PerlPrimer

[pst@…]

Please add PerlPrimer to MacPorts. It is an open-source PCR primer design program. (​http://perlprimer.sourceforge.net/)

Thanks!! Paul

[MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)]

Cc Me!

[(none)]

Milestone Port Requests deleted

[pst@…]

Can anyone let me know the status of this request? Is there any hope that after 10 months this might be ported? I DO appreciate the work that MacPorts does. Thanks Paul

[danielluke (Daniel J. Luke)]

Macports is all volunteers.

The best way to get a port added is to write the portfile yourself. It's not too difficult, and people on the mailing list are happy to help you figure things out.

If you're interested, the guide (​http://guide.macports.org) is a good place to start.

[blb@…]

Looks simple enough, so added in r52110 (make sure your p5-tk is 804.028_1 or newer).

[pst@…]

Replying to blb@…:

Looks simple enough, so added in r52110 (make sure your p5-tk is 804.028_1 or newer).

Thanks so much for porting. However, after doing a selfupdate and installing, I get the helpful error message "Bus Error" when I type "perlprimer.pl" on the command line. Now what should I try? (24" iMac 2.8gh, OSX10.5.7, 4gigs ram). I assume that all dependencies are installed and that the most recent versions of programs would be installed by the installer.

Paul

[blb@…]

It worked fine for me (just a quick bit of testing) on 10.5.7, MacBook Pro, Xcode 3.1.2. Since you've already done selfupdate, check the output from port outdated as you may have some ports in need of upgrading.

[pst@…]

Replying to blb@…:

It worked fine for me (just a quick bit of testing) on 10.5.7, MacBook Pro, Xcode 3.1.2. Since you've already done selfupdate, check the output from port outdated as you may have some ports in need of upgrading.

I ran port outdated and it said "No installed ports are outdated". So, I uninstalled macports completely, reinstalled the DevTools 3.1.2, reinstalled macports, installed 1 port that was working before just to test the new installation of macports, and that port worked just fine. I installed perlprimer and it looked like it installed just fine. I tried to run it from the command line and got the same error message as before "Bus error". I ran port outdated again, it said no ports are outdated. Not sure what to try now...

[blb@…]

I'm guessing you're running 10.5 if you're using Xcode 3.1.2...what is the result of running the following?

$ port installed p5-tk perl5.8 tk
$ otool -L /opt/local/lib/perl5/vendor_perl/5.8.9/darwin-thread-multi-2level/auto/Tk/Tk.bundle
$ otool -L /opt/local/lib/libtk8.5.dylib

[pst@…]

Replying to blb@…:

I'm guessing you're running 10.5 if you're using Xcode 3.1.2...what is the result of running the following? $ port installed p5-tk perl5.8 tk $ otool -L /opt/local/lib/perl5/vendor_perl/5.8.9/darwin-thread-multi-2level/auto/Tk/Tk.bundle $ otool -L /opt/local/lib/libtk8.5.dylib

Here is the output: pst@USDA-3402-GenoMac, 10:38 AM ~/] port installed p5-tk perl5.8 tk The following ports are currently installed:

p5-tk @804.028_1 (active) perl5.8 @5.8.9_3 (active) tk @8.5.6_1 (active)

[pst@USDA-3402-GenoMac, 10:38 AM ~/] otool -L /opt/local/lib/perl5/vendor_perl/5.8.9/darwin-thread-multi-2level/auto/Tk/Tk.bundle otool: can't open file: /opt/local/lib/perl5/vendor_perl/5.8.9/darwin-thread-multi-2level/auto/Tk/Tk.bundle (No such file or directory) [pst@USDA-3402-GenoMac, 10:39 AM ~/] otool -L /opt/local/lib/libtk8.5.dylib /opt/local/lib/libtk8.5.dylib:

/opt/local/lib/libtk8.5.dylib (compatibility version 8.5.0, current version 8.5.6) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 476.18.0) /opt/local/lib/libX11.6.dylib (compatibility version 9.0.0, current version 9.0.0) /opt/local/lib/libXss.1.dylib (compatibility version 2.0.0, current version 2.0.0) /opt/local/lib/libXext.6.dylib (compatibility version 11.0.0, current version 11.0.0) /opt/local/lib/libXft.2.dylib (compatibility version 4.0.0, current version 4.13.0) /opt/local/lib/libfreetype.6.dylib (compatibility version 10.0.0, current version 10.20.0) /opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /opt/local/lib/libfontconfig.1.dylib (compatibility version 5.0.0, current version 5.0.0) /opt/local/lib/libexpat.1.dylib (compatibility version 7.0.0, current version 7.2.0) /opt/local/lib/libXrender.1.dylib (compatibility version 5.0.0, current version 5.0.0) /opt/local/lib/libXau.6.dylib (compatibility version 7.0.0, current version 7.0.0) /opt/local/lib/libXdmcp.6.dylib (compatibility version 7.0.0, current version 7.0.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4)

[pst@USDA-3402-GenoMac, 10:39 AM ~/]

