problems compiling packages in R | 3.3.0-5 | EL6
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 Some packages I use give me a warning that '3.2.5 is out of date', or some such, but no fatal errors.