Opened 7 years ago

Closed 7 years ago

Last modified 7 years ago

#39619 closed submission (fixed)

Submission gnome-chemistry-utils

Reported by: c.herbig@… Owned by: neverpanic (Clemens Lang)
Priority: Normal Milestone:
Component: ports Version:
Keywords: Cc:
Port: gnome-chemistry-utils

Description

This package provides several programs useful to chemists and students. GChem3D displays molecule structures in 3D, GChemCalc provides calculations for chemistry, GChemPaint draws 2D chemical structures and reactions, GChemTable provides the periodic table of the elements, GCrystal displays and edits 3D crystal structures, GSpectrum displays spectra files (NMR, IR, etc).

Attachments (10)

Portfile (2.3 KB) - added by c.herbig@… 7 years ago.
Portfile.2 (1.3 KB) - added by c.herbig@… 7 years ago.
goffice 0.10.x
Portfile.3 (2.1 KB) - added by c.herbig@… 7 years ago.
Applied formatting fixes to gnome-chemistry-utils portfile
Portfile.4 (2.1 KB) - added by c.herbig@… 7 years ago.
removed archs
Portfile.5 (2.2 KB) - added by c.herbig@… 7 years ago.
adds goffice and gnumeric plugins
Portfile.6 (2.2 KB) - added by c.herbig@… 7 years ago.
Reordered keywords so that port will live in the gnome tree instead of the science tree
Portfile.7 (2.2 KB) - added by c.herbig@… 7 years ago.
Adds depends_run port:yelp to comply with recent gnome changes
Portfile.7.patch (776 bytes) - added by neverpanic (Clemens Lang) 7 years ago.
Portfile.8 (2.4 KB) - added by c.herbig@… 7 years ago.
Portfile-gnome-chemistry-utils.diff (1.3 KB) - added by c.herbig@… 7 years ago.
Added gtkglext dep, changed compiler settings, changed some whitespace

Download all attachments as: .zip

Change History (38)

Changed 7 years ago by c.herbig@…

Attachment: Portfile added

Changed 7 years ago by c.herbig@…

Attachment: Portfile.2 added

goffice 0.10.x

comment:1 Changed 7 years ago by c.herbig@…

I forgot, you'll need to use Portfile.2 for the goffice 0.10 dependency.

comment:2 Changed 7 years ago by ryandesign (Ryan Schmidt)

The port says "supported_archs x86_64 i386". So it definitely does not work on PowerPC?

In the long description, you may benefit from inserting newlines. See the moreutils port for an example.

You don't need to specify "depends_extract port:xz"; saying "use_xz yes" does that automatically.

You should not declare a dependency on port:xorg-server. That port provides X11.app, which is but one way that users can access X11 programs. (Other ways include using Apple's X11.app, or the one from XQuartz, or using an X11 server on a different computer.) You should however declare dependencies on any individual X11 libraries this port links with; there are individual ports for each.

The lines of hash marks should be removed from the notes. The notes should just be a paragraph (or paragraphs) of text. If you feel MacPorts does not draw sufficient attention to the notes in the installation output, then that is a global issue that should be addressed by changing MacPorts base, not by changing each individual port.

You've attached a second portfile, of goffice. We already have a port of goffice. If you're proposing to update the goffice port in some way, file a new ticket, and attach a unified diff of your changes to it. First consult any existing open tickets about goffice to see if they relate.

comment:3 in reply to:  2 ; Changed 7 years ago by c.herbig@…

Replying to ryandesign@…:

The port says "supported_archs x86_64 i386". So it definitely does not work on PowerPC?

I have absolutely no idea, and I don't have a PPC mac to test it...

In the long description, you may benefit from inserting newlines. See the moreutils port for an example.

Thanks, that actually what I wanted it to look like.

You don't need to specify "depends_extract port:xz"; saying "use_xz yes" does that automatically.

Fixed.

You should not declare a dependency on port:xorg-server. That port provides X11.app, which is but one way that users can access X11 programs. (Other ways include using Apple's X11.app, or the one from XQuartz, or using an X11 server on a different computer.) You should however declare dependencies on any individual X11 libraries this port links with; there are individual ports for each.

Perhaps then it doesn't need that line at all, since it needs mesa for OpenGL things, but only needs an X11 display to connect to when it launches...

The lines of hash marks should be removed from the notes. The notes should just be a paragraph (or paragraphs) of text. If you feel MacPorts does not draw sufficient attention to the notes in the installation output, then that is a global issue that should be addressed by changing MacPorts base, not by changing each individual port.

I took them out, I had modeled it after how the dbus port did it.

