Hi Daniel -- Remember that Rsamtools is not even in the devel repository; it is a moving target. The error below requires an update, perhaps from svn, of Rsamtools dependencies, specifically IRanges.
Use the development version of R with these packages. Martin Daniel Klevebring wrote: > Hi all, > > Rsamtools looks very interesting. I tried installing it as described below > but I get > > gcc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include > -I/sw/include -I/usr/local/include > -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include" > -I"/Library/Frameworks/R.framework/Resources/library/IRanges/include" > -D_USE_KNETFILE -Dinline="" -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -c cigar.c > -o cigar.o > cigar.c: In function ‘cigar_to_list_of_IRanges’: > cigar.c:257: error: ‘RangeAEAE’ undeclared (first use in this function) > cigar.c:257: error: (Each undeclared identifier is reported only once > cigar.c:257: error: for each function it appears in.) > cigar.c:257: error: expected ‘;’ before ‘range_aeae’ > cigar.c:262: error: ‘range_aeae’ undeclared (first use in this function) > cigar.c:262: warning: implicit declaration of function ‘new_RangeAEAE’ > cigar.c:279: warning: implicit declaration of function ‘RangeAEAE_asLIST’ > cigar.c:279: warning: assignment makes pointer from integer without a cast > make: *** [cigar.o] Error 1 > ERROR: compilation failed for package ‘Rsamtools’ > * Removing ‘/Library/Frameworks/R.framework/Resources/library/Rsamtools’ > > I'm on Mac OS X 10.6.1 with R 2.9.2 and Rsamtools 0.1.16. Any ideas on this? > > Thanks > Daniel Klevebring > > ________________________________________ > From: [email protected] > [[email protected]] On Behalf Of Martin Morgan > [[email protected]] > Sent: 02 November 2009 14:58 > To: Wu Wei > Cc: [email protected] > Subject: Re: [Bioc-sig-seq] readAligned and BAM format > > Hi Wave -- > > svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools > > R CMD INSTALL --clean Rsamtools > > see the script in Rsamtools/inst/script/readAligned_prototype.R > > e.g., > > source(system.file("script", "readAligned_prototype.R", > package="Rsamtools")) > .readAligned_bam(<...>) # args like the other readAligned > > see ?scanBam for additional ideas. > > Martin > > Wu Wei wrote: >> Hi Martin, >> >> I am also looking for that. Would you please also forward that >> additional info to me. >> >> Thanks, >> Wave >> >> On 2 Nov 2009, at 14:34, Martin Morgan wrote: >> >>> Joern Toedling wrote: >>>> Hi everyone, >>>> >>>> has anybody by chance already written a parser for importing >>>> alignments in >>>> BAM/SAM format into objects of class AlignedRead? This format seems >>>> to be >>>> gaining more and more support, yet it is still absent from the >>>> options in >>>> function readAligned. If one of you already has written such a parsing >>>> function and would not mind sharing it, please let me know. >>> Hi Joern -- there is a package in the Bioc svn repository that does >>> this; it is not yet in the devel branch, there are some limitations in >>> terms of AlignedRead (e.g., AlignedRead currently supports only ungapped >>> alignments, whereas BAM allows gapped). I'll forward additional info >>> off-list. >>> >>> Martin >>>> Best regards, >>>> Joern >>>> >>>> --- >>>> Joern Toedling >>>> Institut Curie -- U900 >>>> 26 rue d'Ulm, 75005 Paris, FRANCE >>>> Tel. +33 (0)156246926 >>>> >>>> _______________________________________________ >>>> Bioc-sig-sequencing mailing list >>>> [email protected] >>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>> >>> -- >>> Martin Morgan >>> 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 >>> >>> _______________________________________________ >>> Bioc-sig-sequencing mailing list >>> [email protected] >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> >> >> Wu Wei >> Postdoctoral Fellow >> Steinmetz Group, EMBL Heidelberg >> Tex: +49 6221 387-8310 (8114) >> Fax: +49 6221 387-8518 >> Email: [email protected] >> >> >> >> > > > -- > Martin Morgan > 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 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
