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

Ranjan Maitra maitra.mbox.ignored at inbox.com
Mon May 11 13:07:41 UTC 2015 

Rolf,

Just curious, but why do you use F17? The disasters that you anticipate may happen will be more and more likely the longer you wait to upgrade to a new F. (And, with no upgrades of any kind, aren't you on line for a greater disaster: for instance, you are not patched for the severe openssl vulnerability that was discovered and all over the news a year or two ago unless you installed it by hand yourself.) 

If on the other hand, you do not want to upgrade as frequently as most of the rest of us here, you should either move to a long-term distribution (such as CentOS or ScientificLinux, which appears to have better support) or to a rolling-release distribution such as ArchLinux (whose installation is, IMO, its Achilles heel so you are better off with ManjaroLinux). With the first set, there also appears to be fewer packages available, but they may be enough for you.

Of course, it would be nicer if there was a rolling-release version of Fedora (precisely for people like you). Rawhide, often offered by some as a rolling-release equivalent, is too unstable to be of value to people who are upgrade-phobic. (Frankly, even I would not touch Rawhide.) Even Windoze is getting rid of upgrades.

Best wishes,
Ranjan



On Mon, 11 May 2015 19:42:53 +1200 Rolf Turner <r.turner at auckland.ac.nz> wrote:

> On 11/05/15 16:19, Tom Callaway wrote:
> > 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.
> 
> It certainly did!  Success.  Thank you hugely!
> 
> But if I may ask a supplementary question:  You say "If you really want 
> to build from source ....".  No, I don't *want* to; I have to.  At least 
> in my understanding.  I run the ancient and beyond end-of-life Fedora 
> 17.  (I haven't the nerve to try to upgrade; my current system may be 
> kludgey, but at least it works.  And I *know* that if I try to upgrade 
> all hell will break loose.)  It is my understanding that "current Fedora 
> releases" *do not* include Fedora 17.  Or do they?
> If so, how would I get my hands on an R binary for Fedora 17?
> 
> That's really just an academic question at present, since I have now 
> managed, thanks to your help, to build R 3.2.0 from source.
> 
> Thanks again.
> 
> cheers,
> 
> Rolf Turner
> 
> >
> > 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
> >>>>
> >>>> _______________________________________________
> >>>> R-SIG-Fedora mailing list
> >>>> 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
> >>
> >> _______________________________________________
> >> R-SIG-Fedora mailing list
> >> 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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