Thanks Martin and Seth for your tricks. I have it working finally. Cheers! -Abhi
-----Original Message----- From: Martin Morgan [mailto:[email protected]] Sent: Tuesday, December 08, 2009 6:52 PM To: Pratap, Abhishek Cc: [email protected] Subject: Re: [Bioc-sig-seq] Probs installing dev version of Rsamtools Hi Abhi -- Pratap, Abhishek wrote: > Hi All > > > > I am starting a new thread since the old issues I believe have been > taken care of. I am trying to install dev version of Rsamtools and > following is what I have done till now. -Abhi > > > > > > 1. R devel install > > 2. BioC devel install ver 2.5.8 > > > > ..CMD:- Rdev CMD INSTALL --clean Rsamtools/ > > > > ****Error:***** > > 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' > As mentioned, this package is under active development; your best bet is to wait for it to mature. As a first step, you must use the 'devel' version of R (sessionInfo below says 2.10.1 RC; you're looking for 2.11.0 Under development), and you'll need to ensure that you are using svn versions of the package dependencies, particularly Biostrings and IRanges. Having checked out IRanges, Biostrings, and Rsamtools, one might svn up IRanges Biostrings Rsamtools R CMD INSTALL --clean IRanges Biostrings Rsamtools even then, the packages may not be functional -- it is not even in 'devel' for a reason! Again, your best bet is to wait for Rsamtools to become more stable. Martin > * removing > '/local/projects/grc/devel/apratap/softwares/R-devel/R-rc/lib64/R/librar > y/Rsamtools' > > > > ======== > > > > > > sessionInfo() > > R version 2.10.1 RC (2009-12-06 r50688) > > x86_64-unknown-linux-gnu > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
