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 [[alternative HTML version deleted]]

----- 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]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor