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 > >> > >> _______________________________________________ > >> 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
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
On Monday 11 May 2015 19:42:53 Rolf Turner wrote:> 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?The list of supported versions is here: https://fedoraproject.org/wiki/Releases In short each version is supported for one month after the release of version N+2. That means in particular that as soon as Fedora 22 is released Fedora will be supported one more month.> 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 TurnerIf you prefer a short release cycle a reasonable approach is CentOS where R is packaged in the EPEL repositories, that belong the Fedora infrastructure. Regards, -- Jos? Ab?lio
On 05/11/2015 09:42 AM, Rolf Turner wrote:> 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.Wow. Well, I can't say that I'm building anything for end-of-lifed Fedora releases, though I understand your predicament. That said, I am still building for EL5, which is older than Fedora 17, so you could try to rebuild the R src.rpm from koji. If it does not work properly, let me know, and I will try to fix the conditionals so that it does. Glad you got it working. :) ~tom =Red Hat