From ripley at stats.ox.ac.uk  Tue Mar  3 10:58:50 2009
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 3 Mar 2009 09:58:50 +0000 (GMT)
Subject: [Rd] execution time of .packages
In-Reply-To: <49ACF094.7010209@dbmail.com>
References: <49ACF094.7010209@dbmail.com>
Message-ID: <alpine.OSX.1.00.0903030927420.6041@tystie.local>

The caching is in the disc system: you need to find and read the 
package metadata for every package.  AFAIK it is not easy to flush the 
disc cache, but quite easy to overwrite it with later reads.  (Google 
for more info.)

If you are not concerned about validity of the installed packages you 
could skip the tests and hence the reads.

Your times are quite a bit slower than mine, so a faster disc system 
might help.  Since my server has just been rebooted (for a new 
kernel), with all of CRAN and most of BioC I get

> system.time( packs <- .packages( all = T ) )
    user  system elapsed
   0.518   0.262  25.042
> system.time( packs <- .packages( all = T ) )
    user  system elapsed
   0.442   0.080   0.522
> length(packs)
[1] 2096

There's a similar issue when installing packages: the Perl code reads 
the indices from every visible package to resolve links, and that can 
be slow the first time.


On Tue, 3 Mar 2009, Romain Francois wrote:

> 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.

It's OK as there are only going to be ca 2000 packages.  Try 
profiling this: .readRDS and grepl take most of the time.

>> .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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] execution time of .packages
Prof Brian Ripley