Version 1.0.8 - Add Rpackages

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: myFun
 Type: Package
 Title: myFun is a collection of my favorite R functions, packaged for simplicity
-Version: 1.0.7
-Date: 2023-01-08
+Version: 1.0.8
+Date: 2024-02-20
 Authors@R: person("Tom", "Lesluyes", email = "[email protected]", role = c("aut", "cre"))
 Author: Tom Lesluyes [aut, cre]
 Maintainer: Tom Lesluyes <[email protected]>
@@ -18,6 +18,7 @@ Imports:
     GenomicRanges,
     IRanges,
     doParallel,
-    foreach
+    foreach,
+    rvest
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(Rpackages)
 export(adjustPositions)
 export(checkGRlist)
 export(computeBAF)
@@ -20,4 +21,5 @@ export(reestimate_ploidy)
 export(reestimate_purity)
 export(splitDF)
 export(summarise_segmetation)
+importFrom(foreach,"%do%")
 importFrom(foreach,"%dopar%")

R/Rpackages.R

@@ -0,0 +1,36 @@
+#' @title Rpackages
+#' @description List installed packages and determine their source
+#' @details This function lists installed packages and determine whether they are base packages or come from CRAN/Bioconductor or if they are external (GitHub, SourceForge, etc.). This function requires an internet connection.
+#' @param CRAN_URL the CRAN URL (default: "http://cran.us.r-project.org")
+#' @param Bioconductor_URL the Bioconductor URL (default: "https://www.bioconductor.org/packages/release/bioc/")
+#' @return A data.frame with the installed packages and an additional column: Source (possible values: Base, CRAN, Bioconductor, External)
+#' @examples head(Rpackages())
+#' @author tlesluyes
+#' @export
+Rpackages=function(CRAN_URL="http://cran.us.r-project.org",
+                   Bioconductor_URL="https://www.bioconductor.org/packages/release/bioc/") {
+  # Pick CRAN packages
+  CRAN=as.data.frame(available.packages(repos=CRAN_URL))[, c("Package"), drop=FALSE]
+  CRAN$Source="CRAN"
+  # Pick Bioconductor packages
+  url=url(Bioconductor_URL, "rb")
+  Bioconductor=as.data.frame(rvest::html_table(rvest::read_html(url))[[1]])[, c("Package"), drop=FALSE]
+  close(url)
+  Bioconductor$Source="Bioconductor"
+  # Pick installed packages
+  myPackages=as.data.frame(installed.packages())
+  # Determine the source of each installed package
+  myPackages$Source=foreach::foreach(i=myPackages$Package, .combine=c) %do% {
+    # Test whether it is from CRAN and/or Bioconductor
+    FROM=c(ifelse(i %in% CRAN$Package, "CRAN", NA),
+           ifelse(i %in% Bioconductor$Package, "Bioconductor", NA))
+    FROM=FROM[!is.na(FROM)]
+    # If it is not from CRAN or Bioconductor, test whether it is a base package
+    if (length(FROM)==0 && i %in% c("base", "compiler", "datasets", "grDevices", "graphics", "grid", "methods", "parallel", "splines", "stats", "stats4", "tcltk", "tools", "utils")) FROM="Base"
+    # Otherwise, it looks like an external package
+    if (length(FROM)==0) FROM="External"
+    # The collapse is needed if a package exists in both CRAN and Bioconductor (not sure this could happen though)
+    return(paste0(FROM, collapse="/"))
+  }
+  return(myPackages)
+}

R/misc.R

@@ -1,2 +1,3 @@
 #' @importFrom foreach %dopar%
+#' @importFrom foreach %do%
 NULL

README.md

@@ -220,4 +220,17 @@ summarise_segmetation(DF, "chr", "pos", "pos", c("logR", "BAF"))
 # 
 # $IDs$`5`
 # [1] "SNP_14" "SNP_15" "SNP_16"
+```
+
+### Where do my packages come from?
+```R
+Rpackages()
+#               Package   ...         Source
+# abind           abind   ...           CRAN
+# aCGH             aCGH   ...   Bioconductor
+# affxparser affxparser   ...   Bioconductor
+# affy             affy   ...   Bioconductor
+# affyio         affyio   ...   Bioconductor
+# anndata       anndata   ...           CRAN
+# ...
 ```