[R-sig-Fedora] problems compiling packages | 3.3.0 | Linux
Evan Cooch
evan.cooch at gmail.com
Sat Jun 4 18:10:16 CEST 2016
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.
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