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Old 01-06-2008, 08:55 PM   #16
jay73
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It looks to me as if GENtle is not satisfied to have the shared libs alone. It seems to want a full MySQL 4.1 too. Try this one:

http://rpm.pbone.net/index.php3/stat....i386.rpm.html

Maybe it will then complain that it also needs the 4.1MySQL-server package. It doesn't look like it but we'll see.

Last edited by jay73; 01-06-2008 at 08:58 PM.
 
Old 01-06-2008, 09:17 PM   #17
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Thanks, again, jay73!

Now, finally, the packages don't want to get along. When I 'rpm -ivh MySQL-client-4.1.21-0.i386.rpm', I get a whole page worth of 'conlict' messages like this:

'file /usr/bin/msql2mysql from install of MySQL-client-4.1.21-0.i386 conflicts with file from package mysql-5.0.45-6.fc8.i386'

Of course, I don't want to get rid of the version 5 package, right?

What do I do next? Thank you for any help!
 
Old 01-06-2008, 10:06 PM   #18
jay73
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Hmm, that was to be feared, it can't have both . You could install MySQL4 in an alternative location - in addition to MySQL5 - but that could get really messy. I think the most convenient option would be to uninstall MySQL5, go to the MySQL site and install version 4.1 (Linux x86 generic static version, Server, Client and libraries):
http://dev.mysql.com/downloads/mysql...x86-32bit-rpms
Of course, if you do need MySQL5, you are out of luck. But do you?

As pointed out before, this is just the sort of thing you are likely to run into when you run a bleeding edge distro like Fedora. It rapidly drops support for older packages because its objective is to be innovative more than anything else. If my solution does not work, you should consider installing a more conservative distro like CentOS 4. Much like Fedora, only more conservative. I see that the MySQL site has RedHat 4 specific rpms., by the way. Those will always work on CentOS 4, too, since the two are (nearly) identical. But you probably wouldn't need them at all as I expect that CentOS will have them in its repositories.

Last edited by jay73; 01-06-2008 at 10:33 PM.
 
Old 01-07-2008, 12:00 AM   #19
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And Thank you,again, jay73!

Wow, that is one stubborn program!

One of the few things I know already about Fedora is how cool 'yum' is. Since I could rely on yum to tell me which dependencies I might mess up before I give the final 'y' on removing something, I had no issues removing mysql 5.0. It did cost me only a few toy programs I never used anyhow.
Then, I installed
MySQL-client-4.1.22-0.i386.rpm,
MySQL-devel-4.1.22-0.i386.rpm and
MySQL-server-4.1.22-0.i386.rpm.

And now get this:

'$ ./GENtle
./GENtle: /usr/lib/libmysqlclient.so.14: version `MYSQL_4.1' not found (required by ./GENtle)'!!!!

My last hope is some weired message I got when installing the 'server' package:
'# rpm -ivh MySQL-server-4.1.22-0.i386.rpm
Preparing... ########################################### [100%]
1:MySQL-server ########################################### [100%]
080106 23:21:20 [Warning] Asked for 196608 thread stack, but got 126976
080106 23:21:20 [Warning] Asked for 196608 thread stack, but got 126976
PLEASE REMEMBER TO SET A PASSWORD FOR THE MySQL root USER !
To do so, start the server, then issue the following commands:
/usr/bin/mysqladmin -u root password 'new-password'
/usr/bin/mysqladmin -u root -h localhost.localdomain password 'new-password'
See the manual for more instructions.'

(I did not yet do that password thing, my computer is no server...)

Why does GENtle not see the MySQL_4.1?

Thanks some more for any help!
 
Old 01-07-2008, 02:35 AM   #20
jay73
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Yes, OK, your computer is not a server but if you want to use MySQL, you'll really need to run the server part as well. The client part comprises only applications that are used to access the database; the database itself is provided by the server. The only time that having just the client installed is when, say, your computer is in a network and it needs to contact a MySQL database that is running on an other computer.

I'm not saying that this is the root of your problem, though. In fact, it may be entirely unrelated. I did a quick look-up and it turns out that you're not the only one having issues with GENtle. I found an Ubuntu user who had the same problem. Unfortunately, no-one appears to have replied to that person yet ...

I would be surprised it it were a conflict of libraries since you installed the static version of mysql, which comes bundled with all that it needs. And since you get the same error message from two different versions of MySQL, it seems very likely that it is a bug in GENTle.

