Commit 14580881 authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Debian changes 2.9.0-4

r-base (2.9.0-4) unstable; urgency=low

  * debian/r-cran.mk: Applied suggestion by Julian Gilbey to correct 
    accidental lowercasing of CRAN package names which can prevent removal
    extra license files					(Closes: #531224)
  
  * debian/README.Atlas: Updated to current packages	(Closes: #531223)
  
  * debian/r-cran.mk: Small correction to previously added 'clean' target

r-base (2.9.0-3) unstable; urgency=low

  * debian/r-cran.mk: Applied patch by Steffen Moeller that adds a 
    'clean' target which is useful if one builds outside of pbuilder.
parent 87c35b87
......@@ -10,41 +10,36 @@ Algebra Software, in order to obtain much faster linear algebra operations.
To make use of Atlas, Debian users need to install the Atlas libraries for
their given cpu architecture. Concretely, one of
atlas2-base - Automatically Tuned Linear Algebra Software
atlas2-p3 - Automatically Tuned Linear Algebra Software
atlas2-p4 - Automatically Tuned Linear Algebra Software
atlas2-athlon - Automatically Tuned Linear Algebra Software
libatlas3gf-base - Automatically Tuned Linear Algebra Software, generic
libatlas3gf-sse - Automatically Tuned Linear Algebra Software, SSE1
libatlas3gf-sse2 - Automatically Tuned Linear Algebra Software, SSE2
libatlas3gf-3dnow - Automatically Tuned Linear Algebra Software, 3dnow
must be installed. Here, 'base' provides generic libraries which run on all
platforms whereas 'p3', 'p4' and 'athlon' stand for the Pentium III and IV as
well as the AMD Athlon, respectively. The actual libraries are installed in
/usr/lib/atlas (in the case of 'base') and in /usr/lib/$arch/atlas for the
cpu-specific versions. Here $arch stands for the cpu code used by the kernel
and shown in /proc/cpuinfo.
platforms whereas 'sse' and 'sse2' stand for the SSE (v1 and v2) extension
available on most Intel cpus, and '3dnow' for those made by AMS.
The Atlas libraries can be loaded dynamically instead of the (non-optimised)
blas libraries against which both Octave and R are compiled.
blas and lapack libraries against which both Octave and R are compiled.
Section III below briefly describes how Atlas libraries can be compiled for
your specific machine to further optimise performance.
II. Using the Atlas libraries
II.A New default behaviour with automatic loading of the Atlas libraries
In order to have the libraries loaded at run-time, the location needs to be
communicated to the dynamic linker/loader. As of the Debian release
libc6_2.2.4-5 of the glibc library, a patch to ldconfig automates the use of
the Atlas library. If an Atlas package is installed, and correctly registered
in /etc/ld.so.conf as done by its postinst script, ldconfig will
automatically load the Atlas' version of the Blas instead of the (slower)
default Blas.
Users have to make no changes whatsoever as the Atlas library will be loaded
instead of the standard blas and lapack libraries.
The following text is hence only relevant for systems which have not yet
upgraded to libc6_2.2.4-5 or later.
An example such as the script below can be useful to test the performance.
II.B Old behaviour requiring LD_LIBRARY_PATH for Octave
[ NB: This section has long been obsolete is kept for the historical record
only. ]
For Octave, use the variable LD_LIBRARY_PATH. On a computer with the
atlas2-base package:
......@@ -87,6 +82,7 @@ Lastly, it should be pointed out that it is probably worthwhile to locally
compile, and thereby optimise, the Atlas libraries if at least a moderately
intensive load is expected. This is described in the next section.
III. Locally compiling the Atlas libraries
The Debian Atlas packages have been setup to allow for local recompilation of
......@@ -96,11 +92,11 @@ this can increase performance by a further 12% on the examples above.
Detailed instructions are in /usr/share/doc/atlas2-base/README.debian.gz but
the process is essentially the following [ courtesy of Doug Bates ]
apt-get source atlas2-base
cd atlas2-$VERSION
fakeroot debian/rules/custom
apt-get source libatlas3gf-base
cd atlas-$VERSION
fakeroot debian/rules custom
# wait for a *very* long time
dpkg -i ../atlas2-base*.deb
dpkg -i ../libatlas3gf-base*.deb
IV. See also
......@@ -124,3 +120,6 @@ Initial version
First updated
-- Dirk Eddelbuettel <edd@debian.org> Sun, 11 Nov 2001 11:03:19 -0600
Major update
-- Dirk Eddelbuettel <edd@debian.org> Sun, 31 May 2009 21:04:47 -0500
r-base (2.9.0-4) unstable; urgency=low
* debian/r-cran.mk: Applied suggestion by Julian Gilbey to correct
accidental lowercasing of CRAN package names which can prevent removal
extra license files (Closes: #531224)
* debian/README.Atlas: Updated to current packages (Closes: #531223)
* debian/r-cran.mk: Small correction to previously added 'clean' target
-- Dirk Eddelbuettel <edd@debian.org> Sun, 31 May 2009 21:15:27 -0500
r-base (2.9.0-3) unstable; urgency=low
* debian/r-cran.mk: Applied patch by Steffen Moeller that adds a
'clean' target which is useful if one builds outside of pbuilder.
-- Dirk Eddelbuettel <edd@debian.org> Sat, 16 May 2009 18:07:02 -0500
r-base (2.9.0-2) unstable; urgency=low
* debian/r-base-core.prerm: Remove /etc/R/Renviron on remove or purge to
......
......@@ -14,11 +14,12 @@ include /usr/share/cdbs/1/class/langcore.mk
## include /usr/share/cdbs/1/rules/dpatch.mk
include /usr/share/cdbs/1/rules/simple-patchsys.mk
# awk command to extract word after Package or Bundle, lowercased
awkString := "'/^(Package|Bundle):/ {print tolower($$2) }'"
# awk command to extract word after Package or Bundle, not lowercased
awkString := "'/^(Package|Bundle):/ {print $$2 }'"
# apply it to the upstream meta-info file DESCRIPTION
cranName := $(shell awk "$(awkString)" DESCRIPTION)
# apply it to the upstream meta-info file DESCRIPTION, also generate a lc version
cranNameOrig := $(shell awk "$(awkString)" DESCRIPTION)
cranName := $(shell echo "$(cranNameOrig)" | tr A-Z a-z)
## if no debRreposname is known, set default to cran -- thanks, Steffen!
ifeq ($(debRreposname),)
......@@ -72,11 +73,31 @@ R_any_arch:
fi
## remove extra files which are present in some packages
rm -vf $(debRlib)/R.css \
$(debRlib)/$(cranName)/COPYING \
$(debRlib)/$(cranName)/LICENSE.txt
$(debRlib)/$(cranNameOrig)/COPYING \
$(debRlib)/$(cranNameOrig)/LICENSE.txt
## if we have an overrides file for lintian, install it
if test -f debian/overrides; then \
install -d $(lintiandir) ; \
install -m 0644 debian/overrides \
$(lintiandir)/$(package); \
fi
## clean target from patch by Steffen Moeller on 16 May 2009
clean::
## the re-invocation of a build process should not
## leave a footprint in Debian's diff.gz.
if test -d src; then \
find src -name "*.o" -o "*.so" \
| xargs -r rm; \
fi
rm -f config.log config.status
## the configure file is provided by upstream but
## could be recreated by a call to 'autoconf'.
#if [ -r configure.in ]; then \
# rm -f configure \
#fi
##
if [ -r src/Makevars.in ]; then \
rm -f src/Makevars; \
fi
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