I am a system admin who has been asked by a user to install GenomicRanges, however it is failing. I know absolutely nothing about R, so I'd like some (gentle!) help on how to install it. This is on CentOS6, with gcc 4.4.7, R2.15.1. The error I get is: bash-4.1$ /usr/local/R/2.15.1/lib64/R/bin/Rcmd INSTALL GenomicRanges_1.14.3.tar.gz * installing to library '/usr/local/R/2.15.1/lib64/R/library' * installing *source* package 'GenomicRanges' ... ** libs gcc -std=gnu99 -I/usr/local/R/2.15.1/lib64/R/include -DNDEBUG -I/usr/local/include -I"/usr/local/R/2.15.1/lib64/R/library/IRanges/include" -I"/usr/local/R/2.15.1/lib64/R/library/XVector/include" -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o In file included from /usr/local/R/2.15.1/lib64/R/include/Rdefines.h:25, from /usr/local/R/2.15.1/lib64/R/library/IRanges/incl ude/IRanges_defines.h:18, from /usr/local/R/2.15.1/lib64/R/library/IRanges/incl ude/IRanges_interface.h:12, from /usr/local/R/2.15.1/lib64/R/library/IRanges/incl ude/_IRanges_stubs.c:1, from IRanges_stubs.c:1: /usr/local/R/2.15.1/lib64/R/include/R_ext/Memory.h:27:38: error: stddef.h: No such file or directory Stddef.h does exist and is installed, this simple C program compiles correctly. [hornenj at c6build64 tmp]$ cat std.c #include <stddef.h> main() { } Thanks, -Nigel

On Tue, Nov 26, 2013 at 12:09 PM, Horne, Nigel (NIH/NLM/NCBI) [C] < nigel.horne@nih.gov> wrote: > I am a system admin who has been asked by a user to install GenomicRanges, > however it is failing. I know absolutely nothing about R, so I'd like some > (gentle!) help on how to install it. > > This is on CentOS6, with gcc 4.4.7, R2.15.1. The error I get is: > > bash-4.1$ /usr/local/R/2.15.1/lib64/R/bin/Rcmd INSTALL > GenomicRanges_1.14.3.tar.gz > Hi, Nigel. It turns out that the Bioconductor packages (of which GenomicRanges is one) are matched to the version of R. You are trying to install on a fairly old version of R and the GenomicRanges version does not match. While R does not change too quickly, Bioconductor does continue to add features, so my suggestion is to first install the most recent version of R (3.0.2, I believe) so that your users have the most updated release. Then install using the instructions here: http://www.bioconductor.org/packages/2.13/bioc/html/GenomicRanges.html Let us know how it goes. Sean > * installing to library '/usr/local/R/2.15.1/lib64/R/library' > * installing *source* package 'GenomicRanges' ... > ** libs > gcc -std=gnu99 -I/usr/local/R/2.15.1/lib64/R/include -DNDEBUG > -I/usr/local/include > -I"/usr/local/R/2.15.1/lib64/R/library/IRanges/include" > -I"/usr/local/R/2.15.1/lib64/R/library/XVector/include" -fpic -g -O2 -c > IRanges_stubs.c -o IRanges_stubs.o > In file included from /usr/local/R/2.15.1/lib64/R/include/Rdefines.h:25, > from > /usr/local/R/2.15.1/lib64/R/library/IRanges/include/IRanges_defines. h:18, > from > /usr/local/R/2.15.1/lib64/R/library/IRanges/include/IRanges_interfac e.h:12, > from > /usr/local/R/2.15.1/lib64/R/library/IRanges/include/_IRanges_stubs.c :1, > from IRanges_stubs.c:1: > /usr/local/R/2.15.1/lib64/R/include/R_ext/Memory.h:27:38: error: stddef.h: > No such file or directory > > Stddef.h does exist and is installed, this simple C program compiles > correctly. > > [hornenj@c6build64 tmp]$ cat std.c > #include <stddef.h> > > main() > { > } > > Thanks, > > -Nigel > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

On Wed, Nov 27, 2013 at 8:00 AM, Horne, Nigel (NIH/NLM/NCBI) [C] < nigel.horne@nih.gov> wrote: > Sean, > > On Tue, Nov 26, 2013 at 12:09 PM, Horne, Nigel (NIH/NLM/NCBI) [C] < > nigel.horne@nih.gov> wrote: > >> I am a system admin who has been asked by a user to install >> GenomicRanges, however it is failing. I know absolutely nothing about R, >> so I'd like some (gentle!) help on how to install it. >> >> This is on CentOS6, with gcc 4.4.7, R2.15.1. The error I get is: >> >> bash-4.1$ /usr/local/R/2.15.1/lib64/R/bin/Rcmd INSTALL >> GenomicRanges_1.14.3.tar.gz >> > > Hi, Nigel. > > It turns out that the Bioconductor packages (of which GenomicRanges is > one) are matched to the version of R. You are trying to install on a > fairly old version of R and the GenomicRanges version does not match. > While R does not change too quickly, Bioconductor does continue to add > features, so my suggestion is to first install the most recent version of R > (3.0.2, I believe) so that your users have the most updated release. Then > install using the instructions here: > > http://www.bioconductor.org/packages/2.13/bioc/html/GenomicRanges.html > > > Thanks for your answer. I wondered if that could be the case, though > the page you mentioned says it works with "R (>= 2.10)", so I assumed it > would work with 2.15.1. I will try to convince the user to use a different > version – wish me good luck on that one! Perhaps I could also suggest that > the page correctly reflect the minimum version of R that's required? That > would make my life easier when trying to convince her! > > Hi, Nigel. Sorry for the confusion, but suffice it to say that the Bioconductor releases are coordinated to R so that a specific version of Bioconductor is tied to the associated R release. Some packages may run in earlier versions of R (hence, the R>=2.10 in the package DESCRIPTION), but that use case is not supported by Bioconductor. Following the installation instructions on the Bioconductor website minimizes the chance of getting into trouble with non-matching package versions. In any case, if the user wants to use a specific version of R, the appropriate package version should always be installed using biocLite as detailed on the Bioconductor website. Sean [[alternative HTML version deleted]]