Opened 6 years ago

Last modified 22 months ago

#43092 new defect

atlas: Atlas could not detect any fortran compiler

Reported by: gbacareza@… Owned by: Veence (Vincent)
Priority: Normal Milestone:
Component: ports Version: 2.2.1
Keywords: Cc: petrrr, jkordani (Joshua Kordani), MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)
Port: atlas

Description

Just installed Macports with the intention of using it to install Octave. Obviously I'm very new as I'm a first timer.

When attempting to install Octave with command: sudo port install octave +atlas+docs, I get the Error: Processing of port octave failed.

Questions:

  1. Does this mean that Octave was not installed at all?

1a. Or does it mean that only the failed dependencies, (eg Error: The following dependencies were not installed: SuiteSparse atlas arpack gcc48 cctools ... ) were not installed? 1b. If on the contrary Octave was installed except for dependencies, where could I find executable?

  1. What happened to all the dependencies that were installed eg Installing libxml2 @2.9.1_0 which had no errors?

2a. Where were they installed?

  1. What do terms "Activating" and "Cleaning" (eg ---> Installing libtool @2.4.2_3 ---> Activating libtool @2.4.2_3) actually do?

3a. Do they overwrite libraries and files already there before this operation?

  1. If I decide to not attempt the port installation of Octave and try other means, how do I clean up?

Attachments (3)

main.log (201.0 KB) - added by gbacareza@… 6 years ago.
Main log file
main.2.log (15.1 KB) - added by gbacareza@… 6 years ago.
Main.log of atlas, dependency port that failed
main.3.log (9.2 KB) - added by jkordani (Joshua Kordani) 5 years ago.

Download all attachments as: .zip

Change History (13)

Changed 6 years ago by gbacareza@…

Attachment: main.log added

Main log file

comment:1 Changed 6 years ago by ryandesign (Ryan Schmidt)

The issue tracker is for reporting problems. It appears that on your system, octave could not be installed, because one of its dependencies failed to install. That's a problem, and you should attach the main.log file of the port that failed to install. (You attached the log for octave, which tells us nothing.)

As to the rest of your questions, they're best asked and answered on the macports-users mailing list.

Changed 6 years ago by gbacareza@…

Attachment: main.2.log added

Main.log of atlas, dependency port that failed

comment:2 Changed 6 years ago by gbacareza@…

attached correct file

comment:3 Changed 6 years ago by ryandesign (Ryan Schmidt)

Owner: changed from macports-tickets@… to vince@…
Port: atlas added
Summary: port install octave +atlas+docs processing failedatlas: Atlas could not detect any fortran compiler

The log is fairly straightforward; the error message it contains describes what you have to do:

Atlas could not detect any fortran compiler. If you really don’t need the fortran interface to be built, please use the +nofortran option, else install a fortran compiler (e.g. gcc4X) before building Atlas.

comment:4 in reply to:  3 Changed 6 years ago by jad11@…

Replying to ryandesign@…:

The log is fairly straightforward; the error message it contains describes what you have to do:

Atlas could not detect any fortran compiler. If you really don’t need the fortran interface to be built, please use the +nofortran option, else install a fortran compiler (e.g. gcc4X) before building Atlas.

At risk of hijacking the ticket, but in the hope that my experiences will assist in solving the problem, I wanted to report that I am also having similar problems with the atlas install. Having read your advice, I have made several further attempts with and without gcc48 but without success. In my most recent attempt, I started from a brand new macports installation, and performed just:

sudo port selfupdate
sudo port upgrade outdated
sudo port install gcc48
sudo port install atlas +gcc48

The terminal output for the final command is:

jad11:~$ sudo port install atlas +gcc48
Password:
--->  Computing dependencies for atlas
--->  Fetching archive for atlas
--->  Attempting to fetch atlas-3.10.1_5+gcc48.darwin_13.x86_64.tbz2 from http://packages.macports.org/atlas
--->  Attempting to fetch atlas-3.10.1_5+gcc48.darwin_13.x86_64.tbz2 from http://lil.fr.packages.macports.org/atlas
--->  Attempting to fetch atlas-3.10.1_5+gcc48.darwin_13.x86_64.tbz2 from http://nue.de.packages.macports.org/macports/packages/atlas
--->  Fetching distfiles for atlas
--->  Attempting to fetch atlas3.10.1.tar.bz2 from http://aarnet.dl.sourceforge.net/project/math-atlas/Stable/3.10.1
--->  Attempting to fetch lapack-3.4.2.tgz from http://www.netlib.org/lapack
--->  Verifying checksums for atlas
--->  Extracting atlas
--->  Applying patches to atlas
--->  Configuring atlas
Selected C compiler: /opt/local/bin/gcc-mp-4.8
Selected F77 compiler: gfortran48
Warning: GCC compilers on MacOS do not support AVX: downgrading.
Error: org.macports.configure for port atlas returned: configure failure: command execution failed
Please see the log file for port atlas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port atlas failed

