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google-deepmind / alphafold

Open source code for AlphaFold 2.
Apache License 2.0
12.94k stars 2.29k forks source link

Errors when Building Docker Image #544

Closed DannySaba closed 2 years ago

DannySaba commented 2 years ago

Running into a few dependency build issues:

Scanning dependencies of target ffindex_apply
[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o
[ 30%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o
/tmp/hh-suite/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry':
/tmp/hh-suite/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'int64_t {aka long int}' [-Wformat=]
             fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status));
                                                  ~~~^                                                    ~~~~~~~~~~~
                                                  %ld

Scanning dependencies of target HH_OBJECTS
[ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o
[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o
[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o
[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o
[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o
[ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o
[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o
[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o
[ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o
[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o
[ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o
[ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o
[ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o
[ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o
[ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o
[ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o
/tmp/hh-suite/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])':
/tmp/hh-suite/src/hhalignment.cpp:1596:5: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=]
 int Alignment::Filter2(char keep[], int coverage, int qid, float qsc,
     ^~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6361,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/fstream:38,
                 from /tmp/hh-suite/src/hhalignment.h:6,
                 from /tmp/hh-suite/src/hhalignment.cpp:8:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: '__builtin___sprintf_chk' output between 47 and 4142 bytes into a destination of size 100
       __bos (__s), __fmt, __va_arg_pack ());
                                           ^
[ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o
[ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o
[ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o
[ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o
[ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o
[ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o
[ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o
[ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o
[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o
[ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o
[ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o
[ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o
[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o
[ 79%] Linking CXX static library libHH_OBJECTS.a
[ 79%] Built target HH_OBJECTS
Scanning dependencies of target hhblits_ca3m
Scanning dependencies of target hhsearch_omp
Scanning dependencies of target hhblits_omp
Scanning dependencies of target hhalign_omp
[ 81%] Building CXX object src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o
[ 81%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o
[ 82%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o
[ 83%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o
/tmp/hh-suite/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)':
/tmp/hh-suite/src/hhblits_ca3m.cpp:80:5: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
 int main(int argc, const char **argv) {
     ^~~~
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6361,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/fstream:38,
                 from /tmp/hh-suite/src/hhblits.h:11,
                 from /tmp/hh-suite/src/hhblits_ca3m.cpp:8:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
[ 84%] Linking CXX executable hhblits_ca3m
/tmp/hh-suite/src/hhblits_omp.cpp: In function 'int main(int, const char**)':
/tmp/hh-suite/src/hhblits_omp.cpp:80:5: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
 int main(int argc, const char **argv) {
     ^~~~
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6361,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/fstream:38,
                 from /tmp/hh-suite/src/hhblits.h:11,
                 from /tmp/hh-suite/src/hhsearch.h:34,
                 from /tmp/hh-suite/src/hhblits_omp.cpp:8:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
/tmp/hh-suite/src/hhblits_omp.cpp: In function 'int main(int, const char**)':
/tmp/hh-suite/src/hhblits_omp.cpp:80:5: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
 int main(int argc, const char **argv) {
     ^~~~
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6361,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/fstream:38,
                 from /tmp/hh-suite/src/hhblits.h:11,
                 from /tmp/hh-suite/src/hhsearch.h:34,
                 from /tmp/hh-suite/src/hhblits_omp.cpp:8:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
[ 85%] Linking CXX executable hhsearch_omp
/tmp/hh-suite/src/hhblits_omp.cpp: In function 'int main(int, const char**)':
/tmp/hh-suite/src/hhblits_omp.cpp:80:5: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
 int main(int argc, const char **argv) {
     ^~~~
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6361,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/fstream:38,
                 from /tmp/hh-suite/src/hhblits.h:11,
                 from /tmp/hh-suite/src/hhsearch.h:34,
                 from /tmp/hh-suite/src/hhblits_omp.cpp:8:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
        __bos (__s), __fmt, __va_arg_pack ());
tomwardio commented 2 years ago

Hi @DannySaba,

Thanks for the report, these are compilation warnings when building hh-suite rather than AlphaFold. They should be mostly benign, but if you find any issues, I'm sure the owners would welcome any feedback!