One potential pitfall with earlier versions of Fedora and MySQL was SELINUX. I don't think it is a problem any longer but who knows . Maybe you should try disabling Selinux, remove your MysQL packages, reboot and reinstall them. Do not forget to start your mysql-server as it doesn't start itself automatically (although it will keep running once it has been started as a service). When you have verified that MySQL is running properly, SELINUX should be re-enabled again. Still, my MySQL5 installed and started just fine with SELINUX enabled so I can't guarantee - at all - that it is going to help.
 
Old 01-08-2008, 12:16 AM   #21
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Thanks, jay73!

To quote my previous post: that is one stubborn program!

Golly!

I am tempted to report this thing as a bug at th GENtle home page (http://sourceforge.net/tracker/?atid...80&func=browse), even though I think this does not strictly fall under the bug reporting rules.

Oh yeah, and I will do a very serious search for a similar software, even though I have little hope, after all: it took me forever to find this.

Short of installing a whole new operating system: what else remains there to do?

Thanks, again, and please let me know if you have any new suggestions.
 
Old 01-08-2008, 01:32 AM   #22
jay73
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OK, here are two more things that could come in handy. The ldd command will show what shared libraries are required by a program. When I run ldd GENtle/GENtle (you have to run it on the binary file), I get:
Quote:
linux-gate.so.1 => (0xffffe000)
libwx_gtk2u_xrc-2.6.so.0 => /usr/lib/libwx_gtk2u_xrc-2.6.so.0 (0xf7f4a000)
libwx_gtk2u_qa-2.6.so.0 => /usr/lib/libwx_gtk2u_qa-2.6.so.0 (0xf7f2a000)
libwx_gtk2u_html-2.6.so.0 => /usr/lib/libwx_gtk2u_html-2.6.so.0 (0xf7e9d000)
libwx_gtk2u_adv-2.6.so.0 => /usr/lib/libwx_gtk2u_adv-2.6.so.0 (0xf7dfc000)
libwx_gtk2u_core-2.6.so.0 => /usr/lib/libwx_gtk2u_core-2.6.so.0 (0xf7b0d000)
libwx_baseu_xml-2.6.so.0 => /usr/lib/libwx_baseu_xml-2.6.so.0 (0xf7b03000)
libwx_baseu_net-2.6.so.0 => /usr/lib/libwx_baseu_net-2.6.so.0 (0xf7ad6000)
libwx_baseu-2.6.so.0 => /usr/lib/libwx_baseu-2.6.so.0 (0xf79a0000)
libsqlite.so.0 => not found
libsqlite3.so.0 => /usr/lib/libsqlite3.so.0 (0xf7935000)
libmysqlclient.so.14 => not found
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x03d3e000)
libm.so.6 => /lib/libm.so.6 (0x00cb5000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00805000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00ce0000)
libc.so.6 => /lib/libc.so.6 (0x00b53000)
libz.so.1 => /lib/libz.so.1 (0x00cfb000)
libdl.so.2 => /lib/libdl.so.2 (0x00cae000)
libgtk-x11-2.0.so.0 => /usr/lib/libgtk-x11-2.0.so.0 (0x03fe1000)
libgdk-x11-2.0.so.0 => /usr/lib/libgdk-x11-2.0.so.0 (0x00643000)
libatk-1.0.so.0 => /usr/lib/libatk-1.0.so.0 (0x00709000)
