Hi, I am trying to install package GenomicRanges version 1.17.18 and get the following error. Is there a solution for this? R CMD INSTALL ./GenomicRanges_1.17.18.tar.gz * installing to library ‘/nethome/mshah/R/x86_64-unknown-linux-gnu-library/3.1’ * installing *source* package ‘GenomicRanges’ ... ** libs gcc -std=gnu99 -I/data/NYGC/Software/R/R-3.1.0/lib64/R/include -DNDEBUG -I/usr/local/include -I"/nethome/mshah/R/x86_64-unknown-linux-gnu- library/3.1/S4Vectors/include" -I"/nethome/mshah/R/x86_64-unknown-linux-gnu- library/3.1/IRanges/include" -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -I/data/NYGC/Software/R/R-3.1.0/lib64/R/include -DNDEBUG -I/usr/local/include -I"/nethome/mshah/R/x86_64-unknown-linux-gnu- library/3.1/S4Vectors/include" -I"/nethome/mshah/R/x86_64-unknown-linux-gnu- library/3.1/IRanges/include" -fpic -g -O2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o gcc -std=gnu99 -I/data/NYGC/Software/R/R-3.1.0/lib64/R/include -DNDEBUG -I/usr/local/include -I"/nethome/mshah/R/x86_64-unknown-linux-gnu- library/3.1/S4Vectors/include" -I"/nethome/mshah/R/x86_64-unknown-linux-gnu- library/3.1/IRanges/include" -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu99 -I/data/NYGC/Software/R/R-3.1.0/lib64/R/include -DNDEBUG -I/usr/local/include -I"/nethome/mshah/R/x86_64-unknown-linux-gnu- library/3.1/S4Vectors/include" -I"/nethome/mshah/R/x86_64-unknown-linux-gnu- library/3.1/IRanges/include" -fpic -g -O2 -c transcript_utils.c -o transcript_utils.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o installing to /nethome/mshah/R/x86_64-unknown-linux-gnu- library/3.1/GenomicRanges/libs ** R ** inst ** preparing package for lazy loading Error : .onLoad failed in loadNamespace() for 'XVector', details: call: get(name, envir = asNamespace(pkg), inherits = FALSE) error: object 'setDefaultSlotValue' not found ERROR: lazy loading failed for package ‘GenomicRanges’ Thanks, Minita [[alternative HTML version deleted]]

Hi, On Sun, Jun 15, 2014 at 9:47 PM, Minita Shah <shah.minita at="" gmail.com=""> wrote: > Hi, > > I am trying to install package GenomicRanges version 1.17.18 and get the > following error. Is there a solution for this? > > R CMD INSTALL ./GenomicRanges_1.17.18.tar.gz [snip] It look like you are installing the development version of GenomicRanges -- are you doing so intentionally? If yes: are the rest of the Bioconductor packages using the devel version? Why don't you install using biocLite? There are some tips on how to run with devel here: http://bioconductor.org/developers/how-to/useDevel/ and in the help file you get when you run this in your R console: `?BiocInstaller::useDevel` In particular, note the instructions in the help file for having different directories for each bioconductor version, which it seems like you aren't doing given the choice of destination directory you are installing into here: > * installing to library > '/nethome/mshah/R/x86_64-unknown-linux-gnu-library/3.1' HTH, -steve -- Steve Lianoglou Computational Biologist Genentech