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nishant thakur
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10
@nishant-thakur-6275
Last seen 10.5 years ago
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 cachedXVectorListIn 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 cachedCharSeqIn 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 cachedCharSeqmake: *** [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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