Question: [DEVELOPMENT] Trying to use development version of Bioconductor, needs R 3.6?...
0
gravatar for Casper Peters
4 months ago by
Kampen, Netherlands
Casper Peters0 wrote:

So I am trying to make a package for Bioconductor, but I have to use the latest Bioc-devel. When I tried installing this, it told me I'd need R 3.6? R 3.6 has not been released yet and is a development stage. I tried compiling the latest R devel version but am having issues. Mainly getting the following error;

/usr/bin/ld: CommandLineArgs.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
CommandLineArgs.o: error adding symbols: Bad value
collect2: error: ld returned 1 exit status

I know this is more of an issue with R rather than Bioc, but I wanted to ask/verify anyway if 3.6 is really needed.

Thanks in advance for any response.

bioc-devel developers • 152 views
ADD COMMENTlink written 4 months ago by Casper Peters0
1

Please ask questions about package development on the bioc-devel mailing list. Often the devel version of R does not need to be built from source but is available as a binary version; what are the details of your operating system?

ADD REPLYlink written 4 months ago by Martin Morgan ♦♦ 23k

I am using Ubuntu 16.04 Desktop. I will be sure to ask the bioc-devel mailing instead :). Can you maybe point towards the devel binaries of 3.6? I can't seen to find this anywhere. If they don't exist, I'll still have to try fix my compilation.

ADD REPLYlink written 4 months ago by Casper Peters0

maybe I misspoke about availability; instructions for building from source are at https://cran.r-project.org/bin/linux/debian/#installing-r-devel-or-a-release-branch-from-svn . If there are problems then problably it would be useful to see more of the output, especially the command used to compile and link CommandLineArgs, if that continues to be the problem.

I see you've posted to bioc-devel, so let's continue there...

ADD REPLYlink modified 4 months ago • written 4 months ago by Martin Morgan ♦♦ 23k

Yes, the development of the packages are currently developed and checked with what will become R 3.6, as they will be released when R 3.6 will be released too.

ADD REPLYlink written 4 months ago by Lluís Revilla Sancho460

Alright, thanks :)

ADD REPLYlink written 4 months ago by Casper Peters0
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