[BioC] Rsamtools installation error

[Dan Tenenbaum]

----- Original Message -----
> From: "nishant thakur" <nishantthakur7g at gmail.com>
> To: bioconductor at r-project.org
> Sent: Tuesday, December 3, 2013 7:04:35 AM
> Subject: [BioC] Rsamtools installation error
> 
> 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> 


You might want to try upgrading to BioC 2.13 as suggested by this message.
?BiocUpgrade
will tell you how.

Dan


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
> 
> 	[[alternative HTML version deleted]]
> 
> 
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