Comments (7)
Hi, thanks again for this amazing software. I also ran into this problem and I believe it is because you defined an inline function in a .cpp file, which I think is not supposed to be done this way. See here:
https://stackoverflow.com/questions/5057021/why-are-c-inline-functions-in-the-header
For me, simply removing the "inline" keyword from the definition of the function "comp_nt_int" fixed this issue, and I was able to compile Igor without having to downgrade my compiler. (This was on a Linux system.)
I think the compiler can decide for itself whether or not to inline this function, so it's not too bad to remove this keyword. Another solution would be to move the definition of this function too Aligner.h, and then include that in Deletion.h
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I tried gcc-7 (Homebrew GCC 7.5.0_1) 7.5.0
, it also works.
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I got the same error with gcc-11
would be great to update the code for modern compilers
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Hi @zacmontague ,
Thank your for submitting a bug report. It's the second time this error is reported and I was not able to diagnose the exact reason the first time. Last time the user also had a Mac (although more recent) and GCC 8.1. I had asked whether downgrading to a more ancient version of, e.g GCC 7.3 (the one I'm personally using) solved the problem and did not hear back from the problem. Could you try downgrading your GCC see if this solves your problem?
Also: does your make.log file also contain the error stream? If not could you create a log file containing both the stdout and error stream using:
make >>make.log 2>&1
Thanks!
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Hi,
I attached two logs, one using GCC 8.1 and one using GCC 7.3, using the command you instructed me to use. I think the make
and make install
have been successful now by using GCC 7.3. Executing make check
gives an error, however:
Making check in cdf
/Library/Developer/CommandLineTools/usr/bin/make test
gcc-7 -DHAVE_CONFIG_H -I. -I.. -I.. -g -O2 -MT test.o -MD -MP -MF .deps/test.Tpo -c -o test.o test.c
mv -f .deps/test.Tpo .deps/test.Po
make[4]: *** No rule to make target
../randist/libgslrandist.la', needed by test'. Stop.
make[3]: *** [check-am] Error 2
make[2]: *** [check-recursive] Error 1
make[1]: *** [check-recursive] Error 1
make: *** [check-recursive] Error 1
Navigating to igor_src and doing igor -help
returns the manual and igor run_demo
executes fine. So I'm guessing that, despite the make check
error, things will work.
Therefore, I suppose it's the new GCC that causes whatever not to be linked correctly.
Thanks,
Zach
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Great to hear that changing your compiler did "solve" your problem!
I had a quick look at the new logs, I'm still not sure why this compilation fails with GCC 8, i'll try and look into it, I'll leave this issue open meanwhile.
Thanks!
Quentin
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I got the same error and was able to fix it with @jtextor suggestion. Thank you!
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Related Issues (20)
- File not found when IGoR is installed locally HOT 1
- Errors: python to parse the output results? HOT 2
- Model edge gene choice relations differ HOT 1
- Chain IGoR commands HOT 1
- Missing unknown subargument error for -output HOT 1
- Using the --coverage output subarg HOT 1
- using the --coverage error
- make new database HOT 2
- make check failures but make install worked HOT 1
- Segmentation Fault in -run_demo HOT 5
- Limiting IGoR's CPU usage HOT 1
- Install error HOT 2
- How to get everyone sequence clonotype ?
- the result file foo_indexed_CDR3s.csv HOT 1
- segfault with gcc > 7 HOT 2
- IGoR over-estimating TCR V deletions?
- installation from source
- All 0 output in infer and question about L_thresh
- Remove superfluous IMGT information in TCR beta model parms file
- Undefined reference error during compling
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