#include <zlib.h> in libsrc/InputFile.h throwing compilation error & possible solution

[pjawinski]

Hi there,

for some reason, METAL didn't compile successfully on our linux cluster (although it did on another linux cluster and on my own mac), throwing the following error:

[ 80%] Building CXX object libsrc/CMakeFiles/goncalo.dir/StringArray.cpp.o                                                                                                                                                                                                                
[ 82%] Building CXX object libsrc/CMakeFiles/goncalo.dir/StringBasics.cpp.o                                                                                                                                                                                                               
[ 84%] Building CXX object libsrc/CMakeFiles/goncalo.dir/StringHash.cpp.o                                                                                                                                                                                                                 
[ 86%] Building CXX object libsrc/CMakeFiles/goncalo.dir/StringMap.cpp.o                                                                                                                                                                                                                  
[ 89%] Building CXX object libsrc/CMakeFiles/goncalo.dir/TraitTransformations.cpp.o                                                                                                                                                                                                       
[ 91%] Linking CXX static library libgoncalo.a                                                                                                                                                                                                                                            
make[2]: Leaving directory '/fast/software/METAL/build'                                                                                                                                                                                                                                   
[ 91%] Built target goncalo                                                                                                                                                                                                                                                               
make[2]: Entering directory '/fast/software/METAL/build'                                                                                                                                                                                                                                  
Scanning dependencies of target metal                                                                                                                                                                                                                                                     
make[2]: Leaving directory '/fast/software/METAL/build'                                                                                                                                                                                                                                   
make[2]: Entering directory '/fast/software/METAL/build'                                                                                                                                                                                                                                  
[ 93%] Building CXX object metal/CMakeFiles/metal.dir/Main.cpp.o                                                                                                                                                                                                                          
In file included from /fast/software/METAL/metal/Main.h:25,                                                                                                                                                                                                                               
                 from /fast/software/METAL/metal/Main.cpp:18:                                                                                                                                                                                                                             
/fast/software/METAL/libsrc/InputFile.h:31:10: fatal error: zlib.h: No such file or directory                                                                                                                                                                                             
   31 | #include <zlib.h>                                                                                                                                                                                                                                                                 
      |          ^~~~~~~~                                                                                                                                                                                                                                                                 
compilation terminated.                                                                                                                                                                                                                                                                   
make[2]: *** [metal/CMakeFiles/metal.dir/build.make:63: metal/CMakeFiles/metal.dir/Main.cpp.o] Error 1                                                                                                                                                                                    
make[2]: Leaving directory '/fast/software/METAL/build'                                                                                                                                                                                                                                   
make[1]: *** [CMakeFiles/Makefile2:146: metal/CMakeFiles/metal.dir/all] Error 2                                                                                                                                                                                                           
make[1]: Leaving directory '/fast/software/METAL/build'                                                                                                                                                                                                                                   
make: *** [Makefile:141: all] Error 2  

I've been using a conda environment, but received the same error without conda. In advance, cmake -DCMAKE_BUILD_TYPE=Release .. showed the correct ZLIB header directory and ZLIB library path (within the conda environment). Moreover, all build files written to ../build contained correct references to zlib.h in the activated conda environment. Still, #include <zlib.h> in libsrc/InputFile.h produced an error.

In my case, I solved this problem by manually changing #include <zlib.h> in line 31 of libsrc/InputFile.h to #include </path/to/my/conda/environment/include/zlib.h>. Hope this helps someone else who's experiencing the same issue. Maybe there's a more elegant solution or anything you can do to prevent this error.

Best wishes,
Philippe

[jonathonl]

Try adding include_directories(${ZLIB_INCLUDE_DIR}) to line 14 of CMakeLists.txt (https://github.com/statgen/METAL/blob/master/CMakeLists.txt#L14).

[pjawinski]

Many thanks, that also worked out!