On 22 Feb 2016, at 08:34, William Hsiao <[email protected]> wrote:
> Thanks for your help. Below is the output you requested. Btw, I was able to
> get Samtools to compile by issuing "sudo make LDFLAGS="-L/usr/local/lib”,
> where a newer version of zlib (libz.so.1.2.8) is available. Could it be that
> the version that came with RHEL 6.2 just doesn't have the gzopen64 defined?
[...]
> I still have trouble getting pysam to recognize the new version of libz and
> as a result, I still get a gzopen64 error when pysam is invoked. If you have
> any suggestion for this problem
> (https://github.com/pysam-developers/pysam/issues/235), I would greatly
> appreciate it as well.
[...]
> sudo gcc -H -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I.
> -Ihtslib-1.3 -c -o bedidx.o bedidx.c
[...]
> . /usr/local/include/zlib.h
The problem is that you were mixing the headers (/usr/local/include/zlib.h)
from the newer zlib with the library (/usr/lib64/libz.so) from the older
RHEL-package zlib. And so you were pulling in functions that the old library
(of course) didn't supply.
As you have found, you can work around this by adding LDFLAGS=-L/usr/local/lib
to bump the newer library up the path so that you are linking with the
/usr/local/lib/libz.so corresponding to the headers you are using. To work
around your pysam runtime problem, it may help to also add
-Wl,-rpath,/usr/local/lib so the right zlib library is found at runtime.
The real underlying problem here is that your machine has two copies of
development zlib files on it. Due to vagaries of compiler paths, the headers
from /usr/local are found first by the compiler but the libraries from /usr are
found first by the linker. This matters when you have incompatible copies of
headers/libraries for the same library in the two locations. This is something
that your local system administrators are in a position to fix: ideally there
should only be one copy of the zlib development files in the system paths, and
the current situation is a bug on your local machine that they should fix.
John
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