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ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.
http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html
GNU General Public License v3.0
49 stars 25 forks source link

Error 2 during compilation #306

Open stanedav opened 4 years ago

stanedav commented 4 years ago

Hello I have problem during compilation (in develop branch):

my commands were:

cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_EXTERNAL_PROJECTS=1 ..
-- Compiling with build type 'Release'.
-- DeNovoGear version: 1.1.1-unknown.
-- Building HTSLIB 1.3.1 as external dependency
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dnalab/bioinformatics/denovogear-develop/build

make -j4
Scanning dependencies of target ext_htslib
[  2%] Creating directories for 'ext_htslib'
[  5%] Performing download step (download, verify and extract) for 'ext_htslib'
-- Downloading...
   dst='/home/dnalab/bioinformatics/denovogear-develop/build/ext_deps/htslib/src/htslib-1.3.1.tar.bz2'
   timeout='none'
-- Using src='http://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2'
-- [download 29% complete]
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-- verifying file...
       file='/home/dnalab/bioinformatics/denovogear-develop/build/ext_deps/htslib/src/htslib-1.3.1.tar.bz2'
-- Downloading... done
-- extracting...
     src='/home/dnalab/bioinformatics/denovogear-develop/build/ext_deps/htslib/src/htslib-1.3.1.tar.bz2'
     dst='/home/dnalab/bioinformatics/denovogear-develop/build/ext_deps/htslib/src/ext_htslib'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 10%] No update step for 'ext_htslib'
[ 10%] No patch step for 'ext_htslib'
[ 13%] Performing configure step for 'ext_htslib'
checking for gcc... /usr/bin/cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/cc accepts -g... yes
checking for /usr/bin/cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking how to run the C preprocessor... /usr/bin/cc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
[ 15%] Performing build step for 'ext_htslib'
make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
[ 18%] Performing install step for 'ext_htslib'
make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
[ 21%] Completed 'ext_htslib'
[ 21%] Built target ext_htslib
Scanning dependencies of target libdng
[ 23%] Building CXX object src/lib/CMakeFiles/libdng.dir/bam.cc.o
[ 28%] Building CXX object src/lib/CMakeFiles/libdng.dir/genotyper.cc.o
[ 28%] Building CXX object src/lib/CMakeFiles/libdng.dir/call_mutations.cc.o
[ 31%] Building CXX object src/lib/CMakeFiles/libdng.dir/probability.cc.o
[ 34%] Building CXX object src/lib/CMakeFiles/libdng.dir/pedigree.cc.o
[ 36%] Building CXX object src/lib/CMakeFiles/libdng.dir/mutation.cc.o
[ 39%] Building CXX object src/lib/CMakeFiles/libdng.dir/newick.cc.o
[ 42%] Building CXX object src/lib/CMakeFiles/libdng.dir/peeling.cc.o
[ 44%] Building CXX object src/lib/CMakeFiles/libdng.dir/regions.cc.o
[ 47%] Building CXX object src/lib/CMakeFiles/libdng.dir/relationship_graph.cc.o
[ 50%] Building CXX object src/lib/CMakeFiles/libdng.dir/stats.cc.o
[ 52%] Building CXX object src/lib/CMakeFiles/libdng.dir/utility.cc.o
[ 55%] Building CXX object src/lib/CMakeFiles/libdng.dir/task/call.cc.o
[ 57%] Building CXX object src/lib/CMakeFiles/libdng.dir/task/loglike.cc.o
[ 60%] Linking CXX static library libdng.a
[ 60%] Built target libdng
src/CMakeFiles/dng-phaser.dir/build.make:85: *** target pattern contains no '%'.  Stop.
src/CMakeFiles/dng-dnm.dir/build.make:190: *** target pattern contains no '%'.  Stop.
CMakeFiles/Makefile2:305: recipe for target 'src/CMakeFiles/dng-phaser.dir/all' failed
make[1]: *** [src/CMakeFiles/dng-phaser.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
CMakeFiles/Makefile2:333: recipe for target 'src/CMakeFiles/dng-dnm.dir/all' failed
make[1]: *** [src/CMakeFiles/dng-dnm.dir/all] Error 2
src/CMakeFiles/dng-call.dir/build.make:85: *** target pattern contains no '%'.  Stop.
CMakeFiles/Makefile2:361: recipe for target 'src/CMakeFiles/dng-call.dir/all' failed
make[1]: *** [src/CMakeFiles/dng-call.dir/all] Error 2
src/CMakeFiles/dng-loglike.dir/build.make:85: *** target pattern contains no '%'.  Stop.
CMakeFiles/Makefile2:389: recipe for target 'src/CMakeFiles/dng-loglike.dir/all' failed
make[1]: *** [src/CMakeFiles/dng-loglike.dir/all] Error 2
Makefile:162: recipe for target 'all' failed
make: *** [all] Error 2
`

Could you help me to compile it properly?

Here is CMakeError.log

Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:
Change Dir: /home/dnalab/bioinformatics/denovogear-develop/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_66480/fast && /usr/bin/make -f CMakeFiles/cmTC_66480.dir/build.make CMakeFiles/cmTC_66480.dir/build
make[1]: Entering directory '/home/dnalab/bioinformatics/denovogear-develop/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_66480.dir/src.c.o
/usr/bin/cc   -DCMAKE_HAVE_LIBC_PTHREAD   -o CMakeFiles/cmTC_66480.dir/src.c.o   -c /home/dnalab/bioinformatics/denovogear-develop/build/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTC_66480
/snap/cmake/252/bin/cmake -E cmake_link_script CMakeFiles/cmTC_66480.dir/link.txt --verbose=1
/usr/bin/cc  -DCMAKE_HAVE_LIBC_PTHREAD    -rdynamic CMakeFiles/cmTC_66480.dir/src.c.o  -o cmTC_66480 
CMakeFiles/cmTC_66480.dir/src.c.o: In function `main':
src.c:(.text+0x3e): undefined reference to `pthread_create'
src.c:(.text+0x4a): undefined reference to `pthread_detach'
src.c:(.text+0x5b): undefined reference to `pthread_join'
src.c:(.text+0x6f): undefined reference to `pthread_atfork'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_66480.dir/build.make:86: recipe for target 'cmTC_66480' failed
make[1]: *** [cmTC_66480] Error 1
make[1]: Leaving directory '/home/dnalab/bioinformatics/denovogear-develop/build/CMakeFiles/CMakeTmp'
Makefile:121: recipe for target 'cmTC_66480/fast' failed
make: *** [cmTC_66480/fast] Error 2

Source file was:
#include <pthread.h>

void* test_func(void* data)
{
  return data;
}

int main(void)
{
  pthread_t thread;
  pthread_create(&thread, NULL, test_func, NULL);
  pthread_detach(thread);
  pthread_join(thread, NULL);
  pthread_atfork(NULL, NULL, NULL);
  pthread_exit(NULL);

  return 0;
}
reedacartwright commented 4 years ago

Can you test the latest version of develop? There were issues with dependencies not being resolved by CMake. See #310.