A friend of mine was having trouble building the latest version of R on RHEL 6.8. The trouble was that the configure script could not verify the updated zlib. I gave him some advice, but nothing seemed to work. Typically I’ve solved this with a simple update of the LD_LIBRARY_PATH.
Last night, I provisioned a RHEL 6.8 VM, downloaded the latest version of R, and tried building it myself. As expected, the configure script reported that I did not have zlib 1.2.5 installed.
checking if zlib version >= 1.2.5... no checking whether zlib support suffices... configure: error: zlib library and headers are required
This is simple, just download an updated zlib, build and install. I installed zlib 1.2.11 in /usr/local/lib64. Re-ran configure and go the same result as above. I set LD_LIBRARY_PATH=/usr/local/lib64:$LD_LIBRARY_PATH, configure still complained about not finding an updated zlib.
Updated zlib is installed, LD_LIBRARY_PATH is set. I ran sudo ldconfig -p | grep libz. It shows it can be found in /usr/local/lib64. So frustrating that everything seems to be in order and yet configure doesn’t see it.
My friend was using a blog post to help him out, when I looked at it the author didn’t see to have a problem with configure after updating zlib.
What in the world is the configure script doing to determine what version of zlib we are using?
if test "${have_zlib}" = yes; then
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if zlib version >= 1.2.5" >&5
$as_echo_n "checking if zlib version >= 1.2.5... " >&6; }
if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
else
if test "$cross_compiling" = yes; then :
r_cv_header_zlib_h=no
else
cat confdefs.h - <conftest.$ac_ext
/* end confdefs.h. */
#include
#include
#include
int main() {
#ifdef ZLIB_VERSION
/* Work around Debian bug: it uses 1.2.3.4 even though there was no such
version on the master site zlib.net */
exit(strncmp(ZLIB_VERSION, "1.2.5", 5) < 0);
#else
exit(1);
#endif
}
So it’s writing out a C program to verify the library. That’s when I saw it.
exit(strncmp(ZLIB_VERSION, "1.2.5", 5) < 0);
ZLIB_VERSION is “1.2.11”. So they are comparing the first 5 characters. So that means “1.2.1” vs “1.2.5” and as you can see “1.2.1” is LESS THAN “1.2.5”. Well that would be a problem and never work. So I tried fixing it by changing it to use 6 characters. Well, “1.2.11” in lexicographic order is before “1.2.5”. So that breaks too.
I know there has to be a better way, but since this isn’t my code I just wanted to it to build. I changed it to:
exit(strncmp(ZLIB_VERSION, "1.2.05", 6) < 0);
Why in the world would they use strncmp to compare versions? Aren’t there much better ways to determine libraries installed on a RHEL system? I was astounded this ever made it out to the wild.
zeusville 