Added CompoundDb for optional internal helpers

taxonomicallyinformedannotation · Aug 2, 2024 · c13efed · c13efed
1 parent 200920d
commit c13efed
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Showing 2 changed files with 53 additions and 52 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -19,6 +19,7 @@ Depends:
 Imports:
  bs4Dash (>= 2.3.3),
  cli (>= 3.6.3),
+ CompoundDb (>=1.6.0),
  crayon (>= 1.5.3),
  docopt (>= 0.7.1),
  dplyr (>= 1.1.4),
@@ -60,7 +61,6 @@ Imports:
  yaml (>= 2.3.10)
 Suggests: 
  BiocManager,
- CompoundDb,
  knitr,
  pkgload,
  shinytest2,

diff --git a/codemeta.json b/codemeta.json
@@ -55,18 +55,6 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=BiocManager"
  },
- {
- "@type": "SoftwareApplication",
- "identifier": "CompoundDb",
- "name": "CompoundDb",
- "provider": {
- "@id": "https://www.bioconductor.org",
- "@type": "Organization",
- "name": "Bioconductor",
- "url": "https://www.bioconductor.org"
- },
- "sameAs": "https://bioconductor.org/packages/release/bioc/html/CompoundDb.html"
- },
  {
  "@type": "SoftwareApplication",
  "identifier": "knitr",
@@ -163,6 +151,19 @@
  "sameAs": "https://CRAN.R-project.org/package=cli"
  },
  "4": {
+ "@type": "SoftwareApplication",
+ "identifier": "CompoundDb",
+ "name": "CompoundDb",
+ "version": ">=1.6.0",
+ "provider": {
+ "@id": "https://www.bioconductor.org",
+ "@type": "Organization",
+ "name": "Bioconductor",
+ "url": "https://www.bioconductor.org"
+ },
+ "sameAs": "https://bioconductor.org/packages/release/bioc/html/CompoundDb.html"
+ },
+ "5": {
  "@type": "SoftwareApplication",
  "identifier": "crayon",
  "name": "crayon",
@@ -175,7 +176,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=crayon"
  },
- "5": {
+ "6": {
  "@type": "SoftwareApplication",
  "identifier": "docopt",
  "name": "docopt",
@@ -188,7 +189,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=docopt"
  },
- "6": {
+ "7": {
  "@type": "SoftwareApplication",
  "identifier": "dplyr",
  "name": "dplyr",
@@ -201,7 +202,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=dplyr"
  },
- "7": {
+ "8": {
  "@type": "SoftwareApplication",
  "identifier": "DT",
  "name": "DT",
@@ -214,7 +215,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=DT"
  },
- "8": {
+ "9": {
  "@type": "SoftwareApplication",
  "identifier": "fs",
  "name": "fs",
@@ -227,7 +228,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=fs"
  },
- "9": {
+ "10": {
  "@type": "SoftwareApplication",
  "identifier": "glue",
  "name": "glue",
@@ -240,7 +241,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=glue"
  },
- "10": {
+ "11": {
  "@type": "SoftwareApplication",
  "identifier": "gt",
  "name": "gt",
@@ -253,7 +254,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=gt"
  },
- "11": {
+ "12": {
  "@type": "SoftwareApplication",
  "identifier": "httr2",
  "name": "httr2",
@@ -266,7 +267,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=httr2"
  },
- "12": {
+ "13": {
  "@type": "SoftwareApplication",
  "identifier": "igraph",
  "name": "igraph",
@@ -279,7 +280,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=igraph"
  },
- "13": {
+ "14": {
  "@type": "SoftwareApplication",
  "identifier": "import",
  "name": "import",
@@ -292,7 +293,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=import"
  },
- "14": {
+ "15": {
  "@type": "SoftwareApplication",
  "identifier": "installr",
  "name": "installr",
@@ -305,7 +306,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=installr"
  },
- "15": {
+ "16": {
  "@type": "SoftwareApplication",
  "identifier": "jsonlite",
  "name": "jsonlite",
@@ -318,7 +319,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=jsonlite"
  },
- "16": {
+ "17": {
  "@type": "SoftwareApplication",
  "identifier": "lifecycle",
  "name": "lifecycle",
@@ -331,7 +332,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=lifecycle"
  },
- "17": {
+ "18": {
  "@type": "SoftwareApplication",
  "identifier": "MetaboCoreUtils",
  "name": "MetaboCoreUtils",
@@ -344,7 +345,7 @@
  },
  "sameAs": "https://bioconductor.org/packages/release/bioc/html/MetaboCoreUtils.html"
  },
- "18": {
+ "19": {
  "@type": "SoftwareApplication",
  "identifier": "MsBackendMgf",
  "name": "MsBackendMgf",
@@ -357,7 +358,7 @@
  },
  "sameAs": "https://bioconductor.org/packages/release/bioc/html/MsBackendMgf.html"
  },
- "19": {
+ "20": {
  "@type": "SoftwareApplication",
  "identifier": "MsBackendMsp",
