[R-SIG-Mac] R 3.0, rgdal, and the oft unloved Mac OS

[Simon Urbanek]

It seems that gdal gets confused with internal and external libraries in a static build - likely causing API mismatch which demonstrated itself in the crash. After re-building gdal with minimal dependencies it seems to work. The rgdal binary is up.

Cheers,
Simon


On Apr 11, 2013, at 9:55 AM, Simon Urbanek wrote:

> On Apr 10, 2013, at 3:26 PM, Ian Fellows wrote:
> 
>> On a related note to the lme4 query∑ There was a glorious period of time where rgdal binaries (with it's external dependancies) were available on CRAN for the mac. Unfortunately, with the introduction of R 3.0 this is no longer the case. It now requires a rather protracted install process (installing GDAL, then PROJ4, then installing rgdal from source using the proper configuration arguments). I understand that this is a known issue https://stat.ethz.ch/pipermail/r-sig-geo/2013-April/017989.html, and was wondering whether CRAN is planning on supporting a binary distribution in the future. If not, is CRAN Extras planning on hosting it?
>> 
> 
> rgdal fails the checks, it segfaults:
> http://www.R-project.org/nosvn/R.check/r-release-macosx-x86_64/rgdal-00check.html
> 
> Here is the output of valgrind:
> 
>> logo <- system.file("pictures/logo.jpg", package="rgdal")[1]
>> x <- new("GDALReadOnlyDataset", logo)
> ==41210== Syscall param sigprocmask(set) points to uninitialised byte(s)
> ==41210==    at 0x41D0FA: sigprocmask (in /usr/lib/libSystem.B.dylib)
> ==41210==    by 0x75756E1: jpeg_CreateDecompress (jdapimin.c:38)
> ==41210==    by 0x6FBFAA1: JPGDataset::Open(GDALOpenInfo*) (jpgdataset.cpp:1833)
> ==41210==    by 0x70EF3F5: GDALOpenInternal(GDALOpenInfo&, char const* const*) (gdaldataset.cpp:2236)
> ==41210==    by 0x70EF5C0: GDALOpenInternal(char const*, GDALAccess, char const* const*) (gdaldataset.cpp:2208)
> ==41210==    by 0x6E731A0: RGDAL_OpenDataset (gdal-bindings.cpp:574)
> ==41210==    by 0x89032: do_dotcall (dotcode.c:585)
> ==41210==    by 0xB1D66: Rf_eval (eval.c:612)
> ==41210==    by 0xBFACF: do_begin (eval.c:1534)
> ==41210==    by 0xB1BD5: Rf_eval (eval.c:584)
> ==41210==    by 0xBED3C: applydefine (eval.c:1689)
> ==41210==    by 0xB1BD5: Rf_eval (eval.c:584)
> ==41210==  Address 0x7fff5fbfb870 is on thread 1's stack
> ==41210== 
> --41210:0:syswrap- WARNING: Ignoring sigreturn( ..., UC_RESET_ALT_STACK );
> ==41210== Warning: client switching stacks?  SP change: 0x7fff5fbfb888 --> 0x100207c48
> ==41210==          to suppress, use: --max-stackframe=140730502691904 or greater
> ==41210== Conditional jump or move depends on uninitialised value(s)
> ==41210==    at 0x41D1A9: _longjmp (in /usr/lib/libSystem.B.dylib)
> ==41210==    by 0x1000BBDC7: ???
> ==41210==    by 0x100207C17: ???
> ==41210==    by 0x100F6C7E7: ???
> ==41210== 
> 
> .. followed by a crash. Possibly some incompatibility between jpeg and gdal? I may have a look later unless the maintainers have some insight...
> 
> Cheers,
> Simon
> 
> 
>> I'm currently in the process of updating the OpenStreetMap package, and was planning on moving rgdal from a suggest to a depends, but would like to know the lay of the land before proceeding.
>> 
>> Best,
>> Ian
>> 	[[alternative HTML version deleted]]
>> 
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