Build failure when using non-system zlib

[d-cameron]

When building on Linux version 2.6.32-358.el6.x86_64 (mockbuild@c6b8.bsys.dev.centos.org) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-3) (GCC) ), build fails due to attempt to link samtools against the system zlib version (1.2.3) when a different version is specified using all of CPATH LIBRARY_PATH CMAKE_LIBRARY_PATH CMAKE_INCLUDE_PATH.

cmake .. outputs

-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Looking for include files CMAKE_HAVE_PTHREAD_H
-- Looking for include files CMAKE_HAVE_PTHREAD_H - found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
No CMAKE_BUILD_TYPE specified, defaulting to release
-- Found ZLIB: /usr/local/bioinfsoftware/zlib/zlib_1.2.8/lib/libz.so (found version "1.2.8")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/users/allstaff/cameron.d/src/somatic-sniper/1.0.5.0/build

which shows that cmake is detecting the correct library version. But make deps outputs

[  3%] Creating directories for 'samtools-lib'
[  7%] Performing download step (verify and extract) for 'samtools-lib'
-- verifying file...
     file='/home/users/allstaff/cameron.d/src/somatic-sniper/1.0.5.0/vendor/samtools-0.1.6.tar.gz'
-- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
-- extracting...
     src='/home/users/allstaff/cameron.d/src/somatic-sniper/1.0.5.0/vendor/samtools-0.1.6.tar.gz'
     dst='/home/users/allstaff/cameron.d/src/somatic-sniper/1.0.5.0/build/vendor/samtools'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 10%] Performing patch step for 'samtools-lib'
patching file Makefile
[ 14%] No update step for 'samtools-lib'
[ 17%] Performing configure step for 'samtools-lib'
Building samtools, build log at /home/users/allstaff/cameron.d/src/somatic-sniper/1.0.5.0/build/vendor/samtools/build.log
[ 21%] Performing build step for 'samtools-lib'
make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Error 2
make[1]: *** [CMakeFiles/samtools-lib.dir/all] Error 2
make: *** [all] Error 2

Looking for details, cd vendor/samtools ; make results in

make[1]: Entering directory `/wehisan/home/allstaff/c/cameron.d/src/somatic-sniper/1.0.5.0/build/vendor/samtools'
gcc -g -Wall -O2  -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o -lm  -lcurses  -L. -lbam -lz
./libbam.a(bam_import.o): In function `__bam_get_lines':
/home/users/allstaff/cameron.d/src/somatic-sniper/1.0.5.0/build/vendor/samtools/bam_import.c:75: undefined reference to `gzopen64'
./libbam.a(bam_import.o): In function `sam_open':
/home/users/allstaff/cameron.d/src/somatic-sniper/1.0.5.0/build/vendor/samtools/bam_import.c:502: undefined reference to `gzopen64'
./libbam.a(bam_import.o): In function `sam_header_read2':
/home/users/allstaff/cameron.d/src/somatic-sniper/1.0.5.0/build/vendor/samtools/bam_import.c:125: undefined reference to `gzopen64'
collect2: ld returned 1 exit status
make[1]: *** [samtools] Error 1
make[1]: Leaving directory `/wehisan/home/allstaff/c/cameron.d/src/somatic-sniper/1.0.5.0/build/vendor/samtools'
make: *** [all-recur] Error 1

Indicating samtools is being linked against the system zlib, not the zlib detected by cmake.

Manually editing the samtools Makefile to explicitly add zlib via -L works for the samtools build, but results in a link error when building bam-somaticsniper.

Are you able to update your build process to respect the zlib library path detected by cmake?

[leiendeckerlu]

Is there a solution for this error? Just encountered the same error with no immediate solution...