The pertinent section from the atlas install log would appear to be:

:info:configure /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/..//CONFIG/include/atlconf.h:4:19: fatal error: stdio.h: No such file or directory
:info:configure  #include <stdio.h>
:info:configure                    ^
:info:configure compilation terminated.
:info:configure make: *** [atlconf_misc.o] Error 1
:info:configure ./xconfig -d s /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build/../ -d b /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build  -Si lapackref 1 -O 12 -v 5 -D c -DATL_DYLIBS -A 26 -V 448 -Si omp 0 -C acg /opt/local/bin/gcc-mp-4.8 -A 25 -F acg '-fomit-frame-pointer -mfpmath=sse -O3 -fno-schedule-insns2 -fPIC -msse4.2' -C if /opt/local/bin/gfortran-mp-4.8 -F if '-fomit-frame-pointer -mfpmath=sse -O3 -fno-schedule-insns2 -fPIC -msse4.2' -Ss f77lib /opt/local/lib/gcc48/libgfortran.dylib -b 64 -D c -DPentiumCPS=2800
:info:configure /bin/sh: line 1: ./xconfig: No such file or directory
:info:configure xconfig exited with 127
:info:configure Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/work/ATLAS/build" && ../configure --prefix=/opt/local --with-netlib-lapack-tarfile=/opt/local/var/macports/distfiles/atlas/lapack-3.4.2.tgz -O 12 -v 5 --dylibs -A 26 -V 448 -Si omp 0 -C acg /opt/local/bin/gcc-mp-4.8 -A 25 -F acg '-fomit-frame-pointer -mfpmath=sse -O3 -fno-schedule-insns2 -fPIC -msse4.2' -C if /opt/local/bin/gfortran-mp-4.8 -F if '-fomit-frame-pointer -mfpmath=sse -O3 -fno-schedule-insns2 -fPIC -msse4.2' -Ss f77lib /opt/local/lib/gcc48/libgfortran.dylib -b 64 -D c -DPentiumCPS=2800 
:info:configure Exit code: 127
:error:configure org.macports.configure for port atlas returned: configure failure: command execution failed
:debug:configure Error code: NONE
:debug:configure Backtrace: configure failure: command execution failed
    while executing
"$procedure $targetname"
:info:configure Warning: targets not executed for atlas: org.macports.activate org.macports.configure org.macports.build org.macports.destroot org.macports.install
:notice:configure Please see the log file for port atlas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log

Thanks for your help Andy

comment:5 Changed 6 years ago by Veence (Vincent)

Sorry to chime in a bit lately. This last error is caused by a problem in the Xcode installation. The Fortran compiler is detected all right, but something is wrong with the C compiler. It's not the first time this happens. I am a bit swamped lately, so I have little time, but if you do a quick scan through the tickets archives and look for Atlas, you'll 100% sure find a similar case.

comment:6 Changed 6 years ago by petrrr

Cc: Peter.Danecek@… added

Cc Me!

comment:7 Changed 5 years ago by Ionic (Mihai Moldovan)

Cc: joshua.kordani@… added

Adding #48482 reporter to CC.

Changed 5 years ago by jkordani (Joshua Kordani)

Attachment: main.3.log added

comment:8 Changed 5 years ago by jkordani (Joshua Kordani)

fresh install of 10.10, xcode, macports, port install octave fails due to atlas. console log selects /usr/bin/clang as the c compiler, atlas port could not detect a fortran compiler. Per iconic, sudo port clean atlas, followed by port install octave result in new main log. also, on my system, port info atlas shows that the default variant is clang, not gcc47. so what is supposed to be happening here?

comment:9 Changed 5 years ago by jkordani (Joshua Kordani)

Wow here to report that it is still not fixed. another fresh install of 10.10 and a fresh install of macports and here we are again. Also please bump or include macports version 2.3.3 as it is present in this version as well as the OP reported version.

comment:10 Changed 22 months ago by MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)

Cc: MarcusCalhoun-Lopez added
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