So I take it that something is not installed correctly. The installer for perlprimer indicated that everything was installed. Also the "installed" command gives the following: pst@USDA-3402-GenoMac, 10:42 AM ~/] port installed The following ports are currently installed:

expat @2.0.1_0 (active) fontconfig @2.6.0_2+macosx (active) freetype @2.3.9_0+macosx (active) gperf @3.0.4_0 (active) libiconv @1.12_2 (active) mapm3 @3.0_3+large_datasets (active) p5-compress-raw-zlib @2.015_0 (active) p5-compress-zlib @2.015_0 (active) p5-crypt-ssleay @0.57_0 (active) p5-html-parser @3.60_0 (active) p5-html-tagset @3.20_0 (active) p5-io-compress-base @2.015_0 (active) p5-io-compress-zlib @2.015_0 (active) p5-libwww-perl @5.826_0 (active) p5-term-readkey @2.30_0 (active) p5-tk @804.028_1 (active) p5-uri @1.38_0 (active) perl5 @5.8.9_0 (active) perl5.8 @5.8.9_3 (active) perlprimer @1.1.17_0 (active) pkgconfig @0.23_1 (active) tcl @8.5.6_0 (active) tk @8.5.6_1 (active) Xft2 @2.1.13_1 (active) xorg-bigreqsproto @1.0.2_0 (active) xorg-inputproto @1.5.0_0 (active) xorg-kbproto @1.0.3_0 (active) xorg-libX11 @1.2.1_0 (active) xorg-libXau @1.0.4_0 (active) xorg-libXdmcp @1.0.2_0 (active) xorg-libXext @1.0.5_1 (active) xorg-libXScrnSaver @1.1.3_0 (active) xorg-renderproto @0.9.3_0 (active) xorg-scrnsaverproto @1.1.0_0 (active) xorg-xcmiscproto @1.1.2_0 (active) xorg-xextproto @7.0.5_0 (active) xorg-xf86bigfontproto @1.1.2_0 (active) xorg-xproto @7.0.15_0 (active) xorg-xtrans @1.2.3_0 (active) xrender @0.9.4_5 (active) zlib @1.2.3_2 (active)

[pst@USDA-3402-GenoMac, 10:42 AM ~/]

[pst@…]

Replying to pst@…:

Replying to blb@…:

I'm guessing you're running 10.5 if you're using Xcode 3.1.2...what is the result of running the following? $ port installed p5-tk perl5.8 tk $ otool -L /opt/local/lib/perl5/vendor_perl/5.8.9/darwin-thread-multi-2level/auto/Tk/Tk.bundle $ otool -L /opt/local/lib/libtk8.5.dylib

Here is the output:

I did find a TK.bundle in a different folder: [pst@USDA-3402-GenoMac, 01:08 PM ~/] otool -L /opt/local/lib/perl5/vendor_perl/5.8.9/darwin-2level/auto/Tk/Tk.bundle

/opt/local/lib/perl5/vendor_perl/5.8.9/darwin-2level/auto/Tk/Tk.bundle:

/opt/local/lib/libX11.6.dylib (compatibility version 9.0.0, current version 9.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4)

Is this in the wrong place? Any ideas? Thanks

[blb@…]

Ah, my perl5.8 port is installed with the +shared variant instead of the default like yours, so the paths to Tk.bundle (and other compiled bundles) will be different.

However, that led me to try something and I have found the problem, namely, that perlprimer appears to crash with a perl5.8 which isn't build with the +shared variant. This is unfortunate since ports can't currently cause another to be built with a variant like that (ticket #126). If you really want to get this working you'll need to uninstall all the p5-* ports, perlprimer, and perl5.8, then reinstall perl5.8 with +shared (sudo port install perl5.8 +shared), then finally install perlprimer again.

[pst@…]

Replying to blb@…:

Ah, my perl5.8 port is installed with the +shared variant instead of the default like yours, so the paths to Tk.bundle (and other compiled bundles) will be different.

However, that led me to try something and I have found the problem, namely, that perlprimer appears to crash with a perl5.8 which isn't build with the +shared variant. This is unfortunate since ports can't currently cause another to be built with a variant like that (ticket #126). If you really want to get this working you'll need to uninstall all the p5-* ports, perlprimer, and perl5.8, then reinstall perl5.8 with +shared (sudo port install perl5.8 +shared), then finally install perlprimer again.

That fixed it!! I uninstalled everything, installed perl5.8+shared, then perlprimer. MANY THANKS BLB for your help!!

Now, will the perl5.8+shared variant screw-up future installs of ports that need perl???

[pst@…]

I just noticed that copy and paste do not seem to be working in perlprimer nor does copy from another program allow pasting into perlprimer. Does it work for you? Paul

[blb@…]

Seems to work here, by using the 'Emulate three button mouse' X11 option (since my middle button is captured by the OS before it makes it to X11).

[pst@…]

I do have 'Emulate three button mouse' on. I tried various key combinations too. It is some X11 to Mac problem, not perlprimer. I can't even copy and paste from the X11 term into any mac program or from mac programs into X11. I even installed xclipboard, but that made no difference.

Thanks again for all of the help!! Paul

[blb@…]

Do you have ​Xquartz installed? I do and perhaps that helps with it...

[pst@…]

I just installed the dev tools 3.1.3 and that made no change. I then installed Xquartz and no change. I can only copy from X11 and paste back into X11, but not between X11 and Mac apps.