'syscall' is deprecated during installing jellyfish kmer counting
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2.5 years ago

I have zero knowledge in bioinformatics. I'm using MacOS monterey and bash terminal for bioinformatics. Trying to install jellyfish to count kmer prior to DNA assembly. I'm using http://www.cs.cmu.edu/~ckingsf/software/jellyfish/README to help me install the tool. Can only do ./configure and already stuck in step 2, make. Don't know what to do, did googled it and none of the solutions are helpful. Please help!

(assembly) rna-bio@RNA-Bios-Mac-Pro jellyfish-1.1.6 % make
/Library/Developer/CommandLineTools/usr/bin/make  all-am
  CXX    jellyfish/libjellyfish_la-square_binary_matrix.lo
  CXX    jellyfish/libjellyfish_la-err.lo
  CXX    jellyfish/libjellyfish_la-misc.lo
  CXX    jellyfish/libjellyfish_la-storage.lo
  CXX    jellyfish/libjellyfish_la-thread_exec.lo
  CXX    jellyfish/libjellyfish_la-time.lo
  CXX    jellyfish/libjellyfish_la-file_parser.lo
  CXX    jellyfish/libjellyfish_la-read_parser.lo
  CXX    jellyfish/libjellyfish_la-parse_read.lo
  CXX    jellyfish/libjellyfish_la-half.lo
  CXX    jellyfish/libjellyfish_la-mapped_file.lo
  CXX    jellyfish/libjellyfish_la-parse_dna.lo
  CXX    jellyfish/libjellyfish_la-parse_quake.lo
  CXX    jellyfish/libjellyfish_la-parse_qual_dna.lo
  CXX    jellyfish/libjellyfish_la-sequence_parser.lo
  CXX    jellyfish/libjellyfish_la-seq_qual_parser.lo
  CXX    jellyfish/libjellyfish_la-backtrace.lo
  CXX    jellyfish/libjellyfish_la-floats.lo
  CXX    jellyfish/libjellyfish_la-dbg.lo
jellyfish/dbg.cc:44:34: error: 'syscall' is deprecated: first deprecated in macOS 10.12 - syscall(2) is unsupported; please switch to a supported interface. For SYS_kdebug_trace use kdebug_signpost(). [-Werror,-Wdeprecated-declarations]
  pid_t gettid() { return (pid_t)syscall(SYS_gettid); }
                                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/unistd.h:746:6: note: 'syscall' has been explicitly marked deprecated here
int      syscall(int, ...);
         ^
1 error generated.
make[1]: *** [jellyfish/libjellyfish_la-dbg.lo] Error 1
make: *** [all] Error 2
jellyfish • 651 views
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Hello, I am facing the same problem while doing the installation of jellyfish. Have you solved it and how?

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