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...ompiled 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...

...tests in tests/no-segfault.R could be added. -------------------------------------------- On Mon, 2/20/17, Martin Maechler <maechler at stat.math.ethz.ch> wrote: Subject: Re: [Rd] another fix for R crashes under enable-strict-barrier, lto, trunk at 72156 To: "Hin-Tak Leung" <htl10 at users.sourceforge.net> Cc: r-devel at r-project.org, "bonsai list" <outmodedbonsai-announce at lists.sourceforge.net> Date: Monday, February 20, 2017, 9:56 AM >>>>> Hin-Tak Leung <htl10 at users.sourceforge.net> >>>>>? ???on Sat, 11 F...

...9; Error in untar2(tarfile, files, list, exdir) : unsupported entry type ?g? ------------------ This happens with both R 2.12.2 (x86 linux) and R svn (x86_64 linux). Since R CMD check does install as part of the check process, there is probably a bug somewhere. The tar ball is uploaded at: http://htl10.users.sourceforge.net/tmp/Matrix_0.999375-48.tar.gz and tar -xzpvf works. It is possible to do R CMD INSTALL from the untar'ed data, so I am a bit lost at where the problem is. The tar ball was generated with git archive ... | gzip > package.tar.gz similar to the example at the bottom...

Found the simpliest way of seeing I bug I encountered doing "R CMD check --use-gct": Just launch R (with --vanilla), and do this: > ?gctorture # this work > gctorture() > ?gctorture Error in gzfile(file, "rb") : can only weakly reference/finalize reference objects # this does not It seems that when gctorture() is on gzfile() doesn't work.

repost from the subscribed address... --- On Fri, 1/4/11, Hin-Tak Leung <htl10 at users.sourceforge.net> wrote: > --- On Wed, 30/3/11, Douglas Bates > <bates at stat.wisc.edu> > wrote: > > > I isolated the problem and tested then committed a > fix. I > > am going to > > ask Martin to upload the new release as I have gotten > out...

...ion: Page Group detected which pdfTeX can't handle. Ignoring it. ================== I am fairly sure that this is too late to be included in R 2.14 (already in code freeze and due in less than 10 days..), but harmless enough to go into trunk and 2.14.1? --- On Sat, 22/10/11, Hin-Tak Leung <htl10 at users.sourceforge.net> wrote: > I have had some fun in the last few > days trying to put together an annotated map of China with R > and some public GIS data: > > http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/1.17.7.11/China_Choropleth_Maps.pdf/downloa...

I finally got round to look at a little problem I have - most of the time when I use R I would be using snpMatrix (now part of bioconductor, I wrote a substantial part of), so I had $HOME/.Rprofile to save some typing. Upgrading, switching versions used to work fine with R 2.8 then it broke with 2.9.. Apparently it is because most of SHLIB, INSTALL, etc used to be fairly extensive shell scripts

...will do both and see which one is better at some point. The package uploads (12 in all, 2 packages x 3 R versions x 2 builds) are now divided by R versions - those in unversion'ed directories are still for R 2.x. -------------------------------------------- On Wed, 21/1/15, Hin-Tak Leung <htl10 at users.sourceforge.net> wrote: R.framework-Versions-Resources-library-grDevices-libs-cairo_20150120.tgz in http://sourceforge.net/projects/outmodedbonsai/files/R/ are dropped in replacement to the cairo.so's in the official R binaries (2.15.3, 3.0.3, 3.1.2). updated to cairo-1.12.1...

I haven' t touched R for some 18 months, and so I have no idea if this is a recent problems or not; but it certainly did not segfault two years ago. Since it has been crashing (segfault) under 'make check-all' for over a month, I reckon I'll have to look at it myself, to have it fixed. I have been having the ' --enable-memory-profiling --enable-strict-barrier

------------------------------ On Sat, May 16, 2015 2:33 PM BST Marc Schwartz wrote: > >> On May 16, 2015, at 6:11 AM, Hin-Tak Leung <htl10 at users.sourceforge.net> wrote: >> >> >> >> ------------------------------ >> On Sat, May 16, 2015 8:04 AM BST Uwe Ligges wrote: >> >> Not sure why this goes to R-devel. You just could have asked the >> maintainer. Terry Therneau is aware of...

