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build fails on ubuntu #14

Open splaisan opened 5 years ago

splaisan commented 5 years ago

Something wrong with bamtools! not expert enough to make sense of this, can you please help! Thanks

using code cloned fresh from current github version and instruction as in the MD

-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Check for working C compiler: /opt/biotools/miniconda2/envs/atwork3/bin/x86_64-conda_cos6-linux-gnu-cc
-- Check for working C compiler: /opt/biotools/miniconda2/envs/atwork3/bin/x86_64-conda_cos6-linux-gnu-cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /opt/biotools/miniconda2/envs/atwork3/bin/x86_64-conda_cos6-linux-gnu-c++
-- Check for working CXX compiler: /opt/biotools/miniconda2/envs/atwork3/bin/x86_64-conda_cos6-linux-gnu-c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /opt/biotools/TIDDIT/build
(atwork3) u0002316@gbw-s-pacbio01:/opt/biotools/TIDDIT/build$ make
Scanning dependencies of target BamTools
[  1%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o
[  2%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o
[  3%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o
[  4%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o
[  6%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o
[  7%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o
[  8%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o
[  9%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o
[ 10%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o
[ 12%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o
[ 13%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o
[ 14%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o
[ 15%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o
[ 16%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o
[ 18%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o
[ 19%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o
[ 20%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o
[ 21%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o
[ 22%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o
[ 24%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 25%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o
[ 26%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o
[ 27%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o
[ 28%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o
[ 30%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o
/opt/biotools/TIDDIT/lib/bamtools/src/api/internal/io/BgzfStream_p.cpp:20:10: fatal error: zlib.h: No such file or directory
 #include "zlib.h"
          ^~~~~~~~
compilation terminated.
lib/bamtools/src/api/CMakeFiles/BamTools.dir/build.make:638: recipe for target 'lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o' failed
make[2]: *** [lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o] Error 1
CMakeFiles/Makefile2:148: recipe for target 'lib/bamtools/src/api/CMakeFiles/BamTools.dir/all' failed
make[1]: *** [lib/bamtools/src/api/CMakeFiles/BamTools.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2

I then tried using the build 0.9

which fails because of the boost version 1.58.0 could it be that I need a higher boost to build? Ubuntu stops at 1.58.0 and I do not dare to build boost from source at higher versions (should I? and which version? 1.7?)

$ sudo apt install libboost-dev
[sudo] password for u0002316: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
libboost-dev is already the newest version (1.58.0.1ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

$ sudo apt install libboost-all-dev
Reading package lists... Done
Building dependency tree       
Reading state information... Done
libboost-all-dev is already the newest version (1.58.0.1ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Check for working C compiler: /opt/biotools/miniconda2/envs/atwork3/bin/x86_64-conda_cos6-linux-gnu-cc
-- Check for working C compiler: /opt/biotools/miniconda2/envs/atwork3/bin/x86_64-conda_cos6-linux-gnu-cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /opt/biotools/miniconda2/envs/atwork3/bin/x86_64-conda_cos6-linux-gnu-c++
-- Check for working CXX compiler: /opt/biotools/miniconda2/envs/atwork3/bin/x86_64-conda_cos6-linux-gnu-c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Error at /usr/share/cmake-3.5/Modules/FindBoost.cmake:1677 (message):
  Unable to find the requested Boost libraries.

  Boost version: 1.58.0

  Boost include path: /usr/include

  Could not find the following Boost libraries:

          boost_program_options
          boost_system
          boost_filesystem

  No Boost libraries were found.  You may need to set BOOST_LIBRARYDIR to the
  directory containing Boost libraries or BOOST_ROOT to the location of
  Boost.
Call Stack (most recent call first):
  CMakeLists.txt:10 (find_package)
splaisan commented 5 years ago

Apparently worked after replacing the bamtools src and CMakeLists.txt (edited at its end as shown below) by those from the bamtools latest release (https://github.com/pezmaster31/bamtools/releases/tag/v2.5.1)

# -------------------------------------------

# add our includes root path
include_directories( src )

# list subdirectories to build in
add_subdirectory( src )

changed to (no other changes)

# -------------------------------------------

# add our includes root path
include_directories( bamtools/src )

# list subdirectories to build in
add_subdirectory( bamtools/src/api )