if (nrow(entry) == 0)
next
return(repos)
}
fmt <- "renv %s is not available from your declared package repositories"
stop(sprintf(fmt, version))
}
renv_bootstrap_download_cran_archive <- function(version) {
name <- sprintf("renv_%s.tar.gz", version)
repos <- getOption("repos")
repos <- renv_bootstrap_repos()
urls <- file.path(repos, "src/contrib/Archive/renv", name)
destfile <- file.path(tempdir(), name)
message("* Downloading renv ", version, " from CRAN archive ... ", appendLF = FALSE)
message("* Downloading renv ", version, " ... ", appendLF = FALSE)
for (url in urls) {
@@ -194,7 +276,7 @@ local({
return(FALSE)
}
message("Done!")
message("OK")
return(destfile)
}
@@ -226,7 +308,7 @@ local({
}
renv_bootstrap_prefix <- function() {
renv_bootstrap_platform_prefix <- function() {
# construct version prefix
version <- paste(R.version$major, R.version$minor, sep = ".")
@@ -245,8 +327,8 @@ local({
components <- c(prefix, R.version$platform)
# include prefix if provided by user
prefix <- Sys.getenv("RENV_PATHS_PREFIX")
if (nzchar(prefix))
prefix <- renv_bootstrap_platform_prefix_impl()
if (!is.na(prefix) && nzchar(prefix))
components <- c(prefix, components)
# build prefix
@@ -254,6 +336,152 @@ local({
}
renv_bootstrap_platform_prefix_impl <- function() {
# if an explicit prefix has been supplied, use it
prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA)
if (!is.na(prefix))
return(prefix)
# if the user has requested an automatic prefix, generate it
auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
if (auto %in% c("TRUE", "True", "true", "1"))
return(renv_bootstrap_platform_prefix_auto())
# empty string on failure
""
}
renv_bootstrap_platform_prefix_auto <- function() {
prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity)
if (inherits(prefix, "error") || prefix %in% "unknown") {
msg <- paste(
"failed to infer current operating system",
"please file a bug report at https://github.com/rstudio/renv/issues",
sep = "; "
)
warning(msg)
}
prefix
}
renv_bootstrap_platform_os <- function() {
sysinfo <- Sys.info()
sysname <- sysinfo[["sysname"]]
# handle Windows + macOS up front
if (sysname == "Windows")
return("windows")
else if (sysname == "Darwin")
return("macos")
# check for os-release files
for (file in c("/etc/os-release", "/usr/lib/os-release"))
if (file.exists(file))
return(renv_bootstrap_platform_os_via_os_release(file, sysinfo))
# check for redhat-release files
if (file.exists("/etc/redhat-release"))
return(renv_bootstrap_platform_os_via_redhat_release())
"unknown"
}
renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) {
# read /etc/os-release
release <- utils::read.table(
file = file,
sep = "=",
quote = c("\"", "'"),
col.names = c("Key", "Value"),
comment.char = "#",
stringsAsFactors = FALSE
)
vars <- as.list(release$Value)
names(vars) <- release$Key
# get os name
os <- tolower(sysinfo[["sysname"]])
# read id
id <- "unknown"
for (field in c("ID", "ID_LIKE")) {
if (field %in% names(vars) && nzchar(vars[[field]])) {
id <- vars[[field]]
break
}
}
# read version
version <- "unknown"
for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
if (field %in% names(vars) && nzchar(vars[[field]])) {
version <- vars[[field]]
break
}
}
# join together
paste(c(os, id, version), collapse = "-")
}
renv_bootstrap_platform_os_via_redhat_release <- function() {
# read /etc/redhat-release
contents <- readLines("/etc/redhat-release", warn = FALSE)
# infer id
id <- if (grepl("centos", contents, ignore.case = TRUE))
"centos"
else if (grepl("redhat", contents, ignore.case = TRUE))
"redhat"
else
"unknown"
# try to find a version component (very hacky)
version <- "unknown"
parts <- strsplit(contents, "[[:space:]]")[[1L]]
for (part in parts) {
nv <- tryCatch(numeric_version(part), error = identity)
if (inherits(nv, "error"))
next
version <- nv[1, 1]
break
}
paste(c("linux", id, version), collapse = "-")
}
renv_bootstrap_library_root_name <- function(project) {
# use project name as-is if requested
asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
if (asis)
return(basename(project))
# otherwise, disambiguate based on project's path
id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
paste(basename(project), id, sep = "-")
}
renv_bootstrap_library_root <- function(project) {
path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
@@ -261,10 +489,13 @@ local({
return(path)
path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
if (!is.na(path))
return(file.path(path, basename(project)))
if (!is.na(path)) {
name <- renv_bootstrap_library_root_name(project)
return(file.path(path, name))
}
file.path(project, "renv/library")
prefix <- renv_bootstrap_profile_prefix()
paste(c(project, prefix, "renv/library"), collapse = "/")
}
@@ -283,8 +514,8 @@ local({
paste("renv", loadedversion, sep = "@")
fmt <- paste(
"renv %1$s was loaded from project library, but renv %2$s is recorded in lockfile.",
"Use `renv::record(\"%3$s\")` to record this version in the lockfile.",
"renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
"Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
"Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
sep = "\n"
)
@@ -296,6 +527,16 @@ local({
}
renv_bootstrap_hash_text <- function(text) {
hashfile <- tempfile("renv-hash-")
on.exit(unlink(hashfile), add = TRUE)
writeLines(text, con = hashfile)
tools::md5sum(hashfile)
}
renv_bootstrap_load <- function(project, libpath, version) {
# try to load renv from the project library
@@ -311,12 +552,69 @@ local({
TRUE
}
renv_bootstrap_profile_load <- function(project) {
# if RENV_PROFILE is already set, just use that
profile <- Sys.getenv("RENV_PROFILE", unset = NA)
if (!is.na(profile) && nzchar(profile))
return(profile)
# check for a profile file (nothing to do if it doesn't exist)
path <- file.path(project, "renv/local/profile")
if (!file.exists(path))
return(NULL)
# read the profile, and set it if it exists
contents <- readLines(path, warn = FALSE)
if (length(contents) == 0L)
return(NULL)
# set RENV_PROFILE
profile <- contents[[1L]]
if (nzchar(profile))
Sys.setenv(RENV_PROFILE = profile)
profile
}
renv_bootstrap_profile_prefix <- function() {
profile <- renv_bootstrap_profile_get()
if (!is.null(profile))
return(file.path("renv/profiles", profile))
}
renv_bootstrap_profile_get <- function() {
profile <- Sys.getenv("RENV_PROFILE", unset = "")
renv_bootstrap_profile_normalize(profile)
}
renv_bootstrap_profile_set <- function(profile) {
profile <- renv_bootstrap_profile_normalize(profile)
if (is.null(profile))
Sys.unsetenv("RENV_PROFILE")
else
Sys.setenv(RENV_PROFILE = profile)
}
renv_bootstrap_profile_normalize <- function(profile) {
if (is.null(profile) || profile %in% c("", "default"))
return(NULL)
profile
}

