compile error fresh install kyotocabinet

[FantasticMrFux]

Can't compile a fresh pulled progressiveCactus. After executing make it fails with the following execpetion:

make[2]: Entering directory '/home/fux/progressiveCactus/submodules/kyotocabinet' g++ -c -I. -I/home/fux/progressiveCactus/submodules/kyotocabinet/include -I/usr/local/include -DNDEBUG -D_GNU_SOURCE=1 -D_FILE_OFFSET_BITS=64 -D_REENTRANT -DEXTENSIONS -D_MYZLIB -D_MYGCCATOMIC -D_KC_PREFIX="\"/home/fux/progressiveCactus/submodules/kyotocabinet\"" -D_KC_INCLUDEDIR="\"/home/fux/progressiveCactus/submodules/kyotocabinet/include\"" -D_KC_LIBDIR="\"/home/fux/progressiveCactus/submodules/kyotocabinet/lib\"" -D_KC_BINDIR="\"/home/fux/progressiveCactus/submodules/kyotocabinet/bin\"" -D_KC_LIBEXECDIR="\"/home/fux/progressiveCactus/submodules/kyotocabinet/libexec\"" -D_KC_APPINC="\"-I/home/fux/progressiveCactus/submodules/kyotocabinet/include\"" -D_KC_APPLIBS="\"-L/home/fux/progressiveCactus/submodules/kyotocabinet/lib -lkyotocabinet -lz -lstdc++ -lrt -lpthread -lm -lc \"" -O3 -m64 -O3 -g -Wall -funroll-loops -DNDEBUG -I /home/fux/progressiveCactus/submodules/sonLib/lib -I /home/fux/progressiveCactus/submodules/tokyocabinet/include -DHAVE_TOKYO_CABINET=1 -I/home/fux/progressiveCactus/submodules/kyotocabinet/include -I/home/fux/progressiveCactus/submodules/kyototycoon/include -DHAVE_KYOTO_TYCOON=1 -I/home/fux/progressiveCactus/submodules/zlib/include -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter kcdbext.cc

In file included from kcdbext.cc:16:0:

kcdbext.h: In member function ‘char kyotocabinet::IndexDB::get(const char, size_t, size_t*)’:

kcdbext.h:1281:14: error: cannot convert ‘bool’ to ‘char*’ in return return false;

make[2]: *** [Makefile:76: kcdbext.o] Error 1

[jasonsydes]

Hi there, I'm getting exactly the same error.

I'm trying to build under easybuild's intel/2017a and foss/2017a if that provides any addition insight...

The error happens both under intel and gcc compilers.

Thank you!!

In file included from kcdbext.cc:16:0:
kcdbext.h: In member function ‘char* kyotocabinet::IndexDB::get(const char*, size_t, size_t*)’:
kcdbext.h:1281:14: error: cannot convert ‘bool’ to ‘char*’ in return
       return false;
              ^~~~~
make[2]: *** [kcdbext.o] Error 1
make[2]: Leaving directory `/gpfs/projects/ebb/dir_build/intel/eb.mod/progressiveCactus-2017-10-06-f102445-intel-2017a.eb/progressiveCactus-2017-10-06-f102445/submodules/kyotocabinet'
make[1]: *** [kyotocabinetRule] Error 2
make[1]: Leaving directory `/gpfs/projects/ebb/dir_build/intel/eb.mod/progressiveCactus-2017-10-06-f102445-intel-2017a.eb/progressiveCactus-2017-10-06-f102445/submodules'
make: *** [all] Error 2

[robsyme]

I ran into the same troubles. It looks to be because of gcc versions (6/7) being less lenient about these type conversions.

Workaround in a comment here: https://github.com/glennhickey/progressiveCactus/issues/76#issuecomment-334714835

Note that once the fix is applied to kcdbext.h, you'll probably run into the same trouble with ktremotedb.h and ktulog.h in kyototycoon. I've got a couple of patches here: https://github.com/robsyme/nf-annotate/tree/master/patches

[FantasticMrFux]

Thanks Robert for your help. With the patches the first errors disappeared and the compilation went one but in the end new errors occurred, which are related with the patches:

