R SIG Fedora - Jun 2016 - problems compiling packages | 3.3.0 | Linux

Updated my R install on my GNU/Linux boxes (running CentOS 6.8) from 
3.2.x -> 3.3.0, using latest from epel (i.e., not compiling from 
source), and while said upgrade seemed to go fine, am now (post-upgrade) 
having all sorts of problems with getting some (but not all) packages to 
compile (either during an initial install attempt, or upgrade to 
existing packages).

For example, if I try to update nlme, I get the following errors, which 
are pretty well fatal:

gcc: error: 
/builddir/build/BUILD/R-3.3.0/zlib-1.2.8/target/usr/lib64/libz.a: No 
such file or directory
gcc: error: 
/builddir/build/BUILD/R-3.3.0/bzip2-1.0.6/target/usr/lib64/libbz2.a: No 
such file or directory
gcc: error: 
/builddir/build/BUILD/R-3.3.0/xz-5.2.2/target/usr/lib64/liblzma.a: No 
such file or directory
gcc: error: 
/builddir/build/BUILD/R-3.3.0/pcre-8.38/target/usr/lib64/libpcre.a: No 
such file or directory
gcc: error: 
/builddir/build/BUILD/R-3.3.0/curl-7.48.0/target/usr/lib64/libcurl.a: No 
such file or directory

Even I try this using devtools-4 (which gives me gcc/gfortran 5.2.1), 
same problem.

I think the clue is the version of the libs the installer seems to be 
looking for. For example, zlib-1.2.8. RHEL only supports zlib-1.2.3-29. 
[Interesting, all of the static .a libs aren't on the system, by all the 
.so lib files for each of those listed above are installed].

Serious pain in the butt. R 3.2.5 was working perfectly -- upgrade 
pretty much gummed things up, as far as compiling some packages. What I 
don't understand is -- wouldn't packages like nmle (which are core 
packages in R) be configured for your specific RHEL distribution to have 
dependencies that are compatible? Either that, or I'm missing something 
completely.

Thanks in advance.

On 06/04/2016 12:10 PM, Evan Cooch wrote:
> Updated my R install on my GNU/Linux boxes (running CentOS 6.8) from
> 3.2.x -> 3.3.0, using latest from epel (i.e., not compiling from
> source), and while said upgrade seemed to go fine, am now (post-upgrade)
> having all sorts of problems with getting some (but not all) packages to
> compile (either during an initial install attempt, or upgrade to
> existing packages).
Here's what happened:

In R 3.3.0, R requires much newer versions of zlib, bzip2, lzma/xz.
curl, and pcre than are included in EL5/6. Since I suspected strongly
that people would not like the answer of "upgrade to EL7" (though, to
be
fair, you really should seriously consider that), I endeavoured to hack
in bundled copies of those needed libs, compiled statically into R.
Unfortunately, this process had some leftover noise, which resulted in
my giant pile of custom LDFLAGS getting inherited when you build from CRAN.

3.3.0-5 _should_ resolve all of this and "just work". Please test this
build when it finishes and let me know:

http://koji.fedoraproject.org/koji/taskinfo?taskID=14394314

Thanks,

~tom

=Red Hat

Thanks very much. I had more or less reached the same conclusions -- I 
was just about to rebuild RPMs for source for zlib, etc, and update 
those, and try again, but I've had mixed success in doing that in past. 
Its easy enough to roll back to 3.2.5 (which compiles perfectly against 
all the CentOS 6.x.x libs), but 3.30 plays nice with a few other things 
I work with. Hence my interest in 3.30.

I'll definitely try the latest build later this week.

p.s. I should probably upgrade to RH 7 - but thanks for not beating me 
over the head with the obvious. ;-)


On 6/6/2016 9:55 AM, Tom Callaway wrote:
> On 06/04/2016 12:10 PM, Evan Cooch wrote:
>> Updated my R install on my GNU/Linux boxes (running CentOS 6.8) from
>> 3.2.x -> 3.3.0, using latest from epel (i.e., not compiling from
>> source), and while said upgrade seemed to go fine, am now
(post-upgrade)
>> having all sorts of problems with getting some (but not all) packages
to
>> compile (either during an initial install attempt, or upgrade to
>> existing packages).
> Here's what happened:
>
> In R 3.3.0, R requires much newer versions of zlib, bzip2, lzma/xz.
> curl, and pcre than are included in EL5/6. Since I suspected strongly
> that people would not like the answer of "upgrade to EL7"
(though, to be
> fair, you really should seriously consider that), I endeavoured to hack
> in bundled copies of those needed libs, compiled statically into R.
> Unfortunately, this process had some leftover noise, which resulted in
> my giant pile of custom LDFLAGS getting inherited when you build from CRAN.
>
> 3.3.0-5 _should_ resolve all of this and "just work". Please test
this
> build when it finishes and let me know:
>
> http://koji.fedoraproject.org/koji/taskinfo?taskID=14394314
>
> Thanks,
>
> ~tom
>
> => Red Hat
>