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). 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.
On Jun 2, 2016, at 10:35 AM, Evan Cooch <evan.cooch at 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
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.cooch at 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 > >