Building R-3.2.0 from source.
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