Sorry I could not find the way to install BioC dev version. I was looking here : http://www.bioconductor.org/docs/install/
-Abhi -----Original Message----- From: Sean Davis [mailto:[email protected]] Sent: Tuesday, December 08, 2009 5:30 PM To: Pratap, Abhishek Cc: [email protected] Subject: Re: [Bioc-sig-seq] readAligned and BAM format On Tue, Dec 8, 2009 at 5:26 PM, Pratap, Abhishek <[email protected]> wrote: > If following a hint that I should move to R-devel for testing RSamtools. Yes. You'll need to be using R-devel and the devel branch of bioconductor. > This is while trying to install RSAMTools > > Warning in .completeClassSlots(ClassDef, where) : > undefined slot classes in definition of "Alignments0": > gapped_ranges(class "GappedRanges") > Error in setValidity2("Alignments0", .valid.Alignments0, where = > asNamespace("Rsamtools")) : > unused argument(s) (where = asNamespace("Rsamtools")) > Error : unable to load R code in package 'Rsamtools' > ERROR: lazy loading failed for package 'Rsamtools' > * removing > '/local/projects/grc/devel/apratap/softwares/R-2.10.0/lib64/R/library/Rs > amtools > > > -Abhi > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Pratap, > Abhishek > Sent: Tuesday, December 08, 2009 5:20 PM > To: Martin Morgan > Cc: [email protected] > Subject: Re: [Bioc-sig-seq] readAligned and BAM format > > Thanks Martin. Clearly shows I am just getting started :). > > -Abhi > > -----Original Message----- > From: Martin Morgan [mailto:[email protected]] > Sent: Tuesday, December 08, 2009 5:17 PM > To: Pratap, Abhishek > Cc: Wu Wei; [email protected] > Subject: Re: [Bioc-sig-seq] readAligned and BAM format > > Pratap, Abhishek wrote: >> Hi Martin >> >> Just wondering if people outside the firewall/network without passw >> could download this package ? > > Hi Abhi -- there are short instructions on use of svn, including > password, at > > http://wiki.fhcrc.org/bioc/SvnHowTo > > Important to note that this package is very much under active > development, so subject to frequent and unpredictable change. > > Martin > >> >> >> Thanks, >> -Abhi >> >> -----Original Message----- >> From: [email protected] >> [mailto:[email protected]] On Behalf Of Martin >> Morgan >> Sent: Monday, November 02, 2009 8:58 AM >> 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 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
