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Old 06-11-2019, 01:44 PM   #1
colaneri
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Location: Durham

Join Date: Jul 2012
Posts: 30
Default star 2.7.1a compilation in MacOS Mojave is not working

I was following alexdobin/STAR on Github to compile STAR in my Mac

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
which returned this error:

Code:
*** No rule to make target `STARforMacStatic'.  Stop.
I re run the make command from the source directory :

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.
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
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