'syscall' is deprecated during installing jellyfish kmer counting
0
0
Entering edit mode
23 months 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 • 531 views
ADD COMMENT
0
Entering edit mode

Hello, I am facing the same problem while doing the installation of jellyfish. Have you solved it and how?

ADD REPLY

Login before adding your answer.

Traffic: 1982 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6