[R] Installed packages: Bioconductor vs CRAN?

[Leonard Mada]

[working version]

On 9/25/2021 2:55 AM, Leonard Mada wrote:
> Dear List Members,
>
>
> Is there a way to extract if an installed package is from Bioconductor 
> or if it is a regular Cran package?
>
>
> The information seems to be *not* available in:
>
> installed.packages()

### [updated]

# Basic Info:
info.pkg = function(pkg=NULL, fields="Repository") {
     if(is.null(pkg)) { pkg = installed.packages(fields=fields); }
     else {
         all.pkg = installed.packages();
         pkg = all.pkg[all.pkg[,1] %in% pkg, ];
     }
     p = pkg;
     p = as.data.frame(p);
     p = p[ , c("Package", "Version", "Built", fields, "Imports")];
     return(p);
}


I will think later how to improve the filtering of Bioconductor 
packages. Probably based on biocViews.


Many thanks,


Leonard


>
>
> Sincerely,
>
>
> Leonard
>
> =======
>
> I started to write some utility functions to analyse installed 
> packages. The latest version is on Github:
> https://github.com/discoleo/R/blob/master/Stat/Tools.CRAN.R
>
>
> # Basic Info:
> info.pkg = function(pkg=NULL) {
>     if(is.null(pkg)) { pkg = installed.packages(); }
>     else {
>         all.pkg = installed.packages();
>         pkg = all.pkg[all.pkg[,1] %in% pkg, ];
>     }
>     p = pkg;
>     p = as.data.frame(p);
>     p = p[ , c("Package", "Version", "Built", "Imports")];
>     return(p);
> }
> # Imported packages:
> imports.pkg = function(pkg=NULL, sort=TRUE) {
>     p = info.pkg(pkg);
>     ### Imported packages
>     imp = lapply(p$Imports, function(s) strsplit(s, "[,][ ]*"))
>     imp = unlist(imp)
>     imp = imp[ ! is.na(imp)]
>     # Cleanup:
>     imp = sub("[ \n\r\t]*+\\([-,. >=0-9\n\t\r]++\\) *+$", "", imp, 
> perl=TRUE)
>     imp = sub("^[ \n\r\t]++", "", imp, perl=TRUE);
>     # Tabulate:
>     tbl = as.data.frame(table(imp), stringsAsFactors=FALSE);
>     names(tbl)[1] = "Name";
>     if(sort) {
>         id = order(tbl$Freq, decreasing=TRUE);
>         tbl = tbl[id,];
>     }
>     return(tbl);
> }
>
> match.imports = function(pkg, x=NULL, quote=FALSE) {
>     if(is.null(x)) x = info.pkg();
>     if(quote) {
>         pkg = paste0("\\Q", pkg, "\\E");
>     }
>     # TODO: Use word delimiters?
>     # "(<?=^|[ \n\r\t],)"
>     if(length(pkg) == 1) {
>         isImport = grepl(pkg, x$Imports);
>         return(x[isImport, ]);
>     } else {
>         # TODO: concept?
>         rez = lapply(pkg, function(p) x[grepl(p, x$Imports), ]);
>         return(rez);
>     }
> }
>
> Examples:
>
> p = info.pkg();
> f = imports.pkg();
>
> ### Analyze data
>
> # imported only once: (only in the locally installed packages)
> f$Name[f$Freq == 1]
>
> match.imports("hunspell", p)
> match.imports("labeling", p)
> match.imports("rpart.plot", p)
>
> match.imports(c("pROC", "ROCR"), p)
>