bowtie v 1.2.3

[Minhas61]

I am trying to install bowtie v 1.2.3 on MacOS Monterey version 12.2.1, However, I am getting the following error.

Error: Failed to build bowtie: command execution failed  
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie/bowtie/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets if you believe there is a bug.
Error: Processing of port bowtie failed
--->  Some of the ports you installed have notes:
  python27 has the following notes:
    To make this the default Python or Python 2 (i.e., the version run by the
    'python' or 'python2' commands), run one or both of:
    
        sudo port select --set python python27
        sudo port select --set python2 python27

Could you please guide how can I address this issue

[Minhas61]

Error: Failed to build bowtie: command execution failed  
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie/bowtie/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets if you believe there is a bug.
Error: Processing of port bowtie failed
--->  Some of the ports you installed have notes:
  python27 has the following notes:
    To make this the default Python or Python 2 (i.e., the version run by the
    'python' or 'python2' commands), run one or both of:
    
        sudo port select --set python python27
        sudo port select --set python2 python27

[ryandesign (Ryan Carsten Schmidt)]

Please attach the main.log file so that we can see what happened.

[ryandesign (Ryan Carsten Schmidt)]

Although you haven't attached your log file yet, we do see build failure of this port on our ​Monterey and ​Big Sur buildbot workers so that may be the same problem you're seeing:

/opt/local/include/tbb/compat/thread:45:33: error: target of using declaration conflicts with declaration already in scope
    using tbb::this_tbb_thread::get_id;
                                ^
/opt/local/include/tbb/compat/../tbb_thread.h:331:60: note: target of using declaration
    __TBB_DEPRECATED_IN_VERBOSE_MODE inline tbb_thread::id get_id() { return internal::thread_get_id_v3(); }
                                                           ^

(It also ​fails on the Lion worker but due to a clang segfault which is unrelated to this issue.)

Builds of bowtie 1.2.3 were successful on the buildbot workers for Mac OS X 10.6 through macOS 10.15 inclusive (except Mac OS X 10.7) back in 2019 so something may have changed since then. For example, tbb has been updated several times; maybe bowtie 1.2.3 is incompatible with the new tbb.

bowtie should probably be updated to the latest version, currently 1.3.1. Maybe it already includes a fix for this. I note in its changelog that it mentions removing some third-party library dependencies and that it migrates to python 3.

[catap (Kirill A. Korinsky)]

In 30032d091fbf93d8da5cf5a1f1ec758ce3023a8a/macports-ports (master):

bowtie: update to 1.3.1

Closes: #65312