Installed packages: Bioconductor vs CRAN?

Dear Bert,


The DESCRIPTION file contains additional useful information, e.g.:

1.) Package EBImage:
biocViews: Visualization
Packaged: 2021-05-19 23:53:29 UTC; biocbuild


2.) deSolve
Repository: CRAN


I have verified a few of the CRAN packages, and they seem to include 
the tag:

Repository: CRAN


The Bioconductor packages are different (see e.g. EBImage).

I am wondering if there is already a method to extract this info?


Sincerely,


Leonard


On 9/25/2021 3:06 AM, Bert Gunter wrote:

The help file tells you that installed.packages() looks at the
DESCRIPTION files of packages.
Section 1.1.1 of "Writing R Extensions" tells you what information is
in such files.


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Fri, Sep 24, 2021 at 4:56 PM Leonard Mada via R-help
<r-help at r-project.org> 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()


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)