From htl10 at users.sourceforge.net  Thu Mar 22 04:14:41 2012
From: htl10 at users.sourceforge.net (Hin-Tak Leung)
Date: Thu, 22 Mar 2012 03:14:41 +0000
Subject: [Rd] Thai vignette, cross-compile for Mac OS X,
 universal/multiarch (Fwd: Mac OS X builds of CelQuantileNorm,
 vcftools/samtools/tabix, and snpStats)
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Message-ID: <4F6A9921.2050702@users.sourceforge.net>

FYI.

There is a Thai vignette - and it went a lot further doing some Thai text 
processing in R, than the earlier Chinese/Tibetan/LiangshanYi/Arabic vignette, 
which was in reality just Chinese + Cairo graphics.

Managed to cross-compile an R package for Mac OS X from Linux; and it seems to 
be working. See screenshots below. I'd be interested to know if there are less 
obvious bugs; however numerical difference with native snpStats 1.5.5 is more 
likely because 1.5.5 is buggy than 1.5.5.1 mis-compiled.

Also noticed that R on Mac OS X is universal, with symlinks to the per-arch 
multiarch dylibs. Is there any plans for R packages to switch over to universal 
instead of multi-arch?
(the sentence below as strictly speaking wrong - the R package was 
cross-compiled to multi-arch rather than universal).

FYI a few other not-so-relevant things but may be useful to some.

-------- Original Message --------
Subject: Mac OS X builds of CelQuantileNorm, vcftools/samtools/tabix, and snpStats
Date: Wed, 14 Mar 2012 02:59:42 +0000 (GMT)
From: Hin-Tak Leung <htl10 at users.sourceforge.net>
Reply-To: htl10 at users.sourceforge.net
To: bonsai list <outmodedbonsai-announce at lists.sourceforge.net>

CelQantileNorm, vcftools/samtools/tabix are bult for Mac OS X. These are 
universal binaries and work for all recent variants of Powerpc-, Intel 
32-bit/64-bit Macs.

snpStats 1.5.5 (out a week ago) turned out to be "differently buggy" from 
previous, so there are windows and Mac OS X build of 1.5.5.1 . The Mac OS X 
build is also Universal and was tested for both intel 32-bit/64-bit macs. See also
http://outmodedbonsai.sourceforge.net/InstallingLocalRPackages.html
for a few brief instructions and screenshots for installing R packages from 
downloads.

Here is the new Mac OS X area:
http://sourceforge.net/projects/outmodedbonsai/files/Packages%20for%20Mac%20OS%20X/


-------- Original Message --------
Subject: Two new vignettes, and a bunch of updates here and elsewhere
Date: Tue, 06 Mar 2012 06:39:38 +0000
From: Hin-Tak Leung <htl10 at users.sourceforge.net>
To: outmodedbonsai-announce at lists.sourceforge.net

There is a new vignette, "Algorithms and Thailand", which covers
text/stream/sequence and spatial algorithms, and the use of Thai language in a
vignette.
(Chinese/Tibetan/Arabic/Liangshan Yi was covered in a different vignette
previously).
More on this and emacs's multilingual extension further down.

"snpMatrix Tutorial 2007" was the first ever tutorial written in spring 2007
[1]; it was pre-vignette and therefore had all the hapmap/pedfile output
recorded verbatim; newly revived to work as a testsuite for input/output of
hapmap/ped files (and flaged and fixed a few bugs introduced in the last few
years). The bug fixes will appear in the upcoming snpMatrix 1.19.0.12, which
hopefully will include some continual work to add read.tped() and read.vcf().

The usual suspects:

- new linux and win32 mono 2.10.8.1 builds with the large heap patch;

- "less buggy" snpStats 1.4.1.1, 1.5.2.1, 1.5.4.1 ;

- snpMatrix124 1.2.4.6, fixes a small bug;

- new BeanSprout manual which have a bit more information about various Genome
Studio versions;

- new linux native and non-native build of the whole BeanSprout family against
Genome Studio 2011.1 (they were supposed to happen when I release the android
port, but then I forgot).

There are the 2nd monthly snapshots of win32 and android builds of vcftools,
tabix, samtools. I'd probably continue on a semi-regular monthly basis until
after snpMatrix 1.19.0.12 before I tidy up the adaptations and send upstream.

Besides the two 2.10.8.1 builds, there is a mono 2.11pre snapshot, (mono
2.11pre-push-1480-g0ed3827.x86_64.fc16.tbz2) to address a bug [2].

Lastly, while writing Thai vignette, I fixed a problem which was filed against
emacs [3] ; My notes on 'Typesetting Thai', the emacs lisp script which fixed
that problem and other enhancements mentioned in the notes, a snapshot of
CJK/LaTeX with those enhancements, and perl/python script for unpacking zip
files generated on Chinese windows onto linux/mac's correctly, are housed
elsewhere [4]. While these have nothing to do with science, people processing
non-english data (and specifically Chinese data) may find them useful.

Unless otherwise stated, all of these are somewhere under:
http://sourceforge.net/projects/outmodedbonsai/files/

[1] The original is in the 'historical' section and the updated in 'next/1.19.0.12'.

[2] https://bugzilla.novell.com/show_bug.cgi?id=720031

[3] http://debbugs.gnu.org/cgi/bugreport.cgi?bug=8108

[4] http://htl10.users.sourceforge.net/Languages/



[Rd] Thai vignette, cross-compile for Mac OS X, universal/multiarch (Fwd: Mac OS X builds of CelQuantileNorm, vcftools/samtools/tabix, and snpStats)
Hin-Tak Leung