From romain.francois at dbmail.com  Tue Mar  3 09:55:48 2009
From: romain.francois at dbmail.com (Romain Francois)
Date: Tue, 03 Mar 2009 09:55:48 +0100
Subject: [Rd] execution time of .packages
Message-ID: <49ACF094.7010209@dbmail.com>

Hello,

The first time in a session I call .packages( all.available = T ), it 
takes a long time (I have many packages installed from CRAN):

 > system.time( packs <- .packages( all = T ) )
  user  system elapsed
 0.738   0.276  43.787

When I call it again, the time is now much reduced, so there must be 
some caching somewhere. I would like to try to reduce the  time it takes 
the first time, but I have not been able to identify where the caching 
takes place, and so how I can remove it to try to improve the running 
time without the caching. Without this, I have to restart my computer 
each time to vanish the caching to test a new version of the function 
(this is not going to happen)

Here is the .packages function, I am suspicious about this part : "ans 
<- c(ans, nam)" which grows the ans vector each time a suitable package 
is found, this does not sound right.

 > .packages
function (all.available = FALSE, lib.loc = NULL)
{                                               
    if (is.null(lib.loc))                       
        lib.loc <- .libPaths()                  
    if (all.available) {                        
        ans <- character(0L)                    
        lib.loc <- lib.loc[file.exists(lib.loc)]
        valid_package_version_regexp <- 
.standard_regexps()$valid_package_version                                                                             

        for (lib in lib.loc) 
{                                                
            a <- list.files(lib, all.files = FALSE, full.names = 
FALSE)       
            for (nam in a) 
{                                                  
                pfile <- file.path(lib, nam, "Meta", 
"package.rds")           
                if 
(file.exists(pfile))                                       
                  info <- 
.readRDS(pfile)$DESCRIPTION[c("Package",            
                    
"Version")]                                               
                else 
next                                                     
                if ((length(info) != 2L) || any(is.na(info)))
                  next
                if (!grepl(valid_package_version_regexp, info["Version"]))
                  next
                ans <- c(ans, nam)   ########## suspicious about this
            }
        }
        return(unique(ans))
    }
    s <- search()
    return(invisible(substring(s[substr(s, 1L, 8L) == "package:"],
        9)))
}


 > version
               _
platform       i686-pc-linux-gnu
arch           i686
os             linux-gnu
system         i686, linux-gnu
status         Under development (unstable)
major          2
minor          9.0
year           2009
month          02
day            08
svn rev        47879
language       R
version.string R version 2.9.0 Under development (unstable) (2009-02-08 
r47879)


-- 
Romain Francois
Independent R Consultant
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr



[Rd] execution time of .packages
Romain Francois