R SIG Fedora - Jun 2016 - problems compiling packages in R | 3.3.0-5 | EL6

*All boxes are EL6 x86_64, fully up to date*


Updated to R 3.3.0-3 recently, however just yesterday I tried to update a couple
packages for a user and noticed almost nothing would build. I was (am) getting
the same build errors as another previously posted
(https://stat.ethz.ch/pipermail/r-sig-fedora/2016-June/000452.html). I watched
over the bodhi page for the issue and noticed 3.3.0-5 was pushed to stable
(https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-93778a4eeb), so I
updated this morning. Problem is, I'm still getting the exact same build
errors I was the last couple of days. In fact, I can perfectly replicate the
initial poster's issue: when I try to update nlme, I end up with the
following:


gcc: /builddir/build/BUILD/R-3.3.0/zlib-1.2.8/target/usr/lib64/libz.a: No such
file or directory
gcc: /builddir/build/BUILD/R-3.3.0/bzip2-1.0.6/target/usr/lib64/libbz2.a: No
such file or directory
gcc: /builddir/build/BUILD/R-3.3.0/xz-5.2.2/target/usr/lib64/liblzma.a: No such
file or directory
gcc: /builddir/build/BUILD/R-3.3.0/pcre-8.38/target/usr/lib64/libpcre.a: No such
file or directory
gcc: /builddir/build/BUILD/R-3.3.0/curl-7.48.0/target/usr/lib64/libcurl.a: No
such file or directory
make: *** [nlme.so] Error 1
ERROR: compilation failed for package 'nlme'

My hope is that I'm just doing something wrong/stupid. I updated via
EPEL/YUM, so that's as much interaction as I've had with it. Happy to
provide further info if it helps anyone. To make matters worse, I was going to
just roll back to 3.2.5, but now I cannot find rpms anywhere for that version,
and yum downgrade just wants to take me back to 3.3.0-3, so basically I'm
stuck figuring this out (which, don't get me wrong, is probably the right
thing to do).


Also....I know I should upgrade to EL7 :-) Just too many other things in the
pipe right now.


Thanks all

T

	[[alternative HTML version deleted]]

On 6/8/2016 12:47 PM, TRISTAN J PAUTSCH wrote:
> *All boxes are EL6 x86_64, fully up to date*
>
>
> Updated to R 3.3.0-3 recently, however just yesterday I tried to update a
couple packages for a user and noticed almost nothing would build. I was (am)
getting the same build errors as another previously posted
(https://stat.ethz.ch/pipermail/r-sig-fedora/2016-June/000452.html). I watched
over the bodhi page for the issue and noticed 3.3.0-5 was pushed to stable
(https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-93778a4eeb), so I
updated this morning. Problem is, I'm still getting the exact same build
errors I was the last couple of days. In fact, I can perfectly replicate the
initial poster's issue: when I try to update nlme, I end up with the
following:
>
>
> gcc: /builddir/build/BUILD/R-3.3.0/zlib-1.2.8/target/usr/lib64/libz.a: No
such file or directory
> gcc: /builddir/build/BUILD/R-3.3.0/bzip2-1.0.6/target/usr/lib64/libbz2.a:
No such file or directory
> gcc: /builddir/build/BUILD/R-3.3.0/xz-5.2.2/target/usr/lib64/liblzma.a: No
such file or directory
> gcc: /builddir/build/BUILD/R-3.3.0/pcre-8.38/target/usr/lib64/libpcre.a: No
such file or directory
> gcc: /builddir/build/BUILD/R-3.3.0/curl-7.48.0/target/usr/lib64/libcurl.a:
No such file or directory
> make: *** [nlme.so] Error 1
> ERROR: compilation failed for package 'nlme'
>
> My hope is that I'm just doing something wrong/stupid. I updated via
EPEL/YUM, so that's as much interaction as I've had with it. Happy to
provide further info if it helps anyone. To make matters worse, I was going to
just roll back to 3.2.5, but now I cannot find rpms anywhere for that version,
and yum downgrade just wants to take me back to 3.3.0-3, so basically I'm
stuck figuring this out (which, don't get me wrong, is probably the right
thing to do).
>
>

I rolled back to 3.2.5 without any problems -- but then, I did a compile 
from scratch using the 3.2.5 tarball. Some packages I use give me a 
warning that '3.2.5 is out of date', or some such, but no fatal errors.