R fails to build with visibility on and gcc 4.9's link time optimzation, because of its practice of building part of it as archive first. Specifically it builds some bundled libraries as archive first, the symbols of which are then entirely invisible in gcc 4.9. The Matrix package also does this awful practice, with CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a . One way of fixing R is:

Somebody else had written separately about this before, and so have I a couple of months ago. I assumed this will be fixed before the next R. Since R 3.0 is supposedly only 6 weeks away, even if it is fixed now it doesn't leave much room for testing. Anyway neither Matrix 1.0-11 (current) nor 1.0-9 (sept 2012) build with current R trunk. The last time it did was 1. 0-9 on 3rd october over

..., GNUTARGET are all environment variables - you set them the usual way. The stack probing fix is for passing "make check", when you finish make. ------------------------------ On Thu, Jan 8, 2015 6:14 PM GMT Avraham Adler wrote: >On Thu, Jan 8, 2015 at 10:48 AM, Hin-Tak Leung ><htl10 at users.sourceforge.net> wrote: >> >> The r.dll crash is easy - you need to be using gcc-ar for ar, and gcc-ranlib for ranlib. I also posted a patch to fix the check failure for stack probing, as lto optimizes away the stack probing code, as it should. >> >> yes, lto bui...

------------------------------ On Sat, May 16, 2015 8:04 AM BST Uwe Ligges wrote: >Not sure why this goes to R-devel. You just could have asked the >maintainer. Terry Therneau is aware of it and promised he will fix it. > The quickest fix is to add cmprsk to the recommended list , and that's is an R-devel issue. >On 16.05.2015 07:22, Hin-Tak Leung wrote: >> 'make

Hi, Since upgraded to R 2.15, I have a problem with duplicate S4 class name no longer works (the reason for having duplicate S4 class names is just software forks - they are largely identical but don't have an inheritence relationship, and will never have such). This is happening with "library(mypackage2)" : Error: package slot missing from signature for generic ?[? and classes

I have had some fun in the last few days trying to put together an annotated map of China with R and some public GIS data: http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/1.17.7.11/China_Choropleth_Maps.pdf/download It is done, and rather nice... there are a few issues: - the default pdf() device cannot do CJK with embedded fonts - and cairo_pdf() is not hooked up to

On Thu, Jan 8, 2015 at 10:48 AM, Hin-Tak Leung <htl10 at users.sourceforge.net> wrote: > > The r.dll crash is easy - you need to be using gcc-ar for ar, and gcc-ranlib for ranlib. I also posted a patch to fix the check failure for stack probing, as lto optimizes away the stack probing code, as it should. > > yes, lto build's speed g...

...HeungJun Kim <riverful.kim@samsung.com> Hideki EIRAKU <hdk@igel.co.jp> HighPoint Linux Team <linux@highpoint-tech.com> Hila Gonen <hila.gonen@intel.com> Hillf Danton <dhillf@gmail.com> Himanshu Madhani <himanshu.madhani@qlogic.com> Hin-Tak Leung <htl10@users.sourceforge.net> Hiraku Toyooka <hiraku.toyooka.gu@hitachi.com> Hiral Patel <hiralpat@cisco.com> Hiro Sugawara <hsugawara@nvidia.com> Hiroaki SHIMODA <shimoda.hiroaki@gmail.com> Hiroo MATSUMOTO <matsumoto.hiroo@jp.fujitsu.com> Hiroshi DOYU <hdoy...

...HeungJun Kim <riverful.kim@samsung.com> Hideki EIRAKU <hdk@igel.co.jp> HighPoint Linux Team <linux@highpoint-tech.com> Hila Gonen <hila.gonen@intel.com> Hillf Danton <dhillf@gmail.com> Himanshu Madhani <himanshu.madhani@qlogic.com> Hin-Tak Leung <htl10@users.sourceforge.net> Hiraku Toyooka <hiraku.toyooka.gu@hitachi.com> Hiral Patel <hiralpat@cisco.com> Hiro Sugawara <hsugawara@nvidia.com> Hiroaki SHIMODA <shimoda.hiroaki@gmail.com> Hiroo MATSUMOTO <matsumoto.hiroo@jp.fujitsu.com> Hiroshi DOYU <hdoy...

...eki EIRAKU <hdk@igel.co.jp> Hideyuki Sano <hideyuki.sano.dn@renesas.com> HighPoint Linux Team <linux@highpoint-tech.com> Hila Gonen <hila.gonen@intel.com> Hillf Danton <dhillf@gmail.com> Himanshu Madhani <himanshu.madhani@qlogic.com> Hin-Tak Leung <htl10@users.sourceforge.net> Hiraku Toyooka <hiraku.toyooka.gu@hitachi.com> Hiral Patel <hiralpat@cisco.com> Hiro Sugawara <hsugawara@nvidia.com> Hiroaki SHIMODA <shimoda.hiroaki@gmail.com> Hiroo MATSUMOTO <matsumoto.hiroo@jp.fujitsu.com> Hiroshi DOYU <hdoy...