kmergenie Installation failed. seems got a bug

Question

[xiachongjing]

Hi there:

I was trying to install Kmergenie-1.7038. I type these first:

module load python/2.6.6

module load R/3.2.2

module load autoconf/2.68

module load zlib/1.2.5_gcc

I got this error after typing "make" in kmergenie-1.7016/ directory:

cd ntCard && ./autogen.sh && ./configure && make

+ aclocal

+ autoconf

+ autoheader

+ automake -a

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for gawk... gawk

checking whether make sets $(MAKE)... yes

checking for gawk... (cached) gawk

checking for gcc... /home/modules/apps/compilers/gcc/4.8.3/bin/gcc

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 /home/modules/apps/compilers/gcc/4.8.3/bin/gcc accepts -g... yes

checking for /home/modules/apps/compilers/gcc/4.8.3/bin/gcc option to accept ISO C89... none needed

checking for style of include used by make... GNU

checking dependency style of /home/modules/apps/compilers/gcc/4.8.3/bin/gcc... gcc3

checking how to run the C preprocessor... /home/modules/apps/compilers/gcc/4.8.3/bin/cpp

checking whether we are using the GNU C++ compiler... yes

checking whether /home/modules/apps/compilers/gcc/4.8.3/bin/g++ accepts -g... yes

checking dependency style of /home/modules/apps/compilers/gcc/4.8.3/bin/g++... gcc3

checking for ranlib... ranlib

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 dlfcn.h usability... yes

checking dlfcn.h presence... yes

checking for dlfcn.h... yes

checking fcntl.h usability... yes

checking fcntl.h presence... yes

checking for fcntl.h... yes

checking float.h usability... yes

checking float.h presence... yes

checking for float.h... yes

checking limits.h usability... yes

checking limits.h presence... yes

checking for limits.h... yes

checking stddef.h usability... yes

checking stddef.h presence... yes

checking for stddef.h... yes

checking for stdint.h... (cached) yes

checking for stdlib.h... (cached) yes

checking sys/param.h usability... yes

checking sys/param.h presence... yes

checking for sys/param.h... yes

checking zlib.h usability... yes

checking zlib.h presence... yes

checking for zlib.h... yes

checking for stdbool.h that conforms to C99... yes

checking for _Bool... yes

checking for ANSI C header files... (cached) yes

checking for dup2... yes

checking for gethostname... yes

checking for getopt_long... yes

checking for getpagesize... yes

checking for memset... yes

checking for strdup... yes

checking for strerror... yes

checking for strtoul... yes

checking for pid_t... yes

checking vfork.h usability... no

checking vfork.h presence... no

checking for vfork.h... no

checking for fork... yes

checking for vfork... yes

checking for working fork... yes

checking for working vfork... (cached) yes

checking for stdlib.h... (cached) yes

checking for GNU libc compatible malloc... yes

checking for working memcmp... yes

checking for stdlib.h... (cached) yes

checking for GNU libc compatible realloc... yes

checking for vprintf... yes

checking for _doprnt... no

checking whether byte ordering is bigendian... no

checking for an ANSI C-conforming const... yes

checking for inline... inline

checking for ptrdiff_t... yes

checking for mode_t... yes

checking for pid_t... (cached) yes

checking for size_t... yes

checking for ssize_t... yes

checking for int64_t... yes

checking for uint8_t... yes

checking for uint16_t... yes

checking for uint32_t... yes

checking for uint64_t... yes

checking for sqrt in -lm... yes

checking for pow... yes

checking for sqrt... yes

checking for ceilf... yes

checking for dlsym in -ldl... yes

checking for gzwrite in -lz... yes

checking for /home/modules/apps/compilers/gcc/4.8.3/bin/g++ option to support OpenMP... -fopenmp

configure: creating ./config.status

config.status: creating Makefile

config.status: creating config.h

config.status: config.h is unchanged

config.status: executing depfiles commands

make[1]: Entering directory `/home/plant_pathology/cho.xia/software/kmergenie-1.7038/ntCard'

make  all-am

make[2]: Entering directory `/home/plant_pathology/cho.xia/software/kmergenie-1.7038/ntCard'

if /home/modules/apps/compilers/gcc/4.8.3/bin/g++ -DHAVE_CONFIG_H -I. -I. -I.  -I./Common -I/home/plant_pathology/cho.xia/software/kmergenie-1.7038/ntCard -fopenmp -I/home/modules/apps/compilers/gcc/4.8.3/include -L/home/modules/apps/compilers/gcc/4.8.3/lib -Wall -Wextra -Werror -I/home/modules/apps/compilers/gcc/4.8.3/include -L/home/modules/apps/compilers/gcc/4.8.3/lib -pthread  -D_largeint -DKMER_PRECISION=4 -MT Common/nthll-Uncompress.o -MD -MP -MF "Common/.deps/nthll-Uncompress.Tpo" -c -o Common/nthll-Uncompress.o `test -f 'Common/Uncompress.cpp' || echo './'`Common/Uncompress.cpp; \

