Hi Cristian,
3 things:
1) The current Bioconductor release is BioC 3.1 and it requires R 3.2. Make sure you use these versions. You can check the former by loading the BiocInstaller package:
> library(BiocInstaller)
Bioconductor version 3.1 (BiocInstaller 1.18.1), ?biocLite for help
and the latter by calling sessionInfo()
:
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS
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=en_US.UTF-8 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] BiocInstaller_1.18.1
2) How are you trying to install the IRanges package? You need to show us the command you used. The highly recommended way is to use biocLite()
:
biocLite("IRanges")
Same thing if you were trying to install a package that depends on IRanges: just call biocLite()
on it and that will take care of installing any other package that it depends on.
3) The C code in R packages is expected to conform to the C99 standard and so is the C code in the IRanges package. On Linux platforms, R is usually configured to use the gcc compiler and the -std=gnu99 flag when compiling the C code found in packages. What compiler are you using? You're not showing enough output for us to be able to tell. A simple way to find out is with:
hpages@latitude:~$ R CMD config CC
gcc -std=gnu99
If you have more than one R on your system, make sure you use the same R here as the one you started when you tried to install IRanges with biocLite()
.
Thanks,
H.