Hi, I'm trying to install cummeRbund pakage in my R. In order to work on my RNA-seq data I need to obtain the cummeRbund_2.0.0 release. When I type source("http://bioconductor.org/biocLite.R") biocLite("cummeRbund") on my consolle I'm only able to download the cummeRbund_1.0.0 that lacks a lot of functions. So I downloaded the source cummeRbund_2.0.0.tar.gz solving all the dependencies. But when I installed the pakage Gviz I'm not able to go on. This is my the Gviz error (see section ### 1 ###). Moreover if I try to install from th R consolle the error is the following:(see section ### 2 ###) Any idea to solve my problem??? Many thanks! Valentina -- output of sessionInfo(): ####################### 1 ############################### valentina at valentina-desktop:~/Documenti/Tools/download$ sudo R CMD INSTALL Gviz_1.2.1.tar.gz * installing to library ???/usr/local/lib/R/site-library??? * installing *source* package ???Gviz??? ... ** R ** data ** inst ** preparing package for lazy loading Warning in .simpleDuplicateClass(def, prev) : A specification for S3 class ???connection??? in package ???BiocGenerics??? seems equivalent to one from package ???IRanges??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : A specification for S3 class ???file??? in package ???BiocGenerics??? seems equivalent to one from package ???IRanges??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : A specification for S3 class ???bzfile??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : A specification for class ???characterORconnection??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : A specification for S3 class ???fifo??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : A specification for S3 class ???gzfile??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : A specification for S3 class ???pipe??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : A specification for S3 class ???sockconn??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : A specification for S3 class ???terminal??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : A specification for S3 class ???textConnection??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : A specification for S3 class ???unz??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class Warning in .simpleDuplicateClass(def, prev) : A specification for S3 class ???url??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class Error : requested methods not found in environment/package ???GenomicRanges???: seqnameStyle ERROR: lazy loading failed for package ???Gviz??? * removing ???/usr/local/lib/R/site-library/Gviz??? ################ 2 ############################ > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.2.1, ?biocLite for help > biocLite("Gviz") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'Gviz' Installing package(s) into ???/usr/lib/R/library??? (as ???lib??? is unspecified) Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ???Gviz??? is not available (for R version 2.14.1) This is the R version I used: RKward Version 0.5.7 with KDE 4.8.5 And these are my OS information: Linux valentina-desktop 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux -- Sent via the guest posting facility at bioconductor.org.

Hi Valentina, The dependent Gviz is only available for R >=2.15, as stated in the warning msg, > In getDependencies(pkgs, dependencies, available, lib) : > package ???Gviz??? is not available (for R version 2.14.1) You should have your R installation upgraded. cheers, Dan On Fri, 2013-03-08 at 01:57 -0800, valentina indio [guest] wrote: > Hi, > I'm trying to install cummeRbund pakage in my R. In order to work on my RNA-seq data I need to obtain the cummeRbund_2.0.0 release. > When I type > source("http://bioconductor.org/biocLite.R") > biocLite("cummeRbund") > on my consolle I'm only able to download the cummeRbund_1.0.0 that lacks a lot of functions. > So I downloaded the source cummeRbund_2.0.0.tar.gz solving all the dependencies. But when I installed the pakage Gviz I'm not able to go on. This is my the Gviz error (see section ### 1 ###). > > Moreover if I try to install from th R consolle the error is the following:(see section ### 2 ###) > > Any idea to solve my problem??? > Many thanks! > Valentina > > -- output of sessionInfo(): > > ####################### 1 ############################### > valentina at valentina-desktop:~/Documenti/Tools/download$ sudo R CMD INSTALL Gviz_1.2.1.tar.gz > * installing to library ???/usr/local/lib/R/site-library??? > * installing *source* package ???Gviz??? ... > ** R > ** data > ** inst > ** preparing package for lazy loading > Warning in .simpleDuplicateClass(def, prev) : > A specification for S3 class ???connection??? in package ???BiocGenerics??? seems equivalent to one from package ???IRanges??? and is not turning on duplicate class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > A specification for S3 class ???file??? in package ???BiocGenerics??? seems equivalent to one from package ???IRanges??? and is not turning on duplicate class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > A specification for S3 class ???bzfile??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > A specification for class ???characterORconnection??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > A specification for S3 class ???fifo??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > A specification for S3 class ???gzfile??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > A specification for S3 class ???pipe??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > A specification for S3 class ???sockconn??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > A specification for S3 class ???terminal??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > A specification for S3 class ???textConnection??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > A specification for S3 class ???unz??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class > Warning in .simpleDuplicateClass(def, prev) : > A specification for S3 class ???url??? in package ???rtracklayer??? seems equivalent to one from package ???BiocGenerics??? and is not turning on duplicate class definitions for this class > Error : requested methods not found in environment/package ???GenomicRanges???: seqnameStyle > ERROR: lazy loading failed for package ???Gviz??? > * removing ???/usr/local/lib/R/site-library/Gviz??? > > > > ################ 2 ############################ > > source("http://bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help > > biocLite("Gviz") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'Gviz' > Installing package(s) into ???/usr/lib/R/library??? > (as ???lib??? is unspecified) > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ???Gviz??? is not available (for R version 2.14.1) > > > > This is the R version I used: > RKward Version 0.5.7 with KDE 4.8.5 > And these are my OS information: > Linux valentina-desktop 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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