Bug 93053
| Summary: | sync update of biology/emboss && biology/embassy | ||||||||||||||
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| Product: | Ports & Packages | Reporter: | Fernan Aguero <fernan> | ||||||||||||
| Component: | Individual Port(s) | Assignee: | Thierry Thomas <thierry> | ||||||||||||
| Status: | Closed FIXED | ||||||||||||||
| Severity: | Affects Only Me | ||||||||||||||
| Priority: | Normal | ||||||||||||||
| Version: | Latest | ||||||||||||||
| Hardware: | Any | ||||||||||||||
| OS: | Any | ||||||||||||||
| Attachments: |
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Description
Fernan Aguero
2006-02-08 19:10:08 UTC
Hello Fernan, These ports have been updated since your intial submission, and your patches don't install cleanly any more; could you please update them? Best regards, -- Th. Thomas. +----[ Thierry Thomas <thierry@FreeBSD.org> (16.Mar.2006 18:27): | | Hello Fernan, | | These ports have been updated since your intial submission, and your | patches don't install cleanly any more; could you please update them? | +----] Thierry, yes, the libtool upgrade was the reason of the update. Attached is a new diff against the current emboss port. AFAICS the embassy port was not affected, so the original embassy.diff file should be OK. Let me know if it's not. Thanks, fernan State Changed From-To: open->feedback Thanks for your update. There is a problem with the default config file, still included in plist user $PREFIX/etc: ===> Building package for emboss-3.0.0 tar: etc/emboss.default.sample: Cannot stat: No such file or directory pkg_create: make_dist: tar command failed with code 256 Responsible Changed From-To: freebsd-ports-bugs->thierry Take it. On Mon 20 mar 06 at 17:32:02 +0100, Fernan Aguero <fernan@iib.unsam.edu.ar> wrote: > Sorry about that. Attached is a new diff, Are you running the latest libtool? Emboss installs .la files - and this is normal - but they are not listed in its plist: === Checking filesystem state list of extra files and directories in / (not present before this port was installed but present after it was deinstalled) 291316 4 -rwxr-xr-x 1 root wheel 800 Mar 20 21:11 usr/local/lib/libplplot.la 291363 4 -rwxr-xr-x 1 root wheel 786 Mar 20 21:11 usr/local/lib/libajax.la 291378 4 -rwxr-xr-x 1 root wheel 793 Mar 20 21:11 usr/local/lib/libajaxg.la 291657 4 -rwxr-xr-x 1 root wheel 807 Mar 20 21:11 usr/local/lib/libnucleus.la ================================================================ build ended at Mon Mar 20 21:18:51 UTC 2006 Regards, -- Th. Thomas. +----[ Thierry Thomas <thierry@FreeBSD.org> (20.Mar.2006 18:27): | | > Sorry about that. Attached is a new diff, | | Are you running the latest libtool? Emboss installs .la files - and this | is normal - but they are not listed in its plist: | | === Checking filesystem state | list of extra files and directories in / (not present before this port was installed but present after it was deinstalled) | 291316 4 -rwxr-xr-x 1 root wheel 800 Mar 20 21:11 usr/local/lib/libplplot.la | 291363 4 -rwxr-xr-x 1 root wheel 786 Mar 20 21:11 usr/local/lib/libajax.la | 291378 4 -rwxr-xr-x 1 root wheel 793 Mar 20 21:11 usr/local/lib/libajaxg.la | 291657 4 -rwxr-xr-x 1 root wheel 807 Mar 20 21:11 usr/local/lib/libnucleus.la | ================================================================ | build ended at Mon Mar 20 21:18:51 UTC 2006 | +----] OK, sorry for the delay. I think it should be OK now. Attached is the patch (only for EMBOSS, the patch for biology/embassy already includes .la files in the pkg-plist. Fernan +----[ To Thierry Thomas <fernan@iib.unsam.edu.ar> (28.Mar.2006 16:50): | | OK, sorry for the delay. I think it should be OK now. | | Attached is the patch (only for EMBOSS, the patch for | biology/embassy already includes .la files in the pkg-plist. | | Fernan | +----] Aaarrrghhh ... disregard the last diff, for some reason I forgot to add a couple of essential lines. The correct one is attached (emboss_again.2.diff). I hope this would be the final patch. This has been the most convoluted update I have done in a long time! Sorry for the confusion. Feel free to contact me if you have any questions. Thanks, Fernan On Tue 28 mar 06 at 23:43:40 +0200, Fernan Aguero <fernan@iib.unsam.edu.ar> wrote: > +----[ To Thierry Thomas <fernan@iib.unsam.edu.ar> (28.Mar.2006 16:50): > | > | OK, sorry for the delay. I think it should be OK now. > | > | Attached is the patch (only for EMBOSS, the patch for > | biology/embassy already includes .la files in the pkg-plist. Hello, Embassy depends on /usr/local/include/ajax.h, but it does not find it; then it tries