You've attached a second portfile, of goffice. We already have a port of goffice. If you're proposing to update the goffice port in some way, file a new ticket, and attach a unified diff of your changes to it. First consult any existing open tickets about goffice to see if they relate.

Now here we have a real problem. I forgot that I had been using an updated gnumeric and therefore goffice in a local repository, and that MacPorts still has 0.8.x. They had attempted to update it before, but had to drop it back down because anything above goffice 0.8.x breaks GnuCash (r91843). So after submitting this, I realized if anyone wanted to try it, they would need the updated office 0.10.x portfile, which gnome-chemistry-utils requires. It seems that Fedora deals with the problem by making a separate goffice08 dependency for GnuCash, perhaps someone can take a look at doing that?

Last edited 7 years ago by ryandesign (Ryan Schmidt) (previous) (diff)

Changed 7 years ago by c.herbig@…

Attachment: Portfile.3 added

Applied formatting fixes to gnome-chemistry-utils portfile

comment:4 in reply to:  3 ; Changed 7 years ago by ryandesign (Ryan Schmidt)

Replying to c.herbig@…:

Replying to ryandesign@…:

The port says "supported_archs x86_64 i386". So it definitely does not work on PowerPC?

I have absolutely no idea, and I don't have a PPC mac to test it...

Then you should not presume it won't work. Just omit the supported_archs line to let the default (all archs are supported) take effect. If it turns out not to work on PowerPC, users will bug us about it, and we can address it then.

You've attached a second portfile, of goffice. We already have a port of goffice. If you're proposing to update the goffice port in some way, file a new ticket, and attach a unified diff of your changes to it. First consult any existing open tickets about goffice to see if they relate.

Now here we have a real problem. I forgot that I had been using an updated gnumeric and therefore goffice in a local repository, and that MacPorts still has 0.8.x. They had attempted to update it before, but had to drop it back down because anything above goffice 0.8.x breaks GnuCash (r91843). So after submitting this, I realized if anyone wanted to try it, they would need the updated office 0.10.x portfile, which gnome-chemistry-utils requires. It seems that Fedora deals with the problem by making a separate goffice08 dependency for GnuCash, perhaps someone can take a look at doing that?

That sounds reasonable, and not difficult to accomplish, since there are only two ports currently depending on goffice.

comment:5 in reply to:  4 Changed 7 years ago by c.herbig@…

Replying to ryandesign@…:

Then you should not presume it won't work. Just omit the supported_archs line to let the default (all archs are supported) take effect. If it turns out not to work on PowerPC, users will bug us about it, and we can address it then.

Fixed.

That sounds reasonable, and not difficult to accomplish, since there are only two ports currently depending on goffice.

Shall I assume then that you or one of the other devs will be taking care of that? Meanwhile, the latest gnumeric +quartz has no trouble compiling or running once the latest goffice is installed.

Changed 7 years ago by c.herbig@…

Attachment: Portfile.4 added

removed archs

comment:6 Changed 7 years ago by c.herbig@…

I took the liberty of filing a new ticket (#39628) to address the goffice issue.

Last edited 7 years ago by ryandesign (Ryan Schmidt) (previous) (diff)

comment:7 Changed 7 years ago by mf2k (Frank Schima)

Keywords: science chemistry gnome removed
Version: 2.1.3

comment:8 in reply to:  7 Changed 7 years ago by c.herbig@…

Replying to macsforever2000@…: Was something wrong with the keywords?

comment:9 Changed 7 years ago by mf2k (Frank Schima)

Yes, they were completely unnecessary.

comment:10 Changed 7 years ago by c.herbig@…

Updated the portfile to include the plugins options for goffice and gnumeric. Even if gnumeric is not installed when gnome-chemistry-utils is, the plugins option does not cause errors, it is simply does not create a gnumeric plugin directory. Finally, if Gnumeric is installed afterwards, Gnumeric still checks the goffice plugins directory and uses those to the same effect.

Changed 7 years ago by c.herbig@…

Attachment: Portfile.5 added

adds goffice and gnumeric plugins

Changed 7 years ago by c.herbig@…

Attachment: Portfile.6 added

Reordered keywords so that port will live in the gnome tree instead of the science tree

Changed 7 years ago by c.herbig@…

Attachment: Portfile.7 added

Adds depends_run port:yelp to comply with recent gnome changes

comment:11 Changed 7 years ago by c.herbig@…

Now that goffice supplies a 0.10.x version, there should be no problem compiling and running this in a standard MacPorts setup (no +quartz yet). So, unless there are any issues, I believe this is ready to commit.