libgdk_pixbuf-2.0.so.0 => /usr/lib/libgdk_pixbuf-2.0.so.0 (0x00318000)
libpango-1.0.so.0 => /usr/lib/libpango-1.0.so.0 (0x00600000)
libgobject-2.0.so.0 => /lib/libgobject-2.0.so.0 (0x00564000)
libgmodule-2.0.so.0 => /lib/libgmodule-2.0.so.0 (0x005b4000)
libgthread-2.0.so.0 => /lib/libgthread-2.0.so.0 (0x00727000)
librt.so.1 => /lib/librt.so.1 (0x00acf000)
libglib-2.0.so.0 => /lib/libglib-2.0.so.0 (0x00482000)
libXinerama.so.1 => /usr/lib/libXinerama.so.1 (0x005a6000)
libpng12.so.0 => /usr/lib/libpng12.so.0 (0x008af000)
libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x03242000)
libtiff.so.3 => /usr/lib/libtiff.so.3 (0xf78d9000)
libSDL-1.2.so.0 => /usr/lib/libSDL-1.2.so.0 (0xf783b000)
libexpat.so.1 => /lib/libexpat.so.1 (0x00952000)
/lib/ld-linux.so.2 (0x00b34000)
libpangocairo-1.0.so.0 => /usr/lib/libpangocairo-1.0.so.0 (0x006fd000)
libX11.so.6 => /usr/lib/libX11.so.6 (0x00350000)
libXcomposite.so.1 => /usr/lib/libXcomposite.so.1 (0x00337000)
libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x005ba000)
libcairo.so.2 => /usr/lib/libcairo.so.2 (0x00813000)
libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0x00903000)
libXext.so.6 => /usr/lib/libXext.so.6 (0x00470000)
libXrender.so.1 => /usr/lib/libXrender.so.1 (0x0054e000)
libXi.so.6 => /usr/lib/libXi.so.6 (0x00559000)
libXrandr.so.2 => /usr/lib/libXrandr.so.2 (0x005ab000)
libXcursor.so.1 => /usr/lib/libXcursor.so.1 (0x005c1000)
libpulse-simple.so.0 => /usr/lib/libpulse-simple.so.0 (0xf7834000)
libpulse.so.0 => /usr/lib/libpulse.so.0 (0xf77eb000)
libpangoft2-1.0.so.0 => /usr/lib/libpangoft2-1.0.so.0 (0x005cd000)
libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0x00759000)
libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x0046c000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0x0044e000)
libXau.so.6 => /usr/lib/libXau.so.6 (0x00d70000)
libcap.so.1 => /lib/libcap.so.1 (0xf77e6000)
libSM.so.6 => /usr/lib/libSM.so.6 (0x009e2000)
libICE.so.6 => /usr/lib/libICE.so.6 (0x009ed000)
libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00d75000)
The left column lists every shared library that is "required" by the program, the right one lists the library on your system that will fill that requirement. If you see "not available", it means that your system is missing the shared library in question. In this case, the output shows that only libsqlite.so.0 and mysqlclient14 are missing from my system - but you already knew that Fedora doesn't have these out of the box.
Maybe your should run ldd on your GENTle to find out whether something is wrong. Maybe your freshly installed libmysqlclient.so is simply not getting picked up. Such things can happen (although they rarely do in my experience). If so, try running ldconfig on the mysql package (ldconfig /usr/bin/mysql or /usr/shared/mysql or something like that - it depends on where mysql got installed to).

