[Bioc-devel] ShortRead error

[Martin Morgan]

On 04/28/2010 08:46 AM, Droit Arnaud wrote:
> Hi,
> We find the problems.
> I just add
> #include <errno.h> in read_maq_map.cc  and readBfaToc.cc

Thanks Arnaud; this was caused by a recent change (r51839-51840) to the
development version of R, where R_ext/R.h, R_ext/Rinternals.h no longer
include errno.h.

Martin

> 
> Thanks
> 
> Arnaud.
> 
> 
> On 10-04-28 11:39 AM, "Droit Arnaud" <Arnaud.Droit at ircm.qc.ca> wrote:
> 
> Hi,
> 
> I installed the last R beta  version 2.12.
> When, I try to install the ShortRead package (1.7.0).
> I have the following error message :
> 
> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include  -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fPIC  -g -O2 -c readBfaToc.cc -o readBfaToc.o
> readBfaToc.cc: In function 'SEXPREC* readBfaToc(SEXPREC*)':
> readBfaToc.cc:28: error: 'errno' was not declared in this scope
> make: *** [readBfaToc.o] Error 1
> ERROR: compilation failed for package 'ShortRead'
> * removing '/Library/Frameworks/R.framework/Resources/library/ShortRead'
> 
> Anyone have any idea about the problems ?
> 
> Thanks
> 
> Arnaud.
> 
> 
>> sessionInfo()
> R version 2.12.0 Under development (unstable) (2010-04-28 r51857)
> x86_64-apple-darwin10.2.0
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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