Trying to get this ready has turned into a very educating 2 weeks, I learned more about port files and dependencies than I ever intended to, but I feel that it has paid off. Thank you for your patience as I've learned proper portfile and tracticket policies, and I would especially like to also thank those of you who have taken time out of your day to review, correct and commit the changes to dependencies (which turned out to be more far reaching than I had thought) needed to support this port.

comment:12 Changed 7 years ago by c.herbig@…

Can someone take a look at committing this?

comment:13 Changed 7 years ago by neverpanic (Clemens Lang)

This first failed to fetch for me, now fails to configure. I've attached a patch that fixes the fetch failure, but I don't know how to proceed with the configure failure:

DEBUG: Executing org.macports.configure (gnome-chemistry-utils)
DEBUG: Environment: CPATH='/opt/local/include' CPPFLAGS='-I/opt/local/include' CFLAGS='-pipe -Os -arch x86_64' CXXFLAGS='-pipe -Os -arch x86_64' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.8' F77FLAGS='-m64' CXX='/usr/bin/clang++' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_dports_gnome_gnome-chemistry-utils/gnome-chemistry-utils/work/.CC_PRINT_OPTIONS' F90FLAGS='-pipe -Os -m64' LDFLAGS='-L/opt/local/lib -Wl,-headerpad_max_install_names -arch x86_64' __CFPREFERENCES_AVOID_DAEMON='1' FCFLAGS='-pipe -Os -m64' OBJC='/usr/bin/clang' OBJCXX='/usr/bin/clang++' INSTALL='/usr/bin/install -c' OBJCFLAGS='-pipe -Os -arch x86_64' OBJCXXFLAGS='-pipe -Os -arch x86_64' FFLAGS='-pipe -Os' CC_PRINT_OPTIONS='YES' CC='/usr/bin/clang'
DEBUG: Assembled command: 'cd "/opt/local/var/macports/build/_opt_dports_gnome_gnome-chemistry-utils/gnome-chemistry-utils/work/gnome-chemistry-utils-0.14.2" && ./configure --prefix=/opt/local --disable-scrollkeeper --with-goffice-plugins --with-gnumeric-plugins'
DEBUG: Executing command line:  cd "/opt/local/var/macports/build/_opt_dports_gnome_gnome-chemistry-utils/gnome-chemistry-utils/work/gnome-chemistry-utils-0.14.2" && ./configure --prefix=/opt/local --disable-scrollkeeper --with-goffice-plugins --with-gnumeric-plugins
./configure: This script requires a shell more modern than all
./configure: the shells that I found on your system.
./configure: Please tell bug-autoconf@gnu.org and
./configure: http://savannah.nongnu.org/bugs/?group=gchemutils about
./configure: your system, including any error possibly output before
./configure: this message. Then install a modern shell, or manually
./configure: run the script under such a shell if you do have one.
Command failed:  cd "/opt/local/var/macports/build/_opt_dports_gnome_gnome-chemistry-utils/gnome-chemistry-utils/work/gnome-chemistry-utils-0.14.2" && ./configure --prefix=/opt/local --disable-scrollkeeper --with-goffice-plugins --with-gnumeric-plugins
Exit code: 1

Changed 7 years ago by neverpanic (Clemens Lang)

Attachment: Portfile.7.patch added

comment:14 in reply to:  13 Changed 7 years ago by c.herbig@…

Replying to cal@…:

This first failed to fetch for me, now fails to configure. I've attached a patch that fixes the fetch failure, but I don't know how to proceed with the configure failure:

That's the weirdest thing I've ever seen! Let me play with this a bit. P.S. I am using OS X 10.8.4 with the latest updates to everything installed, in case that matters. Also, for the fetch patch, I was sure I had fixed that. But thanks for finding that.

Last edited 7 years ago by c.herbig@… (previous) (diff)

comment:15 Changed 7 years ago by neverpanic (Clemens Lang)

Don't worry too much about it. I noticed this only happens when using trace mode from trunk, so it's probably a bug in trace mode I should fix. It does configure successfully without trace mode (and I've stopped there for now, since I need to install +x11 before I continue testing).

comment:16 Changed 7 years ago by c.herbig@…

I'm in the middle of installing it in a fresh copy of macports, so I'll see if it works here.

comment:17 Changed 7 years ago by c.herbig@…

I was able to compile and run this portfile on a fresh installation of macports.

