070704 - R, Allegro and Enzo

[easuter]

veki has packaged R, Allegro and Enzo, all of which can be downloaded from the testing repository:

Package: http://vectorlinux.osuosl.org/veclinux-5.8/testing/x-apps/R-2.5.0-i586-1vl58.tlz

Code:

R: R ( R is a free software environment for statistical computing a )
R:
R: R is a free software environment for statistical computing and
R: graphics. R version 2.5.0 has been released on 2007-04-24. R provides
R: a wide variety of statistical (linear and nonlinear modelling,
R: classical statistical tests, time-series analysis, classification,
R: clustering) and graphical techniques, and is highly extensible.
R: Author: Initially written by Robert Gentleman and Ross Ihaka—a
R: Website: http://www.r-project.org
R: License: GPL

Package: http://vectorlinux.osuosl.org/veclinux-5.8/testing/libs/allegro-4.2.1-i586-1vl58.tlz

Code:

allegro: allegro ( a gaming library )
allegro:
allegro: Allegro is a portable library mainly aimed at video game and
allegro: multimedia programming. According to the Oxford Companion to Music,
allegro: Allegro is the Italian for «quick, lively, bright». It is also a
allegro: recursive acronym which stands for «Allegro Low LEvel Game
allegro: ROutines».
allegro: Author: originally started by Shawn Hargreaves
allegro: Website: http://alleg.sourceforge.net/wip.html
allegro: License: free to use, modify, distribute

Package: http://vectorlinux.osuosl.org/veclinux-5.8/testing/libs/enzo-1.0.1-i586-1vl58.tlz

Code:

enzo: enzo ( Enzo is an adaptive mesh refinement. )
enzo:
enzo: Enzo is an adaptive mesh refinement (AMR), grid-based hybrid code
enzo: (hydro + N-Body) which is designed to do simulations of cosmological
enzo: structure formation. It uses the algorithms of Berger & Collela to
enzo: improve spatial and temporal resolution in regions of large
enzo: gradients, such as gravitationally collapsing objects.
enzo: Author: LCA, San Diego California
enzo: Website: http://lca.ucsd.edu/portal/software/enzo
enzo: License: GPL

Post feedback here.

[wcs]

There seems to be something wrong with the R package.

First, after installing it I could not find the executable by typing 'R' or running

Code:

whereis R

.
Downloading the package and doing explodepkg reveals that only stuff that goes in /usr/doc is there.

Second, trying to remove the package leads to quite a dangerous situation. Either trying to remove it in gslapt or typing:

Code:

slapt-get -s -remove R

leads to a huge list of packages ready to be removed:

Code:

The following packages will be REMOVED:
  GConf abiword abiword-plugins libgnomeprint zenity OpenSP aqbanking kmymoney2
  libofx SDL_Pango frozen-bubble SDL_ttf vpackager XML-Parser Xarchiver
  aiksaurus amarok cairo thunar-media-tags-plugin xfce4-battery-plugin
  xfce4-clipman-plugin xfce4-cpu-freq-plugin xfce4-cpugraph-plugin
  xfce4-netload-plugin xfce4-taskmanager xfce4-wavelan-plugin gtk+2 d4x
  gparted gqview gst-plugins-good gtk-smooth-engine2 gtk-theme-switch2
  gtkmathview gtkmm gutenprint libexif-gtk libglade libgnomecanvas pygtk
  xscreensaver mozilla-sunbird mtpaint vasm vlapt plugins poppler sane sgmixer
  vim xine-lib xine-ui qt lyx dbus-glib dbus-python dbus-qt3 pango
  gst-plugins-base conky cvs darkice easytag ffmpeg fusesmb glib2 ORBit2 atk
  enchant gamin gstreamer libgnomecups mc sshfs-fuse gnutls gpgme libgphoto2
  htop icecast ices icon-naming-utils jpilot liblrdf libshout libsigc++
  libtunepimp lm_sensors nano nasm perl-gettext pilot-link pkgtools-tukaani
  psiconv tetradraw texlive wpa_supplicant xalan-c xdm-custom R
0 upgraded, 0 newly installed, 99 to remove and 0 not upgraded.

Luckily, I checked the packages in gslapt before pressing the OK button and used -s when using slapt-get. Uff...

[easuter]

  I'll take a look into this this evening...

[wcs]

Any news on this one?

I was taking a look at the compilation of R and found it to be more straightforward than I thought.
It actually went without any problems. So I'll be uploading a newer version (2.5.1) to the repos.

(I'll be using --with-BLAS, but is it necessary to tell the R ./configure to build a BLAS shared library? I suppose that one is already present in the BLAS package isn't it?)

In any case, the present package seems a bit dangerous if someone actually does a slapt-get --remove without paying much attention. Can anyone replicate this ? (without wrecking your system  )

[easuter]

Yeah, I've been going over this and can't seem to find the cause of it.
If you have a new package for R at hand, please send it along and I'll replace this one with it and see if that fixes anything.

[wcs]

Uploaded 

[wcs]

Oh, the enzo package also seems to have a problem as it only contains the /usr/doc directory.

(the allegro one seems to be fine... although I just did an explodepkg and haven't installed it yet)