# load the renv profile, if any
renv_bootstrap_profile_load(project)

# construct path to library root
root <- renv_bootstrap_library_root(project)

# construct library prefix for platform
prefix <- renv_bootstrap_prefix()
prefix <- renv_bootstrap_platform_prefix()

# construct full libpath
libpath <- file.path(root, prefix)
@@ -325,7 +623,13 @@ local({
if (renv_bootstrap_load(project, libpath, version))
return(TRUE)

# load failed; attempt to bootstrap
# load failed; inform user we're about to bootstrap
prefix <- paste("# Bootstrapping renv", version)
postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "")
header <- paste(prefix, postfix)
message(header)

# perform bootstrap
bootstrap(version, libpath)

# exit early if we're just testing bootstrap
@@ -334,7 +638,7 @@ local({

# try again to load
if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
message("Successfully installed and loaded renv ", version, ".")
message("* Successfully installed and loaded renv ", version, ".")
return(renv::load())
}


+ 0
- 20
resources/renv/renv.lock ファイルの表示

@@ -1,20 +0,0 @@
{
"R": {
"Version": "3.6.3",
"Repositories": [
{
"Name": "CRAN",
"URL": "https://cloud.r-project.org"
}
]
},
"Packages": {
"renv": {
"Package": "renv",
"Version": "0.13.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "9f10d9db5b50400c348920c5c603385e"
}
}
}

書き込み プレビュー
読み込み中…
キャンセル
保存