[MacPorts] #42888: Upgrade of netcdf-fortran fails staging into destroot
#42888: Upgrade of netcdf-fortran fails staging into destroot ------------------------------+-------------------------------- Reporter: david.w.watson@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Keywords: | Port: netcdf-fortran ------------------------------+-------------------------------- See log. -- Ticket URL: <https://trac.macports.org/ticket/42888> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Changes (by macsforever2000@…): * cc: takeshi@… (removed) * owner: macports-tickets@… => takeshi@… -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:1> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by david.w.watson@…): Is anyone working on this? -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by sean@…): Replying to [comment:2 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? -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:3> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by sean@…): 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. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:4> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by david.w.watson@…): 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. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:5> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by 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. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:6> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by sean@…): Replying to [comment:6 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`? -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:7> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by sean@…): Replying to [comment:6 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... -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:8> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by 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. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:9> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by sean@…): Replying to [comment:9 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. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:10> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by david.w.watson@…): 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. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:11> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by cal@…): 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`. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:12> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by david.w.watson@…): Didn't work. Same result. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:13> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by 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. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:14> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by sean@…): Replying to [comment:14 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. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:15> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by cal@…): Replying to [comment:14 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. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:16> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by cal@…): I cannot reproduce either; my build log doesn't show any calls to `makeinfo`. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:17> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by cal@…): 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. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:18> MacPorts <http://www.macports.org/> Ports system for OS X
#42888: Upgrade of netcdf-fortran fails staging into destroot -------------------------------+----------------------- Reporter: david.w.watson@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Resolution: | Keywords: Port: netcdf-fortran | -------------------------------+----------------------- Comment (by david.w.watson@…): 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. -- Ticket URL: <https://trac.macports.org/ticket/42888#comment:19> MacPorts <http://www.macports.org/> Ports system for OS X
participants (1)
-
MacPorts