Bug 70271 - [new port] biology/finchtv a DNA sequence trace viewer
Summary: [new port] biology/finchtv a DNA sequence trace viewer
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: Normal Affects Only Me
Assignee: Thierry Thomas
URL:
Keywords:
Depends on:
Blocks:
 
Reported: 2004-08-10 19:30 UTC by Fernan Aguero
Modified: 2005-03-11 21:17 UTC (History)
0 users

See Also:


Attachments
finchtv.shar (2.89 KB, text/plain)
2004-08-10 19:30 UTC, Fernan Aguero
no flags Details
Makefile (860 bytes, text/plain; charset=us-ascii)
2004-10-15 21:18 UTC, Fernan Aguero
no flags Details
distinfo (99 bytes, text/plain; charset=us-ascii)
2004-10-15 21:18 UTC, Fernan Aguero
no flags Details
finchtv.shar (12.02 KB, text/plain; charset=us-ascii)
2005-03-10 15:04 UTC, Fernan Aguero
no flags Details
finchtv.shar (12.44 KB, application/x-shar)
2005-03-10 20:34 UTC, Thierry Thomas
no flags Details
finchtv.shar (11.97 KB, text/plain; charset=us-ascii)
2005-03-10 22:58 UTC, Fernan Aguero
no flags Details

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Description Fernan Aguero 2004-08-10 19:30:26 UTC
	
	It is a linux binary, it's running fine for me. It comes with
	three DNA sequence trace files (chromatograms) that anyone can
	open to test the program.
Comment 1 Fernan Aguero 2004-10-15 21:18:24 UTC
This PR is getting old!

The attached Makefile and distinfo files bring FinchTV to
1.2.0

Fernan

-- 
Fernan Aguero -  fernan at iib.unsam.edu.ar
Phone: +54 11 4580-7255/7 ext 310, Fax: +54 11 4752-9639
Check http://genoma.unsam.edu.ar/~fernan for more info.
Comment 2 Thierry Thomas freebsd_committer freebsd_triage 2005-02-21 22:26:19 UTC
State Changed
From-To: open->feedback


It seems that this program requires emulators/linux_base-rh-9 
and it depends on several libraries: 

ldd finchtv 
finchtv: 
finchtv: /usr/lib/libstdc++.so.5: version `GLIBCPP_3.2.2' not found (required by finchtv) 
libXft.so.2 => /usr/X11R6/lib/libXft.so.2 (0x285d8000) 
libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0x285ec000) 
libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0x2864d000) 
libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x28672000) 
libexpat.so.0 => /usr/lib/libexpat.so.0 (0x28724000) 
libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x28744000) 
libz.so.1 => /usr/lib/libz.so.1 (0x28797000) 
libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x287a6000) 
libXrender.so.1 => /usr/X11R6/lib/libXrender.so.1 (0x287bc000) 
libXrandr.so.2 => /usr/X11R6/lib/libXrandr.so.2 (0x287c4000) 
libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x287c8000) 
libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x287d1000) 
libdl.so.2 => /lib/libdl.so.2 (0x287e9000) 
libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x287ed000) 
libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x287fc000) 
libm.so.6 => /lib/libm.so.6 (0x288f8000) 
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x28919000) 
libc.so.6 => /lib/libc.so.6 (0x28921000) 
/lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x285c2000) 

Could you please precise its dependencies? 



Comment 3 Thierry Thomas freebsd_committer freebsd_triage 2005-02-21 22:26:19 UTC
Responsible Changed
From-To: freebsd-ports-bugs->thierry


Take it.
Comment 4 Fernan Aguero 2005-03-10 15:04:43 UTC
+----[ Thierry Thomas <thierry@FreeBSD.org> (21.Feb.2005 19:33):
|
| It seems that this program requires emulators/linux_base-rh-9
| and it depends on several libraries:
| 
| ldd finchtv
| finchtv:
| finchtv: /usr/lib/libstdc++.so.5: version `GLIBCPP_3.2.2' not found (required by finchtv)
| 	libXft.so.2 => /usr/X11R6/lib/libXft.so.2 (0x285d8000)

	... [rest of list snipped ]

| Could you please precise its dependencies?
|
+----]

Thierry, the program is distributed as a static binary, all
libraries are included. What happened with version 1.2.0 is
that the authors forgot to include some library, which produced the
error message that you mention above (GLIBCPP_3.2.2 not
found). This was not the case for 1.1.0 (the one originally
submitted in this PR, and is not the case for 1.3.0, the
version I am submitting now in this followup.)