to reinstall emboss one more time and aborts: ===> Patching for embassy-3.0.0 ===> embassy-3.0.0 depends on file: /usr/local/include/ajax.h - not found ===> Verifying install for /usr/local/include/ajax.h in /usr/ports/biology/emboss => EMBOSS-3.0.0.tar.gz doesn't seem to exist in /tmp/distfiles/emboss. => Attempting to fetch from file:///distcache/emboss/. fetch: file:///distcache/emboss/EMBOSS-3.0.0.tar.gz: No such file or directory => Attempting to fetch from ftp://emboss.open-bio.org/pub/EMBOSS/. EMBOSS-3.0.0.tar.gz 15 MB 153 kBps ===> Extracting for emboss-3.0.0 ... ===> Installing for emboss-3.0.0 ===> emboss-3.0.0 depends on shared library: gd.4 - found ===> emboss-3.0.0 depends on shared library: png.5 - found ===> emboss-3.0.0 depends on shared library: Xm.3 - found ===> emboss-3.0.0 depends on shared library: X11.6 - found ===> Generating temporary packing list ===> Checking if biology/emboss already installed ===> emboss-3.0.0 is already installed You may wish to ``make deinstall'' and install this port again by ``make reinstall'' to upgrade it properly. If you really wish to overwrite the old port of biology/emboss without deleting it first, set the variable "FORCE_PKG_REGISTER" in your environment or the "make install" command line. *** Error code 1 Stop in /a/ports/biology/emboss. *** Error code 1 Stop in /a/ports/biology/emboss. *** Error code 1 Stop in /a/ports/biology/embassy. *** Error code 1 Stop in /a/ports/biology/embassy. I suppose that ajax.h should be checked in ${LOCALBASE}/emboss/include but I prefer you to check it. Regards, -- Th. Thomas. On Thu 30 mar 06 at 18:41:28 +0200, Fernan Aguero <fernan@iib.unsam.edu.ar> wrote: > actually, now that look more carefully, something isn't quite > right (I can't make any sense of it). In each Makefile, I > set PREFIX to ${LOCALBASE}/emboss, if it is not already > defined by the user: > > PREFIX?= ${LOCALBASE}/emboss > > then I check ajax.h in PREFIX > > BUILD_DEPENDS= ${PREFIX}/include/ajax.h:${PORTSDIR}/biology/emboss > > which at first sight should do what I intended it to do. > > However, when I do test builds, I build and install ports in > a special PREFIX, so I do set PREFIX manually each time. In > this particular case, I tested both emboss and embassy like > this: > > make install PREFIX=/home/fernan/freebsd/ports/emboss.tmp > > after installation all executables, libraries, etc are > in the expected place (i.e. under emboss.tmp). > However, when I build embassy apps, ajax.h is not looked for > in /home/fernan/freebsd/ports/emboss.tmp/include but in > ${LOCALBASE}/emboss/include. This is what I don't > understand, since PREFIX was defined, it should never be set > to ${LOCALBASE}/emboss. > > Do you have any clue about this? Actually, this is my mistake: I had replaced BUILD_DEPENDS= ${PREFIX}/include/ajax.h:${PORTSDIR}/biology/emboss by BUILD_DEPENDS= ${LOCALBASE}/include/ajax.h:${PORTSDIR}/biology/emboss at the first glance, and then I had forgotten about it... But the problem is that you cannot depend on something installed in ${PREFIX}, because ${PREFIX} is relative to the to-be-installed port. The correct line would be: BUILD_DEPENDS= ${LOCALBASE}/emboss/include/ajax.h:${PORTSDIR}/biology/emboss but we might have a simpler solution: since embassy already depends on emboss through LIB_DEPENDS= nucleus.3:${PORTSDIR}/biology/emboss you could remove this BUILD_DEPENDS line, could'nt you? Regards, -- Th. Thomas. On Thu 30 mar 06 at 21:20:02 +0200, Fernan Aguero <fernan@iib.unsam.edu.ar> wrote: > OK. So can you commit the embassy port removing the > BUILD_DEPENDS line? Or do you want me to submit a revised > diff? Sorry, but embassy cannot be packaged when built with default options: ===> Building package for embassy-3.0.0 tar: %%PLIST_SIM4%%bin/esim4: Cannot stat: No such file or directory tar: %%PLIST_SIM4%%share/EMBOSS/acd/esim4.acd: Cannot stat: No such file or directory pkg_create: make_dist: tar command failed with code 256 Creating package /tmp/packages/All/embassy-3.0.0.tbz Registering depends: emboss-3.0.0 open-motif-2.2.3_2 xorg-libraries-6.9.0 gd-2.0.33_4,1 fontconfig-2.3.2_3,1 imake-6.9.0 jpeg-6b_4 libdrm-2.0_1 libiconv-1.9.2_2 expat-2.0.0_1 perl-5.8.8 freetype2-2.1.10_3 png-1.2.8_3 pkgconfig-0.20. Creating bzip'd tar ball in '/tmp/packages/All/embassy-3.0.0.tbz' *** Error code 1 Stop in /a/ports/biology/embassy. *** Error code 1 Stop in /a/ports/biology/embassy. `make -V PLIST_SUB' does not know PLIST_SIM4, but PLIST_ESIM4. Should I replace PLIST_SIM4 by PLIST_ESIM4? -- Th. Thomas. State Changed From-To: feedback->closed Here we are ;-) Committed, thanks! |
