Message-ID: <17509.63555.958767.122255@stat.math.ethz.ch>
Date: 2006-05-13T15:16:19Z
From: Martin Maechler
Subject: str() with attr(*, "names") is extremely slow for long vectors
In-Reply-To: <000201c6767b$918bc8b0$0400a8c0@mobilix>
>>>>> "Gerhard" == Gerhard Thallinger <Gerhard.Thallinger at tugraz.at>
>>>>> on Sat, 13 May 2006 12:54:10 +0200 writes:
>>>>> "HenrikB" == Henrik Bengtsson (max 7Mb) <hb at stat.berkeley.edu>
>>>>> on Fri, 5 May 2006 11:58:19 -0700 writes:
But have you looked at R 2.3.0-patched at all?
I did acknowledge that str(<long character>) had become unacceptably slow,
and had implemented a simple patch almost "immediately".
Martin
HenrikB> Hi, I noticed some time ago that, for instance,
HenrikB> named vectors that are really makes str() really
HenrikB> slow when displaying the names attribute.
HenrikB> I don't know exactly when this started, but it
HenrikB> wasn't the case say 1-2 years ago. Example (on a
HenrikB> WinXP 1.8GHz):
Gerhard> It got slower with R 2.3.0. Comparing str() for a
Gerhard> big exprSet object from the "Biobase" package I got
Gerhard> the following numbers (system.time(str(anaexp)) on
Gerhard> WinXP 1.8 GHz):
Gerhard> R 2.2.0
Gerhard> 1. 14.64 0.13 14.90 NA NA 2. 4.33 0.09 4.43 NA
Gerhard> NA 3. 4.20 0.15 4.38 NA NA
Gerhard> R 2.3.0
Gerhard> 1. 65.36 0.18 66.12 NA NA 2. 51.75 0.21 52.55
Gerhard> NA NA 3. 51.79 0.17 52.45 NA NA
Gerhard> One can notice a considerable speed-up in the 2nd &
Gerhard> 3rd call to str() in R 2.2.0, which is much less
Gerhard> pronounced in R 2.3.0.
Gerhard> Hth
Gerhard> Gerhard
Gerhard> ------------------------------------------------------------------------
Gerhard> DI Gerhard Thallinger E-mail:
Gerhard> Gerhard.Thallinger at tugraz.at Institute for Genomics
Gerhard> and Bioinformatics Web: http://genome.tugraz.at
Gerhard> Graz University of Technology Tel: +43 316 873 5343
Gerhard> Petersgasse 14/V Fax: +43 316 873 5340 8010 Graz,
Gerhard> Austria Map: http://genome.tugraz.at/Loc.html