Dear all, I just tried to run the example under "readGappedAlignments" from Rsamtools, and get an error message as shown below, I am using the latest R and Rsamtools/GenomicRanges, is it because the dynamic loading is not in the NAMESPACE of GenomicRanges? Thanks in advance! Tengfei ########################### > library(Rsamtools) # because file ex1.bam is in this package Loading required package: IRanges Attaching package: ‘IRanges’ The following object(s) are masked from ‘package:base’: cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union Loading required package: GenomicRanges Loading required package: Biostrings > galn_file <- system.file("extdata", "ex1.bam", package="Rsamtools") > galn <- readGappedAlignments(galn_file) Error in .Call(.NAME, ..., PACKAGE = PACKAGE) : C symbol name "valid_cigar" not in DLL for package "GenomicRanges" > sessionInfo() R Under development (unstable) (2011-08-08 r56671) Platform: x86_64-unknown-linux-gnu (64-bit) 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C 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 other attached packages: [1] Rsamtools_1.5.46 Biostrings_2.21.6 GenomicRanges_1.5.22 [4] IRanges_1.11.18 loaded via a namespace (and not attached): [1] BSgenome_1.21.3 RCurl_1.6-0 rtracklayer_1.13.0 XML_3.4-0 [5] zlibbioc_0.1.7 ################################################ -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[alternative HTML version deleted]]

Hi Sorry that it turn out somehow the package in my repos is broken even though I call svn update it doesn't work, UseDynLib is missing... it's actually in the svn of GenomicRanges, I just clean the repos and check out again, it works now. Regards Tengfei On Mon, Aug 8, 2011 at 2:02 PM, Tengfei Yin <yintengfei@gmail.com> wrote: > Dear all, > > I just tried to run the example under "readGappedAlignments" from > Rsamtools, and get an error message as shown below, I am using the latest R > and Rsamtools/GenomicRanges, is it because the dynamic loading is not in the > NAMESPACE of GenomicRanges? > > Thanks in advance! > > Tengfei > > ########################### > > > library(Rsamtools) # because file ex1.bam is in this package > Loading required package: IRanges > > Attaching package: ‘IRanges’ > > The following object(s) are masked from ‘package:base’: > > cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, > pmin, pmin.int, rbind, rep.int, setdiff, table, union > > Loading required package: GenomicRanges > Loading required package: Biostrings > > galn_file <- system.file("extdata", "ex1.bam", package="Rsamtools") > > galn <- readGappedAlignments(galn_file) > Error in .Call(.NAME, ..., PACKAGE = PACKAGE) : > C symbol name "valid_cigar" not in DLL for package "GenomicRanges" > > sessionInfo() > R Under development (unstable) (2011-08-08 r56671) > Platform: x86_64-unknown-linux-gnu (64-bit) > > 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C 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 > > other attached packages: > [1] Rsamtools_1.5.46 Biostrings_2.21.6 GenomicRanges_1.5.22 > [4] IRanges_1.11.18 > > loaded via a namespace (and not attached): > [1] BSgenome_1.21.3 RCurl_1.6-0 rtracklayer_1.13.0 XML_3.4-0 > > [5] zlibbioc_0.1.7 > > > ################################################ > > > > -- > Tengfei Yin > MCDB PhD student > 1620 Howe Hall, 2274, > Iowa State University > Ames, IA,50011-2274 > Homepage: www.tengfei.name > > > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[alternative HTML version deleted]]