atlas @3.10.2: error: implicit declaration of function 'dgeqlf_' is invalid in C99

[gsarrouh]

I am trying to install Source Extractor v.2.19.5 using the terminal command: >> sudo port install source-extractor

Three dependencies are required: i) atlas; i) fftw-3; iii) fftw-3-single

When I execute the command i get the following output:

gsarrouh$ sudo port install source-extractor
Password:
--->  Computing dependencies for source-extractor
The following dependencies will be installed: 
 atlas
 fftw-3
 fftw-3-single
Continue? [Y/n]: Y
--->  Fetching archive for atlas
--->  Attempting to fetch atlas-3.10.2_2.darwin_19.x86_64.tbz2 from https://packages.macports.org/atlas
--->  Attempting to fetch atlas-3.10.2_2.darwin_19.x86_64.tbz2 from https://ywg.ca.packages.macports.org/mirror/macports/packages/atlas/atlas
--->  Attempting to fetch atlas-3.10.2_2.darwin_19.x86_64.tbz2 from https://mse.uk.packages.macports.org/atlas
--->  Fetching distfiles for atlas
--->  Attempting to fetch atlas3.10.2.tar.bz2 from http://ykf.ca.distfiles.macports.org/MacPorts/mpdistfiles/atlas
--->  Attempting to fetch lapack-3.6.0.tgz from http://ykf.ca.distfiles.macports.org/MacPorts/mpdistfiles/atlas
--->  Verifying checksums for atlas                                                  
--->  Extracting atlas
--->  Applying patches to atlas
--->  Configuring atlas
Selected C compiler: /usr/bin/clang
Selected F77 compiler: gfortrandevel
Warning: reinplace s|-no-cpp-precomp||g didn't change anything in /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/work/ATLAS/CONFIG/src/atlcomp.txt
--->  Building atlas
Error: Failed to build atlas: command execution failed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_atlas/atlas/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets to report a bug.
Error: Processing of port source-extractor failed

I really have no idea why altas is failing the build stage, but I cannot use a different software package other than Source Extractor for my work so I really need this to work!

Thanks for your help in advance,
ghassan

[gsarrouh]

main.log from build failure

[chrstphrchvz (Christopher Chavez)]

The issue is that implicit function declarations used to be considered warnings, but are now considered errors with Xcode 12. The canned response is to downgrade to Xcode 11.x to avoid the errors until MacPorts addresses them.

Existing upstream ticket regarding these implicit function declarations (no feedback yet from developer): ​https://sourceforge.net/p/math-atlas/support-requests/1082/

[michaelld (Michael Dickens)]

Anybody know if there's a PR/fix upstream yet? Guessing not ... this is just sloppy "old school C" programming!

[Veence (Vincent)]

Sorry I’m chiming in a bit late. I don’t think Atlas is maintained anymore. If I had to guess, I'd rather say no than yes. There’s basically a major hurdle to overcome with Atlas. I’m not 100% confident about it, but here it is anyway: Atlas chooses the best "kernel" to perform a given matrix task by testing all the ASM snippets it’s been bundled with, and picking up the fastest one. This results in CPU usage skyrocketing. However, it seems that starting with a MacOS 10.13 or 10.14, I don’t know exactly which one, Apple (or Intel?) bundled a mechanism to temporarily strike down, or even suspend, tasks that draw too much power. This results in the entire sampling process being derailed, and no meaningful result is produced. That might be the reason why Atlas is currently being phased out. I'd recommend linking against the Accelerate framework which, albeit being specific to Apple, is still actively developed.