Changed 7 years ago by c.herbig@…

Attachment: Portfile.8 added

comment:18 Changed 7 years ago by neverpanic (Clemens Lang)

Owner: changed from macports-tickets@… to cal@…
Status: newassigned

Turns out the message above is what happens if you trick configure into thinking that '/' doesn't exist on your system… sorry for the false alarm.

Committed in r108474 with the following changes:

  • added missing build dependencies on intltool, gnome-doc-utils and pkgconfig.
  • remove non-existant ./configure parameters --with-goffice-plugins and --with-gnumeric-plugins
  • use active_variants PortGroup to ensure gtk3 is +x11
  • avoid updating desktop and mime databases in destroot by configuring with --disable-update-databases
  • update desktop and mime databases in post-activate and post-deactivate

gchemtable fails for me:

:( clemens@cSchlepptop:/opt/local$ gchemtable
libc++abi.dylib: terminate called throwing an exception

gchempaint works, but cannot be closed.

comment:19 Changed 7 years ago by neverpanic (Clemens Lang)

Resolution: fixed
Status: assignedclosed

comment:20 in reply to:  18 Changed 7 years ago by c.herbig@…

Replying to cal@…:

gchemtable fails for me:

:( clemens@cSchlepptop:/opt/local$ gchemtable
libc++abi.dylib: terminate called throwing an exception

I don't recall that happening before, but I'll take another look at it

gchempaint works, but cannot be closed.

ditto

comment:21 in reply to:  18 ; Changed 7 years ago by c.herbig@…

Replying to cal@…:

Turns out the message above is what happens if you trick configure into thinking that '/' doesn't exist on your system… sorry for the false alarm.

Committed in r108474 with the following changes:

  • added missing build dependencies on intltool, gnome-doc-utils and pkgconfig.
  • remove non-existant ./configure parameters --with-goffice-plugins and --with-gnumeric-plugins
  • use active_variants PortGroup to ensure gtk3 is +x11
  • avoid updating desktop and mime databases in destroot by configuring with --disable-update-databases
  • update desktop and mime databases in post-activate and post-deactivate

Also, do the gnumeric plugins still show up in local/lib/goffice/0.10/plugins/gchemutils ? I'd check this all now, but I'm waiting for webkit-gtk to compile...

comment:22 Changed 7 years ago by c.herbig@…

I do remember this now. It closes only from the File -> Quit menu. No idea what that's all about... And you're right, gchemtable doesn't work now. I'm rather disappointed by this now.

comment:23 in reply to:  21 ; Changed 7 years ago by neverpanic (Clemens Lang)

Replying to c.herbig@…:

Also, do the gnumeric plugins still show up in local/lib/goffice/0.10/plugins/gchemutils?

I can't check at the moment either, but I'd assume they don't given the configure output I saw "checking for gnumeric... no". If you want to build gnumeric plugins, you should maybe add a dependency on gnumeric?

Replying to c.herbig@…:

I do remember this now. It closes only from the File -> Quit menu. No idea what that's all about...

That didn't work for me either.

And you're right, gchemtable doesn't work now. I'm rather disappointed by this now.

Have you tried using a different compiler, e.g. llvm-gcc-4.2? I think the problem might be two different stdc++ implementations in the same binary, but I'd have to check again to be sure.

comment:24 in reply to:  23 ; Changed 7 years ago by c.herbig@…

Replying to cal@…:

Have you tried using a different compiler, e.g. llvm-gcc-4.2? I think the problem might be two different stdc++ implementations in the same binary, but

I don't know how to do that. I'll try it if you can tell me what to put into the port file to make that happen.

comment:25 Changed 7 years ago by c.herbig@…

It turns out that with or without gnumeric, it still puts a copy of the plugins into the appropriate goffice directory, and gnumeric is smart enough to look there when it loads plugins. So, that's not an issue.

comment:26 in reply to:  24 Changed 7 years ago by neverpanic (Clemens Lang)

Replying to c.herbig@…:

I don't know how to do that. I'll try it if you can tell me what to put into the port file to make that happen.

You can try on the command line first: sudo port install gnome-chemistry-utils configure.compiler=llvm-gcc-4.2. If that works and produces a working gchemtable, I'll have a fix to make the change persistent.

Changed 7 years ago by c.herbig@…

Added gtkglext dep, changed compiler settings, changed some whitespace

comment:27 Changed 7 years ago by c.herbig@…

So, the compiler settings got gchempaint to work as it ought, but still no luck on gchemtable. Somebody at the home_site had gotten gchemtable to compile outside of macports, so I'm waiting to hear if they used any special settings...

comment:28 Changed 7 years ago by c.herbig@…

Actually, since this is closed, I'll just prep a new update ticket and get a .diff for that.

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