  "name": "MsBackendMsp",
@@ -370,7 +371,7 @@
  },
  "sameAs": "https://bioconductor.org/packages/release/bioc/html/MsBackendMsp.html"
  },
- "20": {
+ "21": {
  "@type": "SoftwareApplication",
  "identifier": "msentropy",
  "name": "msentropy",
@@ -383,7 +384,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=msentropy"
  },
- "21": {
+ "22": {
  "@type": "SoftwareApplication",
  "identifier": "pak",
  "name": "pak",
@@ -396,7 +397,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=pak"
  },
- "22": {
+ "23": {
  "@type": "SoftwareApplication",
  "identifier": "pbapply",
  "name": "pbapply",
@@ -409,7 +410,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=pbapply"
  },
- "23": {
+ "24": {
  "@type": "SoftwareApplication",
  "identifier": "pingr",
  "name": "pingr",
@@ -422,7 +423,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=pingr"
  },
- "24": {
+ "25": {
  "@type": "SoftwareApplication",
  "identifier": "R.utils",
  "name": "R.utils",
@@ -435,7 +436,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=R.utils"
  },
- "25": {
+ "26": {
  "@type": "SoftwareApplication",
  "identifier": "rlang",
  "name": "rlang",
@@ -448,7 +449,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=rlang"
  },
- "26": {
+ "27": {
  "@type": "SoftwareApplication",
  "identifier": "rotl",
  "name": "rotl",
@@ -461,7 +462,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=rotl"
  },
- "27": {
+ "28": {
  "@type": "SoftwareApplication",
  "identifier": "shiny",
  "name": "shiny",
@@ -474,7 +475,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=shiny"
  },
- "28": {
+ "29": {
  "@type": "SoftwareApplication",
  "identifier": "shinybusy",
  "name": "shinybusy",
@@ -487,7 +488,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=shinybusy"
  },
- "29": {
+ "30": {
  "@type": "SoftwareApplication",
  "identifier": "shinyhelper",
  "name": "shinyhelper",
@@ -500,7 +501,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=shinyhelper"
  },
- "30": {
+ "31": {
  "@type": "SoftwareApplication",
  "identifier": "shinyjs",
  "name": "shinyjs",
@@ -513,7 +514,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=shinyjs"
  },
- "31": {
+ "32": {
  "@type": "SoftwareApplication",
  "identifier": "shinyvalidate",
  "name": "shinyvalidate",
@@ -526,7 +527,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=shinyvalidate"
  },
- "32": {
+ "33": {
  "@type": "SoftwareApplication",
  "identifier": "shinyWidgets",
  "name": "shinyWidgets",
@@ -539,7 +540,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=shinyWidgets"
  },
- "33": {
+ "34": {
  "@type": "SoftwareApplication",
  "identifier": "Spectra",
  "name": "Spectra",
@@ -552,12 +553,12 @@
  },
  "sameAs": "https://bioconductor.org/packages/release/bioc/html/Spectra.html"
  },
- "34": {
+ "35": {
  "@type": "SoftwareApplication",
  "identifier": "stats",
  "name": "stats"
  },
- "35": {
+ "36": {
  "@type": "SoftwareApplication",
  "identifier": "stringi",
  "name": "stringi",
@@ -570,7 +571,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=stringi"
  },
- "36": {
+ "37": {
  "@type": "SoftwareApplication",
  "identifier": "targets",
  "name": "targets",
@@ -583,7 +584,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=targets"
  },
- "37": {
+ "38": {
  "@type": "SoftwareApplication",
  "identifier": "tidyfst",
  "name": "tidyfst",
@@ -596,7 +597,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=tidyfst"
  },
- "38": {
+ "39": {
  "@type": "SoftwareApplication",
  "identifier": "tidytable",
  "name": "tidytable",
@@ -609,12 +610,12 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=tidytable"
  },
- "39": {
+ "40": {
  "@type": "SoftwareApplication",
  "identifier": "utils",
  "name": "utils"
  },
- "40": {
+ "41": {
  "@type": "SoftwareApplication",
  "identifier": "visNetwork",
  "name": "visNetwork",
@@ -627,7 +628,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=visNetwork"
  },
- "41": {
+ "42": {
  "@type": "SoftwareApplication",
  "identifier": "withr",
  "name": "withr",
@@ -640,7 +641,7 @@
  },
  "sameAs": "https://CRAN.R-project.org/package=withr"
  },
- "42": {
+ "43": {
  "@type": "SoftwareApplication",
  "identifier": "yaml",
  "name": "yaml",
@@ -656,7 +657,7 @@
  "SystemRequirements": null
  },
  "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
- "fileSize": "3178.832KB",
+ "fileSize": "3178.842KB",
  "citation": [
  {
  "@type": "ScholarlyArticle",