installation error

[madhubioinfo]

Hi, I am trying to install smartdenovo for my analysis but it failed with error when i do the make command

This the error i am getting, help me in fixing this

collect2: error: ld returned 1 exit status Makefile:48: recipe for target 'wtlay' failed make: *** [wtlay] Error 1

[ruanjue]

Please give me more backward lines.

[fabiodepa]

Hi @ruanjue I had a similar error while compiling from the github repository.

me@mypc:~/applications$ git clone https://github.com/ruanjue/smartdenovo.git
me@mypc:~/applications$ cd smartdenovo
me@mypc:~/applications/smartdenovo$ make
gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o pairaln file_reader.c ksw.c pairaln.c -lm -lpthread
gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtpre file_reader.c wtpre.c -lm -lpthread
gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtcyc file_reader.c ksw.c wtcyc.c -lm -lpthread
gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtmer file_reader.c wtmer.c -lm -lpthread
gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtzmo file_reader.c ksw.c wtzmo.c -lm -lpthread
gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtobt file_reader.c wtobt.c -lm -lpthread
gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtclp file_reader.c wtclp.c -lm -lpthread
gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtext file_reader.c ksw.c wtext.c -lm -lpthread
gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtgbo file_reader.c ksw.c wtgbo.c -lm -lpthread
gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtlay file_reader.c wtlay.c -lm -lpthread
/tmp/ccFAXTvE.o: In function `merge_bubbles_strgraph':
wtlay.c:(.text+0x984d): undefined reference to `cut_biedge_strgraph2'
wtlay.c:(.text+0x9861): undefined reference to `cut_biedge_strgraph2'
wtlay.c:(.text+0x992d): undefined reference to `cut_biedge_strgraph2'
wtlay.c:(.text+0x994a): undefined reference to `cut_biedge_strgraph2'
collect2: error: ld returned 1 exit status
Makefile:48: recipe for target 'wtlay' failed
make: *** [wtlay] Error 1

Thank you for any help,

Fabio

[fabiodepa]

Update: I tried with the suggestions @ruanjue gave in the issue #18 and now the make get to the end without any error.

Hope it could help, Fabio

[jhernandez1409]

Hi, I am getting the same error. I tried fixing it with comments in Issue #18 but still getting the same error. Please advise.

Thanks,

JoJo

[fabiodepa]

Hi JoJo,

Just trying to help... Did you made all the changes suggested in the five posts by @ruanjue in #18 ? For me, those worked...

Fabio

[jhernandez1409]

Hi Fabio,

Thank you for your reply... yes, I did all the suggested changes in issue #18 but I still get the same error. I tried it multiple times to make sure I was doing it right but still the same error.

JoJo

[jhernandez1409]

Hi! I actually add ´static´ in front of ´inline...´ in line 516 of the wtlay.h file and compiled wtlay again and it worked, just as @ruanjue suggested in issue #22. Hope this helps.

Thanks,

JoJo