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Installed packages: Bioconductor vs CRAN?

6 messages · Bert Gunter, Leonard Mada

Leonard Mada
# 
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)
Bert Gunter
# 
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:
Bert Gunter
# 
Oh, I should have added that packages can be on other repositories
(local, github,...) and I think can be both in CRAN and BIOC . So your
query would not seem to have a clear answer. AFAICS anyway.

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 5:06 PM Bert Gunter <bgunter.4567 at gmail.com> wrote:
Leonard Mada
# 
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:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Leonard Mada
    

    

      
      #
    

  


  

      
Dear Bert,


Indeed, this seems to work:

installed.packages(fields="Repository")


I still need to figure out what variants to expect.


Sincerely,


Leonard

        
On 9/25/2021 3:31 AM, Leonard Mada wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Leonard Mada
    

    

      
      #
    

  


  

      
[working version]

        
On 9/25/2021 2:55 AM, Leonard Mada wrote:

            

      
      
      
    

        
### [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