        then mv -f "Common/.deps/nthll-Uncompress.Tpo" "Common/.deps/nthll-Uncompress.Po"; else rm -f "Common/.deps/nthll-Uncompress.Tpo"; exit 1; fi
if /home/modules/apps/compilers/gcc/4.8.3/bin/g++ -DHAVE_CONFIG_H -I. -I. -I.  -I./Common -I/home/plant_pathology/cho.xia/software/kmergenie-1.7038/ntCard -fopenmp -I/home/modules/apps/compilers/gcc/4.8.3/include -L/home/modules/apps/compilers/gcc/4.8.3/lib -Wall -Wextra -Werror -I/home/modules/apps/compilers/gcc/4.8.3/include -L/home/modules/apps/compilers/gcc/4.8.3/lib -pthread  -D_largeint -DKMER_PRECISION=4 -MT Common/nthll-SignalHandler.o -MD -MP -MF "Common/.deps/nthll-SignalHandler.Tpo" -c -o Common/nthll-SignalHandler.o `test -f 'Common/SignalHandler.cpp' || echo './'`Common/SignalHandler.cpp; \

        then mv -f "Common/.deps/nthll-SignalHandler.Tpo" "Common/.deps/nthll-SignalHandler.Po"; else rm -f "Common/.deps/nthll-SignalHandler.Tpo"; exit 1; fi
if /home/modules/apps/compilers/gcc/4.8.3/bin/g++ -DHAVE_CONFIG_H -I. -I. -I.  -I./Common -I/home/plant_pathology/cho.xia/software/kmergenie-1.7038/ntCard -fopenmp -I/home/modules/apps/compilers/gcc/4.8.3/include -L/home/modules/apps/compilers/gcc/4.8.3/lib -Wall -Wextra -Werror -I/home/modules/apps/compilers/gcc/4.8.3/include -L/home/modules/apps/compilers/gcc/4.8.3/lib -pthread  -D_largeint -DKMER_PRECISION=4 -MT Common/nthll-Fcontrol.o -MD -MP -MF "Common/.deps/nthll-Fcontrol.Tpo" -c -o Common/nthll-Fcontrol.o `test -f 'Common/Fcontrol.cpp' || echo './'`Common/Fcontrol.cpp; \

        then mv -f "Common/.deps/nthll-Fcontrol.Tpo" "Common/.deps/nthll-Fcontrol.Po"; else rm -f "Common/.deps/nthll-Fcontrol.Tpo"; exit 1; fi
/home/modules/apps/compilers/gcc/4.8.3/bin/g++ -Wall -Wextra -Werror -I/home/modules/apps/compilers/gcc/4.8.3/include -L/home/modules/apps/compilers/gcc/4.8.3/lib -pthread  -D_largeint -DKMER_PRECISION=4  -fopenmp  -o nthll  Common/nthll-Uncompress.o Common/nthll-SignalHandler.o Common/nthll-Fcontrol.o nthll-nthll.o  -lz -ldl -lm 
/usr/bin/ld: BFD 2.17.50.0.6-12.el5 20061020 internal error, aborting at ../../bfd/reloc.c line 5054 in bfd_generic_get_relocated_section_contents

/usr/bin/ld: ***Please report this bug.***

collect2: error: ld returned 1 exit status

make[2]: *** [nthll] Error 1

make[2]: Leaving directory `/home/plant_pathology/cho.xia/software/kmergenie-1.7038/ntCard'

make[1]: *** [all] Error 2

make[1]: Leaving directory `/home/plant_pathology/cho.xia/software/kmergenie-1.7038/ntCard'

make: *** [ntcard] Error 2

[WouterDeCoster]

I think 'kmergenie' would be a logical tag for this post, I added this. If you need support of the authors, best to use tags.

[h.mon]

Although the error is different, you could try the suggestion from this post.

Answer 1

[hmohamadi]

Just remove ntcard-ntcard.o and nthll-nthll.o from ntCard folder and then ./autogen.sh && ./configure && make.

You can also get the latest version of ntCard from https://github.com/bcgsc/ntCard.git and replace it with current ntCard folder in KmerGenie.

Answer 2

[Rayan Chikhi]

hi, I've updated kmergenie to version 1.7039, hopefully resolving this compilation issue. Please let me know if it still persists.

Thanks for the help Hamid. Any chance ntCard could get rid of automake/autoconf by the way?