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soedinglab / CCMpred

Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.
http://www.ncbi.nlm.nih.gov/pubmed/25064567
GNU Affero General Public License v3.0
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Errors when using make #37

Open ken0414 opened 1 year ago

ken0414 commented 1 year ago

CMake version is 3.22.1 GNU Make version is 4.3 CMake is running without using CUDA

Errors occured when using command 'make'

kenmarnuls@LAPTOP-Q547HOJF:~/CCMpred$ make [ 7%] Building C object lib/libconjugrad/CMakeFiles/conjugrad.dir/src/conjugrad.c.o In file included from /home/kenmarnuls/CCMpred/lib/libconjugrad/src/conjugrad.c:4: /home/kenmarnuls/CCMpred/lib/libconjugrad/include/conjugrad.h:21:15: error: conflicting types for ‘sqrtf’; have ‘float(double)’ 21 | #define fsqrt sqrtf | ^~~~~ In file included from /home/kenmarnuls/CCMpred/lib/libconjugrad/src/conjugrad.c:4: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:143:1: note: previous declaration of ‘sqrtf’ with type ‘float(float)’ 143 | MATHCALL (sqrt,, (Mdouble x)); | ^~~~~~ make[2]: [lib/libconjugrad/CMakeFiles/conjugrad.dir/build.make:76：lib/libconjugrad/CMakeFiles/conjugrad.dir/src/conjugrad.c.o] Error 1 make[1]: [CMakeFiles/Makefile2:129：lib/libconjugrad/CMakeFiles/conjugrad.dir/all] Error 2 make: *** [Makefile:156：all] Error 2

Can this problem be solved by modifying the code?

ken0414 commented 1 year ago

Hello, my issue is solved, the program was succesfully generated, but there is an another problem when im running CCMpred.

line 4: 240 Segmentation fault

How does it happend? Is there something wrong with my Ubuntu system. Im using the CPU version.

ken0414 commented 1 year ago

Here is the output

(base) kenmarnuls@LAPTOP-Q547HOJF:~/code/SPOT-Contact-Helical-New/inputs$ ccmpred tmp.aln tmp.mat

| | | | | | | --| --| | | | . | | -| . | |__||||| |_| ||| |_|

using CPU (1 thread(s))

Reweighted 3971 sequences with threshold 0.8 to Beff=370.517 weight mean=0.0933057, min=0.000383877, max=1 Segmentation fault

Benny0323 commented 1 year ago

CMake version is 3.22.1 GNU Make version is 4.3 CMake is running without using CUDA

Errors occured when using command 'make'

kenmarnuls@LAPTOP-Q547HOJF:~/CCMpred$ make [ 7%] Building C object lib/libconjugrad/CMakeFiles/conjugrad.dir/src/conjugrad.c.o In file included from /home/kenmarnuls/CCMpred/lib/libconjugrad/src/conjugrad.c:4: /home/kenmarnuls/CCMpred/lib/libconjugrad/include/conjugrad.h:21:15: error: conflicting types for ‘sqrtf’; have ‘float(double)’ 21 | #define fsqrt sqrtf | ^~~ In file included from /home/kenmarnuls/CCMpred/lib/libconjugrad/src/conjugrad.c:4: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:143:1: note: previous declaration of ‘sqrtf’ with type ‘float(float)’ 143 | MATHCALL (sqrt,, (Mdouble x)); | ^~~~ make[2]: [lib/libconjugrad/CMakeFiles/conjugrad.dir/build.make:76：lib/libconjugrad/CMakeFiles/conjugrad.dir/src/conjugrad.c.o] Error 1 make[1]: [CMakeFiles/Makefile2:129：lib/libconjugrad/CMakeFiles/conjugrad.dir/all] Error 2 make: *** [Makefile:156：all] Error 2

Can this problem be solved by modifying the code?

Hi! Could you tell me how to solve this problem. Unluckily, I met it too! Thanks!

lm-jkominek commented 8 months ago

Hi, not sure if you still care, but I also stumbled upon this problem. What worked for me was opening the file "include/conjugrad.h" and simply commenting out the offending line by adding // in front of it.