I was following alexdobin/STAR on Github to compile STAR in my Mac
which returned this error:
I re run the make command from the source directory :
now compilation started but produced a lot of warnings
example:
after that I tried to run star but command was not found
it is possible that those warning are related with the failed compilation?
can someone advice or help
Code:
curl -OL https://github.com/alexdobin/STAR/archive/2.7.1a.tar.gz tar -xzf 2.7.1a.tar.gz cd STAR-2.7.1a
Code:
brew install gcc make STARforMacStatic CXX=/usr/local/Cellar/gcc/9.1.0/bin/g++-9
Code:
*** No rule to make target `STARforMacStatic'. Stop.
Code:
cd source make STARforMacStatic CXX=/usr/local/Cellar/gcc/9.1.0/bin/g++-9
now compilation started but produced a lot of warnings
example:
Code:
1 warning generated. cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o faidx.o faidx.c faidx.c:21:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, faidx1_t) faidx.c:21:1: warning: unused function 'kh_del_s' [-Wunused-function] ./htslib/khash.h:615:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) hts.c:19:5: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT2(, BGZF*, bgzf_read, 65536) 2 warnings generated. cc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o sam.o sam.c sam.c:1335:1: warning: unused function 'kh_clear_olap_hash' [-Wunused-function] KHASH_MAP_INIT_STR(olap_hash, lbnode_t *) vcf.c:15:1: warning: unused function 'kh_del_vdict' [-Wunused-function] ./htslib/khash.h:615:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) cram/cram_io.c:2244:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:311: note: expanded from macro 'itf8_put' ...=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~^~~~~~~~~~~~~~~~~ cram/cram_io.c:2244:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:345: note: expanded from macro 'itf8_put' ...=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~~~~~~^~~~~ cram/cram_io.c:2244:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ cram/cram_io.h:97:367: note: expanded from macro 'itf8_put' ...=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~~~~~~^~~~~ cram/cram_io.c:2244:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ g++-9: warning: parametersDefault.xxd: linker input file unused because linking not done g++-9: warning: htslib: linker input file unused because linking not done Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()': Parameters_openReadsFiles.cpp:33:20: warning: variable 'imate' might be clobbered by 'longjmp' or 'vfork' [-Wclobbered] 33 | for (uint imate=0;imate<readFilesIn.size();imate++) {//open readIn files ld: warning: direct access in function 'operator new[](unsigned long, std::nothrow_t const&) [clone .cold]' from file '/usr/local/Cellar/gcc/9.1.0/lib/gcc/9/gcc/x86_64-apple-darwin18/9.1.0/../../../libstdc++.a(new_opvnt.o)' to global weak symbol 'operator new[](unsigned long, std::nothrow_t const&)' from file '/usr/local/Cellar/gcc/9.1.0/lib/gcc/9/gcc/x86_64-apple-darwin18/9.1.0/../../../libstdc++.a(new_opvnt.o)' means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
it is possible that those warning are related with the failed compilation?
can someone advice or help