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ruanjue / smartdenovo

Ultra-fast de novo assembler using long noisy reads
GNU General Public License v3.0
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smartdenovo make error #18

Closed liguiyang410 closed 6 years ago

liguiyang410 commented 6 years ago

when make in fold smartdenovo, errors were showed as follows: /tmp/ccTfg5aF.o: In function merge_bubbles_strgraph': wtlay.c:(.text+0x984d): undefined reference tocut_biedge_strgraph2' wtlay.c:(.text+0x9861): undefined reference to cut_biedge_strgraph2' wtlay.c:(.text+0x992d): undefined reference tocut_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

ruanjue commented 6 years ago

Please tell me your gcc version. Try to modify https://github.com/ruanjue/smartdenovo/blob/5cc1356bffb87197b0fb9b835cfe1adc5a764dc6/Makefile#L48 into $(CC) $(CFLAGS) -o wtlay file_reader.c wtlay.c wtlay.h $(GLIBS), then make wtlay again.

liguiyang410 commented 6 years ago

GCC 4.8 . I modified the line 48, but still the same errors.

ruanjue commented 6 years ago

Let me think that your compiler is not C but C++. Then try to remove https://github.com/ruanjue/smartdenovo/blob/5cc1356bffb87197b0fb9b835cfe1adc5a764dc6/wtlay.h#L95-L97 https://github.com/ruanjue/smartdenovo/blob/5cc1356bffb87197b0fb9b835cfe1adc5a764dc6/wtlay.h#L832-L834 and compile wtlay again.

ruanjue commented 6 years ago

If there is still error, also try to remove the modifier inline in https://github.com/ruanjue/smartdenovo/blob/5cc1356bffb87197b0fb9b835cfe1adc5a764dc6/wtlay.h#L491-L518

emaleckova commented 4 years ago

I also had trouble installing SMARTdenovo, similar to those described here as well as in issue #22. Since it took me several tries to install successfully, I would like to share what helped in my case:

  1. Changes in the Makefile as mentioned here
  2. Removing lines 95 to 97 and 832 to 834 in wtlay.h as mentioned here
  3. Add static before all five occurrences of inline (lines 491 to 518) in wtlay.h

For completeness, I work on Ubuntu 19.04 and run gcc 8.3.0.

ruanjue commented 4 years ago

Thanks!

miltongr21 commented 2 years ago

@emaleckova

This solved the problem for me! Thanks bro!

cfz1998 commented 1 year ago

I also had trouble installing SMARTdenovo, similar to those described here as well as in issue #22. Since it took me several tries to install successfully, I would like to share what helped in my case:

  1. Changes in the Makefile as mentioned here
  2. Removing lines 95 to 97 and 832 to 834 in wtlay.h as mentioned here
  3. Add static before all five occurrences of inline (lines 491 to 518) in wtlay.h

For completeness, I work on Ubuntu 19.04 and run gcc 8.3.0.

Thanks！