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

Rolf Turner r.turner at auckland.ac.nz
Mon May 11 09:42:53 CEST 2015


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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