On Tue, Dec 8, 2009 at 6:06 PM, Pratap, Abhishek <[email protected]> wrote: > Sorry I could not find the way to install BioC dev version. I was looking > here : http://www.bioconductor.org/docs/install/
Hi, Abhi. Simply install the development version of R (available from the CRAN website) and then use biocLite() as usual. You will get the devel versions of bioconductor packages. Sean > -----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
