OK -- thanks. I used to compile from source routinely, but could never
get thee 'hand rolled' version of R to play nice with some external
applications (specifically, jags, and openbugs).
On 6/2/2016 5:41 PM, Marc Schwartz wrote:
On Jun 2, 2016, at 10:35 AM, Evan Cooch <evan.co...@gmail.com> wrote:
Updated my R install on my GNU/Linux boxes (running RHEL 6.xx), using latest
from CRAN (i.e., not compiling from source), and while said upgrade seemed to
go fine, am having all sorts of problems with getting some packages to compile
(either during an initial install attempt, or upgrade to existing packages).
Just for clarification, if you were NOT installing from source, you were NOT
installing from CRAN. Precompiled RH RPM binaries of R have not been available
from CRAN for quite some time.
Presumably you used 'yum' and were installing via the EPEL using their
precompiled binary RPMs? Those would be configured for your specific RHEL
distribution to have dependencies that are compatible.
The RPMS there would include both "base" R and the additional "recommended"
packages, which are part of the default R distribution and includes nlme.
More below.
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
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 (RHEL, like most
'enterprise distros', is typically 1 step back from 'bleeding edge').
Any way I can force R CMD (or some such) to use system libs, instead of looking
for specific, newer versions? Or, any other suggestions?
Serious pain in the butt. R 3.2.5 was working perfectly -- upgrade pretty much
gummed things up, as far as compiling some packages.
Thanks in advance.
p.s. wasn't sure if this should go to r-help, or r-packages.
Neither one.
You should be posting to R-SIG-Fedora:
https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Please re-post there as both RH/Fedora users and the RH RPM maintainers read
that list, should there be issues with the EPEL RPMs relative to dependencies.
Regards,
Marc Schwartz
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
