cufflinks @0.9.3 - build failure

[graceqy@…]

I was trying to install cufflinks on my Mac OS X Lion 10.7.5 (Xcode 4.3.2)

I used the command: sudo port install cufflinks

Terminal runs as below:

--->  Computing dependencies for cufflinks
--->  Fetching archive for cufflinks
--->  Attempting to fetch cufflinks-0.9.3_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/cufflinks
--->  Attempting to fetch cufflinks-0.9.3_0.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/cufflinks
--->  Attempting to fetch cufflinks-0.9.3_0.darwin_11.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/cufflinks
--->  Fetching distfiles for cufflinks
--->  Verifying checksum(s) for cufflinks
--->  Extracting cufflinks
--->  Configuring cufflinks
--->  Building cufflinks
Error: org.macports.build for port cufflinks returned: command execution failed
Please see the log file for port cufflinks for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port cufflinks failed
graces-macbook-pro:~ Graceqy$ /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/main.log
-bash: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/main.log: Permission denied
graces-macbook-pro:~ Graceqy$ open /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/main.log

The main log is attached.

I did update and upgrade outdated and cleared up the previous attempt of cufflink install ahead.

Could anyone help me figure out the issues, pls?

Thanks.

[mf2k (Frank Schima)]

In the future, please use WikiFormatting and Cc the port maintainer(s) but not yourself. The reporter is automatically Cc'ed.

[ryandesign (Ryan Carsten Schmidt)]

Has duplicate #42119.

[ryandesign (Ryan Carsten Schmidt)]

Probably we just need to update cufflinks to a newer version.

[warren-mcgee@…]

Replying to ryandesign@…:

Probably we just need to update cufflinks to a newer version.

I think you might be right RyanDesign. I realized after I submitted the ticket the discrepancy in the version available through macports and the version available on the developer's website (​link). The cufflinks available on macports is from 2010, and the current version is 2.1.1, updated in April 2013. This outdatedness is also true for TopHat (​link), which is a tool commonly used in conjunction with cufflinks. Anyway, for the time being, I'll install directly from the developer's website, but I would like to see the newer versions updated in mac ports, so I can keep all of my installations within the macports framework. Thanks for your help RyanDesign!

[chrstphrchvz (Christopher Chavez)]

cufflinks was updated to 2.2.1 in 2018. Is this ticket still relevant, or can it be closed?

[neverpanic (Clemens Lang)]

Error is

:info:build /opt/local/include/boost/multi_index/hashed_index.hpp:1254:10: error: no member named 'BOOST_FOREACH' in namespace 'boost'

I believe that's probably solved meanwhile, either by newer compilers, newer boost, or an updated cufflinks.

cufflinks fails to build on newer macOS because its configure script requires python, which is no longer shipped on macOS 12. Additionally, some newer architectures fail to build because they're looking for a copy of bam, and the cufflinks Portfile does not specify a dependency on it. Ryan, could you look into that?