[Bioc-devel] os x binary

Hi Dan

I am on snow leopard. ?We have not made any changes to the C code in
affxparser in over a year I think, and it works on a wide variety of
systems. ?Everyone who has reported this problem seems to be able to
fix it by re-installing the CRAN binary and rebuilding affxparser from
source. ?I am not sure that this includes anyone on Lion.

Have you manually rebuild affxparser? ?We have not bumped the version
number since we have made no changes to the package, so according to
my understanding of the build system it will not get rebuild
automatically.

Kasper

On Thu, Nov 17, 2011 at 4:01 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

Hi Kasper,

On Mon, Nov 14, 2011 at 1:24 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

On Mon, Nov 14, 2011 at 12:57 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:

Some problems with the CRAN binary for OS X has been reported on
r-sig-mac. ?Oliver (cc'ed) reported a problem with affxparser
segfaulting that we solved by
(1) installing an updated R binary
(2) recompiling affxparser from source

It was not enough to do (1) and the reinstall using biocLite and type
= "mac.binary".

The building team might already be aware of this, but in case they are
not I would suggest re-installing the R binary and rebuilding
packages.

Thanks, I will update the R on pitt (Mac machine used for release
builds) as soon as it is finished with the builds it's running now.

The new affxparser produced by the latest R binary is now available,
and on my machine (running Lion) it still produces the same segfault:

R --vanilla -q -e 'library(affxparser);sessionInfo(); h <-
readCdfHeader("Mapping250K_Nsp.cdf")'

library(affxparser);sessionInfo(); h <- readCdfHeader("Mapping250K_Nsp.cdf")

R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base

other attached packages:
[1] affxparser_1.26.2
Abort trap: 6



On a different machine (running Leopard) it works:

compbio$ R --vanilla -q -e 'library(affxparser);sessionInfo(>

library(affxparser);sessionInfo(); h <- readCdfHeader("Mapping250K_Nsp.cdf")

R version 2.14.0 (2011-10-31)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] C

attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base

other attached packages:
[1] affxparser_1.26.2

So I think there may still be a problem.
Dan

Dan

Kasper