[R] [R-sig-Fedora] Building R-3.2.0 from source.

Mon May 11 06:19:16 CEST 2015

I just landed in Paris, and haven't read backwards in this thread, but I've done 3.2.0 builds for all current Fedora releases, they're all in updates-testing (I think the Fedora 22 builds are in updates stable now).

The thing that changed is that R doesn't bundle a number of libraries like it used to. This doesn't affect the official Fedora R package, since we never used the bundled libraries. This is documented in the 3.2.0 release notes.

If you really want to build from source, I think you can run:

yum-builddep R

That will install all the necessary Build Requires to build R from source. You need to have the yum-utils package installed for that command to exist.

Hope that helps.

On May 11, 2015 3:10 AM, Rolf Turner <r.turner at auckland.ac.nz> wrote:
>
> On 11/05/15 12:06, M. Edward (Ed) Borasky wrote: 
> > 1. R 3.2.0 is packaged for Fedora now; it's in Rawhide and Fedora 22. 
> > I'm running Fedora 22 (late beta) and haven't had any problems with R. 
> > RStudio Desktop Preview (0.99.435) from the RStudio Fedora RPM is also 
> > running fine. You might save yourself some hassles by upgrading to 
> > Fedora 22. 
>
> I'm sure I would, but I don't dare.  Everything I see on the Fedora 
> mailing list fills me with terror in respect of the disasters that can 
> occur.  I don't have the skills to cope with such disasters and I have 
> no access to support in respect of Fedora. 
>
> > 2. I have a bash script to build R from source that works on Fedora 
> > 22. It probably also works on Fedora 21 but it's been a while since I 
> > tried it. Note that it installs 'calibre' and makes the ebooks of the 
> > manuals. It also does some packaging things at the end you probably 
> > don't need. 
>
> Thanks, but I don't think it's any help in my situation. 
>
> I had no problem at all building R 3.1.2 from source.  What changed from 
> 3.1.2 to 3.2.0 that would cause those undefined reference problems? 
>
> cheers, 
>
> Rolf Turner 
>
> > 
> > On Sun, May 10, 2015 at 2:52 PM, Rolf Turner <r.turner at auckland.ac.nz> wrote: 
> >> 
> >> I am cross-posting this to r-sig-fedora (I hope that's not an egregious sin) 
> >> in the hope that doing so might provide some source of insight. 
> >> 
> >> I tried 
> >> 
> >>      sudo yum install zlib 
> >> 
> >> and was told 
> >> 
> >>> Package zlib-1.2.5-7.fc17.x86_64 already installed and latest version 
> >> 
> >> 
> >> 
> >> Likewise for "zlib-devel". 
> >> 
> >> I also tried 
> >> 
> >>      sudo yum install bzlib 
> >> 
> >> and was told 
> >> 
> >>> No package bzlib available. 
> >> 
> >> 
> >> Likewise for "bzlib-devel". 
> >> 
> >> Finally I sort of got some joy with "lzma" and "lzma-devel" --- both of 
> >> those yielded an actual installation.  But it didn't help. 
> >> 
> >> I re-did the configure and then the make and got the same errors/complaints 
> >> about undefined references to deflate, inflate, crc32, etc. 
> >> 
> >> Can anyone provide any guidance/suggestions about what else I could try? 
> >> I'm getting very frustrated! :-) 
> >> 
> >> cheers, 
> >> 
> >> Rolf Turner 
> >> 
> >> On 11/05/15 00:50, peter dalgaard wrote: 
> >>> 
> >>> 
> >>>> On 10 May 2015, at 14:15 , Rolf Turner <r.turner at auckland.ac.nz> wrote: 
> >>>> 
> >>>> 
> >>>> 
> >>>> I am just now getting around to upgrading from 3.1.2 to 3.2.0 and am 
> >>>> getting hammered by a problem which is beyond my limited capabilities of 
> >>>> handling. 
> >>>> 
> >>>> I executed 
> >>>> 
> >>>>    ./configure --with-tcltk --with cairo 
> >>>> 
> >>>> which seemed to go just fine, and then did: 
> >>>> 
> >>>>     make 
> >>>> 
> >>>> In fairly short order I started getting  error messages like unto: 
> >>>> 
> >>>>> connections.o: In function `gzcon_write': 
> >>>>> /home/rolf/Desktop/Rinst/R-3.2.0/src/main/connections.c:5469: undefined 
> >>>>> reference to `deflate' 
> >>>> 
> >>>> 
> >>>> There were also complaints about undefined references to inflate, crc32, 
> >>>> deflateEnd, inflateEnd, inflateReset, inflateInit2_, deflateInit2_, 
> >>>> compress, uncompress, and zlibVersion, many of which were issued repeatedly. 
> >>>> It finally gave up, saying: 
> >>>> 
> >>>>> collect2: error: ld returned 1 exit status 
> >>>> 
> >>>> 
> >>>> A bit of googling informed me (I think?) that a workaround was to 
> >>>> configure using --without-system-pcre.  This however achieved nothing in my 
> >>>> case. 
> >>>> 
> >>>> Can anyone point me at what I need to do to fix this?  Install or update 
> >>>> something? 
> >>>> 
> >>>> I am running an (elderly, no-longer-supported) Fedora 17 Linux. 
> >>>> 
> >>>> Thanks for any assistance. 
> >>> 
> >>> 
> >>> PCRE (regular expressions) won't help you with compression algorithms... 
> >>> If anything, it is  --without-system-xz, -zlib, -bzlib that would come into 
> >>> play, but it would be a better idea to ensure that you do have the libraries 
> >>> and headers installed. 
> >>> 
> >>> I'm not completely up to speed on Fedora, but the order of the day is that 
> >>> you need to install some variation of lzma/zlib/bzlib and their -dev/-devel 
> >>> header files etc. Check appendix A.1 and A.2 of the R Installation and 
> >>> Administration manual. 
> >>> 
> >> 
> >> 
> >> -- 
> >> Technical Editor ANZJS 
> >> Department of Statistics 
> >> University of Auckland 
> >> Phone: +64-9-373-7599 ext. 88276 
> >> Home phone: +64-9-480-4619 
> >> 
> >> _______________________________________________ 
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> >> R-SIG-Fedora at r-project.org 
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora 
> > 
> > 
> > 
>
>
> -- 
> Technical Editor ANZJS 
> Department of Statistics 
> University of Auckland 
> Phone: +64-9-373-7599 ext. 88276 
> Home phone: +64-9-480-4619 
>
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