Building R-3.2.0 from source.

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

--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
Home phone: +64-9-480-4619

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

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.