Opened 11 years ago

Last modified 21 months ago

#38969 assigned defect

cufflinks @0.9.3 - build failure

Reported by: graceqy@… Owned by: ryandesign (Ryan Carsten Schmidt)
Priority: Normal Milestone:
Component: ports Version: 2.1.3
Keywords: Cc: warren-mcgee@…, chrstphrchvz (Christopher Chavez)
Port: cufflinks

Description (last modified by mf2k (Frank Schima))

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I did update and upgrade outdated and cleared up the previous attempt of cufflink install ahead.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

Attachments (1)

main.log (48.4 KB) - added by graceqy@… 11 years ago.

Download all attachments as: .zip

Change History (9)

Changed 11 years ago by graceqy@…

Attachment: main.log added

comment:1 Changed 11 years ago by mf2k (Frank Schima)

Cc: graceqy@… removed
Description: modified (diff)
Owner: changed from macports-tickets@… to haroldpimentel@…

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

comment:2 Changed 10 years ago by ryandesign (Ryan Carsten Schmidt)

Cc: warren-mcgee@… added

Has duplicate #42119.

comment:3 Changed 10 years ago by ryandesign (Ryan Carsten Schmidt)

Summary: cufflinks @ 2.1.1 - build failurecufflinks @0.9.3 - build failure

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

comment:4 in reply to:  3 Changed 10 years ago by 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!

comment:5 Changed 7 years ago by kurthindenburg (Kurt Hindenburg)

Owner: haroldpimentel@… deleted
Status: newassigned

comment:6 Changed 21 months ago by chrstphrchvz (Christopher Chavez)

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

comment:7 Changed 21 months ago by chrstphrchvz (Christopher Chavez)

Cc: chrstphrchvz added

comment:8 Changed 21 months ago by neverpanic (Clemens Lang)

Owner: set to ryandesign

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?

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