Opened 6 years ago

Last modified 6 years ago

#42888 new defect

Upgrade of netcdf-fortran fails staging into destroot

Reported by: watsodw Owned by: tenomoto (Takeshi Enomoto)
Priority: Normal Milestone:
Component: ports Version: 2.2.1
Keywords: Cc: cooljeanius (Eric Gallager)
Port: netcdf-fortran

Description

See log.

Attachments (2)

main.log (118.2 KB) - added by watsodw 6 years ago.
main2.log (144.7 KB) - added by watsodw 6 years ago.

Download all attachments as: .zip

Change History (22)

Changed 6 years ago by watsodw

Attachment: main.log added

comment:1 Changed 6 years ago by mf2k (Frank Schima)

Cc: takeshi@… removed
Owner: changed from macports-tickets@… to takeshi@…

comment:2 Changed 6 years ago by watsodw

Is anyone working on this?

comment:3 in reply to:  2 Changed 6 years ago by seanfarley (Sean Farley)

Replying to david.w.watson@…:

Is anyone working on this?

Sorry for dropping the ball on this. The error seems very strange:

1434	:info:build netcdf4_eightbyte.f90:754:0: internal compiler error: Abort trap: 6
1435	:info:build gfortran-mp-4.8: internal compiler error: Abort trap: 6 (program f951)
1436	:info:build ../libtool: line 1150: 16607 Abort trap: 6           /opt/macports/bin/gfortran-mp-4.8 -pipe -Os -m32 -c netcdf4.f90 -fno-common -o .libs/netcdf4.

I just built this from source on my Mountain Lion machine successfully but will try to build on my Mavericks buildbot. In the meantime, have you tried to run the self update, clean, then rebuild dance?

comment:4 Changed 6 years ago by seanfarley (Sean Farley)

This built on my Mavericks bot fine. The only difference I can see is that you have a different prefix /opt/macports instead of the usual /opt/local but that, in theory, shouldn't be a problem.

comment:5 Changed 6 years ago by watsodw

I cleaned and tried again. I don't see the error you referenced. What I see is build failure when trying to stage into destroot. I have attached a new log file.

Changed 6 years ago by watsodw

Attachment: main2.log added

comment:6 Changed 6 years ago by neverpanic (Clemens Lang)

:info:destroot netcdf-f90.texi:2085: warning: @item missing argument
:info:destroot netcdf-f90.texi:6982: raising the section level of @unnumberedsubsec which is too low
:info:destroot make[1]: *** [netcdf-f90.info] Error 1

Likely caused by a newer version of texinfo. Replacing @item with @itemx in the file might help.

comment:7 in reply to:  6 Changed 6 years ago by seanfarley (Sean Farley)

Replying to cal@…:

:info:destroot netcdf-f90.texi:2085: warning: @item missing argument
:info:destroot netcdf-f90.texi:6982: raising the section level of @unnumberedsubsec which is too low
:info:destroot make[1]: *** [netcdf-f90.info] Error 1

Likely caused by a newer version of texinfo. Replacing @item with @itemx in the file might help.

That's what I am thinking too but I still can't reproduce it. David, do you have anything installed in /usr/local?

comment:8 in reply to:  6 Changed 6 years ago by seanfarley (Sean Farley)

Replying to cal@…:

:info:destroot netcdf-f90.texi:2085: warning: @item missing argument
:info:destroot netcdf-f90.texi:6982: raising the section level of @unnumberedsubsec which is too low
:info:destroot make[1]: *** [netcdf-f90.info] Error 1

Likely caused by a newer version of texinfo. Replacing @item with @itemx in the file might help.

There was a patch submitted here for reference:

http://www.unidata.ucar.edu/mailing_lists/archives/netcdfgroup/2013/msg00342.html

comment:9 Changed 6 years ago by watsodw

I don't have anything that would cause this error. I removed /usr/local from my path and tried again, but no luck.

comment:10 in reply to:  9 Changed 6 years ago by seanfarley (Sean Farley)

Replying to david.w.watson@…:

I don't have anything that would cause this error. I removed /usr/local from my path and tried again, but no luck.

You'd have to move /usr/local to another place, like ~/Desktop/usr-local-backup so that it's not automatically found.

comment:11 Changed 6 years ago by watsodw

Moving /usr/local didn't help either. I tried applying the patch mentioned earlier but I had to modify the file in the original tar archive, which changed the checksum, so macports wouldn't unpack the archive.

comment:12 Changed 6 years ago by neverpanic (Clemens Lang)

You can run sudo port extract netcdf-fortran, edit the file below the path returned by port work netcdf-fortran and continue the build using port install netcdf-fortran.

comment:13 Changed 6 years ago by watsodw

Didn't work. Same result.

comment:14 Changed 6 years ago by watsodw

I could extract and edit the file, but when I port install, Macports extracted the archive again, overwriting my edits. If the above patch is a fix, it will have to be applied by Macports itself.

comment:15 in reply to:  14 Changed 6 years ago by seanfarley (Sean Farley)

Replying to david.w.watson@…:

I could extract and edit the file, but when I port install, Macports extracted the archive again, overwriting my edits. If the above patch is a fix, it will have to be applied by Macports itself.

You should probably port clean netcdf-fortran then use port -vs extract netcdf-fortran then apply the patch, then port -vs destroot netcdf-fortran to see if it works.

comment:16 in reply to:  14 Changed 6 years ago by neverpanic (Clemens Lang)

Replying to david.w.watson@…:

I could extract and edit the file, but when I port install, Macports extracted the archive again, overwriting my edits.

It shouldn't do that unless the Portfile changed, and even then you can avoid it by using port -o.

If the above patch is a fix, it will have to be applied by Macports itself.

Yes, in the end that will have to be the way it's done, but it's usually easier to test it that way.

I'm trying to reproduce your problem now.

comment:17 Changed 6 years ago by neverpanic (Clemens Lang)

I cannot reproduce either; my build log doesn't show any calls to makeinfo.

comment:18 Changed 6 years ago by neverpanic (Clemens Lang)

Does /opt/local/bin/makeinfo exist on your system? If yes, what's the output of port provides /opt/local/bin/makeinfo?

Also, what are the file modification dates on $(port work netcdf-fortran)/netcdf-fortran-4.2/man4/netcdf-f77.texi and $(port work netcdf-fortran)/netcdf-fortran-4.2/man4/netcdf-f90.texi?

I also don't understand why the builtin "restore the .info file from the backup if it fails to build from scratch" doesn't kick in here, but I guess we should just apply the patch from upstream linked earlier to fix this.

comment:19 Changed 6 years ago by watsodw

Sorry for taking so long to respond. I did port -vs extract netcdf-fortran, applied the patch, then port -vs destroot netcdf-fortran, and it worked. Thanks again for the help.

comment:20 Changed 6 years ago by cooljeanius (Eric Gallager)

Cc: egall@… added

Cc Me!

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