Hello,
I have been trying to install Rsamtools, but no luck so far.  I am getting
error mentioned below, Is this something related to Ubuntu version or this
is specific to Rsamtools. how can I fix it ?
Thanks in advance

> source("http://bioconductor.org/biocLite.R")Bioconductor version 2.12 (BiocInstaller 1.10.4), ?biocLite for helpA newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help> biocLite("Rsamtools")BioC_mirror: http://bioconductor.orgUsing Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.2.Installing package(s) 'Rsamtools'trying URL 'http://bioconductor.org/packages/2.12/bioc/src/contrib/Rsamtools_1.12.4.tar.gz'Content type 'application/x-gzip' length 2970276 bytes (2.8 Mb)opened URL==================================================downloaded 2.8 Mb
* installing *source* package ‘Rsamtools’ ...** libsgcc -std=gnu99
-I/usr/share/R/include -DNDEBUG
-I"/usr/local/lib/R/site-library/Biostrings/include"
-I"/home/thakur/R/x86_64-pc-linux-gnu-library/3.0/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  -O3 -pipe  -g  -c Biostrings_stubs.c -o Biostrings_stubs.oIn
file included from
/usr/local/lib/R/site-library/Biostrings/include/Biostrings_interface.h:96:0,
                 from
/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:1,
                 from Biostrings_stubs.c:1:
/usr/local/lib/R/site-library/Biostrings/include/Biostrings_defines.h:50:2:
error: unknown type name ‘cachedCharSeq’
/usr/local/lib/R/site-library/Biostrings/include/Biostrings_defines.h:59:1:
error: unknown type name ‘cachedXVectorList’In file included from
/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:1:0,
                 from Biostrings_stubs.c:1:
/usr/local/lib/R/site-library/Biostrings/include/Biostrings_interface.h:119:1:
error: unknown type name
‘cachedCharSeq’/usr/local/lib/R/site-library/Biostrings/include/Biostrings_interface.h:167:2:
error: unknown type name
‘cachedCharSeq’/usr/local/lib/R/site-library/Biostrings/include/Biostrings_interface.h:168:2:
error: unknown type name ‘cachedCharSeq’In file included from
Biostrings_stubs.c:1:0:
/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:78:1:
error: expected declaration specifiers or ‘...’ before ‘*’ token
/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:78:1:
error: unknown type name
‘cachedCharSeq’/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:
In function ‘get_cachedXStringSet_elt’:
/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:78:1:
error: unknown type name ‘__get_cachedXStringSet_elt_funtype__’
/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:78:1:
warning: initialization makes integer from pointer without a cast
[enabled by default]/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:78:1:
warning: comparison between pointer and integer [enabled by
default]/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:81:1:
error: ‘__get_cachedXStringSet_elt_funtype__’ undeclared (first use in
this function)
/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:81:1:
note: each undeclared identifier is reported only once for each
function it appears
in/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:78:1:
error: expected ‘;’ before
‘R_GetCCallable’/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:78:1:
error: called object ‘fun’ is not a
function/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:
At top level:
/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:155:1:
error: unknown type name ‘cachedCharSeq’
/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:155:1:
error: unknown type name ‘cachedCharSeq’
/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:155:1:
error: unknown type name
‘cachedCharSeq’/usr/local/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:155:1:
error: unknown type name ‘cachedCharSeq’make: *** [Biostrings_stubs.o]
Error 1ERROR: compilation failed for package ‘Rsamtools’* removing
‘/home/thakur/R/x86_64-pc-linux-gnu-library/3.0/Rsamtools’
The downloaded source packages are in
	‘/tmp/Rtmp8npPvQ/downloaded_packages’


Nishant

JElab, CIML


France

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