The program is working for me using linux_base-8-8.0_4.
Please test and let me know if something else needs to be
fixed. 

Fernan

PS: see attached shar archive containing 1.3.0
Comment 5 Thierry Thomas freebsd_committer freebsd_triage 2005-03-10 20:34:51 UTC
Le Jeu 10 mar 05 à 16:04:43 +0100, Fernan Aguero <fernan@iib.unsam.edu.ar>
 écrivait :
> Thierry, the program is distributed as a static binary, all
> libraries are included. What happened with version 1.2.0 is
> that the authors forgot to include some library, which produced the
> error message that you mention above (GLIBCPP_3.2.2 not
> found). This was not the case for 1.1.0 (the one originally
> submitted in this PR, and is not the case for 1.3.0, the
> version I am submitting now in this followup.)


OK. Thanks for the follow-up.

> The program is working for me using linux_base-8-8.0_4.
> Please test and let me know if something else needs to be
> fixed. 


Unfortunately, it does not run on my machines (tested on FreeBSD-5.3 and
FreeBSD-4.11), both of them running linux_base-8-8.0_6: it eats CPU
cycles, and nothing appears.

Here is the output of a truss session:

$ truss finchtv
settimeofday(0xbfbff8b0,0x1)			 ERR#1 'Operation not permitted'
open("ÄøÿÃU",0x8696920,00)		 ERR#2 'No such file or directory'
read(0x84b33a1,0x2,0xbfbffa40)			 ERR#9 'Bad file descriptor'
close(2)					 = 0 (0x0)
write(9,0x0,-1077937512)			 ERR#9 'Bad file descriptor'
write(9,0x0,-1077937512)			 ERR#9 'Bad file descriptor'
write(9,0x0,-1077937512)			 ERR#9 'Bad file descriptor'
write(9,0x0,-1077937512)			 ERR#9 'Bad file descriptor'
write(9,0x0,-1077937512)			 ERR#9 'Bad file descriptor'
...

and then there is an infinite loop with these 'write'.

Since I was here, I have made some minor modifications (pkg-message and
pkg-plist), please see the attached shar file.

Regards,
-- 
Th. Thomas.
Comment 6 Fernan Aguero 2005-03-10 22:58:13 UTC
+----[ Thierry Thomas <thierry@FreeBSD.org> (10.Mar.2005 17:39):
|
| > The program is working for me using linux_base-8-8.0_4.
| > Please test and let me know if something else needs to be
| > fixed. 
| 
| Unfortunately, it does not run on my machines (tested on FreeBSD-5.3 and
| FreeBSD-4.11), both of them running linux_base-8-8.0_6: it eats CPU
| cycles, and nothing appears.

[ truss output snipped ]

OK, yes I see the same behaviour with the binary that gets
installed by the port (I should have tested this one before
submitting). However, the binary that is in the
distfile works fine after brandelf. Maybe the problem is
with the stripping? This is the only difference I see
between the two files. 

I have corrected the port to install the binary without
stripping and the installed executable works fine for me.

Please test, but I think that it is ready to be committed
this time!

| Since I was here, I have made some minor modifications (pkg-message and
| pkg-plist), please see the attached shar file.

OK, thanks.

| 
| Regards,
| -- 
| Th. Thomas.
|
+----]
Comment 7 Thierry Thomas freebsd_committer freebsd_triage 2005-03-11 21:16:39 UTC
State Changed
From-To: feedback->closed


New port added, thanks!