Hello Bioconductorians, I just downloaded and installed the new R-devel (without problems) but rtracklayer fails to load. It started by asking me to recompile bitops, which I did. Unfortunately, the problem persists. Please see below. Can anybody think of a solution? Thank you, Ivan $ R --vanilla R Under development (unstable) (2011-11-01 r57541) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(rtracklayer) Loading required package: RCurl Loading required package: bitops Error : classes "file", "connection" are not exported by 'namespace:Biostrings' Error: package/namespace load failed for ?rtracklayer? > sessionInfo() R Under development (unstable) (2011-11-01 r57541) 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] RCurl_1.6-10 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biostrings_2.23.0 BSgenome_1.23.0 GenomicRanges_1.7.0 [4] IRanges_1.13.0 tools_2.15.0 XML_3.4-3 [7] zlibbioc_1.1.0

On 11/02/2011 01:47 PM, Ivan Gregoretti wrote: > Hello Bioconductorians, > > I just downloaded and installed the new R-devel (without problems) but > rtracklayer fails to load. > > It started by asking me to recompile bitops, which I did. > Unfortunately, the problem persists. Please see below. update packages via source('http://bioconductor.org/biocLite.R') biocLite(character()) Martin > > Can anybody think of a solution? > > Thank you, > > Ivan > > > > $ R --vanilla > > R Under development (unstable) (2011-11-01 r57541) > Copyright (C) 2011 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-unknown-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> library(rtracklayer) > Loading required package: RCurl > Loading required package: bitops > Error : classes "file", "connection" are not exported by 'namespace:Biostrings' > Error: package/namespace load failed for ?rtracklayer? >> sessionInfo() > R Under development (unstable) (2011-11-01 r57541) > 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] RCurl_1.6-10 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biostrings_2.23.0 BSgenome_1.23.0 GenomicRanges_1.7.0 > [4] IRanges_1.13.0 tools_2.15.0 XML_3.4-3 > [7] zlibbioc_1.1.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793