On 08/18/2013 07:18 PM, Aric Gregson wrote:
Hello,
I am trying to install Rsamtools but am having difficulty on
R version 3.0.1 Patched (2013-05-26 r62815)
Platform: amd64-portbld-freebsd9.1 (64-bit)
I receive the following error when installing from within R. I suspect
it is a PATH issue, it seems to be in FreeBSD when trying to compile
Bioconductor packages.
[snip]
gcc46 -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include
-I"/usr/local/lib/R/library/Biostrings/include"
-I"/usr/local/lib/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE
-D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit
-Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -O2 -pipe
-Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bcftools/bcfutils.c -o
samtools/bcftools/bcfutils.o
samtools/bcftools/bcfutils.c:3:37: fatal error: alloca.h: No such file or
directory
compilation terminated.
*** [samtools/bcftools/bcfutils.o] Error code 1
Stop in /tmp/Rtmp6FWVKA/R.INSTALL1352730cb1960/Rsamtools/src.
ERROR: compilation failed for package 'Rsamtools'
* removing '/usr/local/lib/R/library/Rsamtools'
Can I provide you with more information to help diagnose the problem? I
have searched google and not found any suggestions. Any help would be
greatly appreciated.
Hi Aric --
I'm cc'ing the Bioc-devel mailing list, since this has been reported and fixed
earlier, but not publicly.
This is fixed (I hope; please let me know if otherwise!!) in devel with
------------------------------------------------------------------------
r79268 | mtmor...@fhcrc.org | 2013-08-06 11:48:27 -0700 (Tue, 06 Aug 2013) | 2
lines
Changed paths:
M /trunk/madman/Rpacks/Rsamtools/DESCRIPTION
M /trunk/madman/Rpacks/Rsamtools/src/samtools/bcftools/bcfutils.c
M /trunk/madman/Rpacks/Rsamtools/src/samtools/bcftools/prob1.c
alloca() in stdlib.h for FreeBSD
so library(BiocInstaller); useDevel(); biocLite(ask=FALSE) with R-3.0.1 should
get you a fix (and perhaps additional grief associated with using devel, so only
do this if an important deadline is imminent).
Martin
Thanks, Aric
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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