In file included from impl/sonLibKVDatabase_KyotoTycoon.cpp:34:0:
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktremotedb.h: In member function ‘char* kyototycoon::RemoteDB::Cursor::get_key(size_t*, bool)’:
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktremotedb.h:301:16: error: ‘nullptr’ was not declared in this scope
         return nullptr;
                ^~~~~~~
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktremotedb.h: In member function ‘char* kyototycoon::RemoteDB::Cursor::get_value(size_t*, bool)’:
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktremotedb.h:353:16: error: ‘nullptr’ was not declared in this scope
         return nullptr;
                ^~~~~~~
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktremotedb.h: In member function ‘char* kyototycoon::RemoteDB::Cursor::get(size_t*, const char**, size_t*, int64_t*, bool)’:
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktremotedb.h:414:16: error: ‘nullptr’ was not declared in this scope
         return nullptr;
                ^~~~~~~
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktremotedb.h: In member function ‘char* kyototycoon::RemoteDB::Cursor::seize(size_t*, const char**, size_t*, int64_t*)’:
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktremotedb.h:484:16: error: ‘nullptr’ was not declared in this scope
         return nullptr;

/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktulog.h: In member function ‘virtual void kyototycoon::UpdateLogger::AutoFlusher::run()’:
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktulog.h:514:27: error: ‘FLUSHWAIT’ was not declared in this scope
         kc::Thread::sleep(FLUSHWAIT);
                           ^~~~~~~~~

In file included from /scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktcommon.h:24:0,
                 from /scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktremotedb.h:19,
                 from impl/sonLibKVDatabase_KyotoTycoon.cpp:34:
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyotocabinet/include/kcdbext.h: In member function ‘char* kyotocabinet::IndexDB::get(const char*, size_t, size_t*)’:
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyotocabinet/include/kcdbext.h:1281:14: error: ‘nullptr’ was not declared in this scope
       return nullptr;
              ^~~~~~~
In file included from /scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktremotedb.h:25:0,
                 from impl/sonLibKVDatabase_KyotoTycoon.cpp:34:
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktulog.h: At global scope:
/scratch/fux/programms/genome_alligner/progressiveCactus/submodules/kyototycoon/include/ktulog.h:51:10: error: ‘constexpr’ does not name a type; did you mean ‘confstr’?
   static constexpr double FLUSHWAIT = 0.1;
          ^~~~~~~~~
          confstr

Here my compiler version:

Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/7/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-redhat-linux
Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,objc,obj-c++,fortran,ada,go,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl --enable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 7.3.1 20180130 (Red Hat 7.3.1-2) (GCC) 

[antoncom]

Hi! I have successfully made: configure / make / make check / make install both Kyoto Cabinet & Kyoto Tycoon by using this fork: https://github.com/carlosefr/kyoto

This way was suggested in "Still mantained" issue: https://github.com/alticelabs/kyoto/issues/31

Sincerely..

[diekhans]

Thanks for the info, I will update, note that progressive cactus is now part of cactus and the official repository is at:

https://github.com/ComparativeGenomicsToolkit/cactus

Anton Gavrilyuk notifications@github.com writes:

Hi! I have successfully made: configure / make / make check / make install both Kyoto Cabinet & Kyoto Tycoon by using this fork: https://github.com/carlosefr/kyoto

This way was suggested in "Still mantained" issue: https://github.com/alticelabs/kyoto/issues/31

Sincerely..

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/glennhickey/progressiveCactus/issues/95#issuecomment-583527084 Hi! I have successfully made: configure / make / make check / make install both Kyoto Cabinet & Kyoto Tycoon by using this fork: https://github.com/carlosefr/kyoto

This way was suggested in "Still mantained" issue: alticelabs/kyoto#31

Sincerely..

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.*

[glennhickey]

Perhaps we want to change the Cactus readme to refer to this version of Kyoto for source builds. I was just having problems building the alticelabs one the other day with a modern gcc.

[diekhans]

Already done in the py3 branch.

Glenn Hickey notifications@github.com writes:

Perhaps we want to change the Cactus readme to refer to this version of Kyoto for source builds. I was just having problems building the alticelabs one the other day with a modern gcc.

-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/glennhickey/progressiveCactus/issues/95#issuecomment-583557607 Perhaps we want to change the Cactus readme to refer to this version of Kyoto for source builds. I was just having problems building the alticelabs one the other day with a modern gcc.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.*