If that still doesn't do it, then I'm afraid that the only option left is to put on your hacker's hat and go hunting through the code for any bugs.

Last edited by jay73; 01-08-2008 at 01:44 AM.
 
Old 01-08-2008, 02:24 AM   #23
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Thanks, again, jay73,

And hunters greetings!

After I treated my computer to ldconfig on mysql and even a re-boot,

GENtle listed no packages missing -- ooh, yeah: except for its little introductory complaint :-)

'ldd GENtle/GENtle
GENtle/GENtle: /usr/lib/libmysqlclient.so.14: version `MYSQL_4.1' not found (required by GENtle/GENtle)
linux-gate.so.1 => (0x00110000)
libwx_gtk2u_xrc-2.6.so.0 => /usr/lib/libwx_gtk2u_xrc-2.6.so.0 (0x00bde000)
libwx_gtk2u_qa-2.6.so.0 => /usr/lib/libwx_gtk2u_qa-2.6.so.0 (0x00c68000)
libwx_gtk2u_html-2.6.so.0 => /usr/lib/libwx_gtk2u_html-2.6.so.0 (0x00111000)
libwx_gtk2u_adv-2.6.so.0 => /usr/lib/libwx_gtk2u_adv-2.6.so.0 (0x020a0000)
libwx_gtk2u_core-2.6.so.0 => /usr/lib/libwx_gtk2u_core-2.6.so.0 (0x06664000)
libwx_baseu_xml-2.6.so.0 => /usr/lib/libwx_baseu_xml-2.6.so.0 (0x00921000)
libwx_baseu_net-2.6.so.0 => /usr/lib/libwx_baseu_net-2.6.so.0 (0x00d9b000)
libwx_baseu-2.6.so.0 => /usr/lib/libwx_baseu-2.6.so.0 (0x002ac000)
libsqlite.so.0 => /usr/lib/libsqlite.so.0 (0x001a3000)
libsqlite3.so.0 => /usr/lib/libsqlite3.so.0 (0x001ef000)
libmysqlclient.so.14 => /usr/lib/libmysqlclient.so.14 (0x00408000)
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x0098d000)
libm.so.6 => /lib/libm.so.6 (0x00565000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00847000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00597000)
libc.so.6 => /lib/libc.so.6 (0x005b0000)
libz.so.1 => /lib/libz.so.1 (0x0025a000)
libdl.so.2 => /lib/libdl.so.2 (0x00590000)
libgtk-x11-2.0.so.0 => /usr/lib/libgtk-x11-2.0.so.0 (0x06184000)
libgdk-x11-2.0.so.0 => /usr/lib/libgdk-x11-2.0.so.0 (0x060e0000)
libatk-1.0.so.0 => /usr/lib/libatk-1.0.so.0 (0x00b2c000)
libgdk_pixbuf-2.0.so.0 => /usr/lib/libgdk_pixbuf-2.0.so.0 (0x00b4a000)
libpango-1.0.so.0 => /usr/lib/libpango-1.0.so.0 (0x00ae9000)
libgobject-2.0.so.0 => /lib/libgobject-2.0.so.0 (0x00a7a000)
libgmodule-2.0.so.0 => /lib/libgmodule-2.0.so.0 (0x00855000)
libgthread-2.0.so.0 => /lib/libgthread-2.0.so.0 (0x0085b000)
librt.so.1 => /lib/librt.so.1 (0x00982000)
libglib-2.0.so.0 => /lib/libglib-2.0.so.0 (0x07209000)
libXinerama.so.1 => /usr/lib/libXinerama.so.1 (0x00826000)
libpng12.so.0 => /usr/lib/libpng12.so.0 (0x007b7000)
libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x00953000)
libtiff.so.3 => /usr/lib/libtiff.so.3 (0x04001000)
libSDL-1.2.so.0 => /usr/lib/libSDL-1.2.so.0 (0x02000000)
libexpat.so.1 => /lib/libexpat.so.1 (0x00794000)
libcrypt.so.1 => /lib/libcrypt.so.1 (0x03f60000)
libnsl.so.1 => /lib/libnsl.so.1 (0x00d1d000)
libnss_files.so.2 => /lib/libnss_files.so.2 (0x00876000)
libnss_dns.so.2 => /lib/libnss_dns.so.2 (0x0026d000)
libresolv.so.2 => /lib/libresolv.so.2 (0x00273000)
/lib/ld-linux.so.2 (0x003eb000)
libpangocairo-1.0.so.0 => /usr/lib/libpangocairo-1.0.so.0 (0x00862000)
libX11.so.6 => /usr/lib/libX11.so.6 (0x00dc9000)
libXcomposite.so.1 => /usr/lib/libXcomposite.so.1 (0x00101000)
libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x00834000)
libcairo.so.2 => /usr/lib/libcairo.so.2 (0x076de000)
libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0x007df000)
libXext.so.6 => /usr/lib/libXext.so.6 (0x00287000)
libXrender.so.1 => /usr/lib/libXrender.so.1 (0x00810000)
libXi.so.6 => /usr/lib/libXi.so.6 (0x0081b000)
libXrandr.so.2 => /usr/lib/libXrandr.so.2 (0x0082b000)
libXcursor.so.1 => /usr/lib/libXcursor.so.1 (0x0083b000)
libpulse-simple.so.0 => /usr/lib/libpulse-simple.so.0 (0x00bd8000)
libpulse.so.0 => /usr/lib/libpulse.so.0 (0x0088c000)
libpangoft2-1.0.so.0 => /usr/lib/libpangoft2-1.0.so.0 (0x008e7000)
libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0x00c89000)
libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x00297000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00549000)
libXau.so.6 => /usr/lib/libXau.so.6 (0x00299000)
libcap.so.1 => /lib/libcap.so.1 (0x00d4d000)
libSM.so.6 => /usr/lib/libSM.so.6 (0x00977000)
libICE.so.6 => /usr/lib/libICE.so.6 (0x00937000)
libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x0029c000)'


I checked, and I know I have libmysqlclient.so.14. Thus I am afraid you are right and I need to look at GENtle as my main suspect. Just please don't hold your breath, that will take me a while, I first have to learn how to do that and what I might be looking at, before I might get a clue what I will be looking for. Give me some study time.

The good news is that even if I will have to go to the common facility and use commercial software to deal with my molecular biology problems, for now, I sure learned a lot about linux!

Thanks!

P.S.:
I just did see something weired: my yum command finds any random package I ask for from that list above, EXCEPT libmysqlclient.so.14, which I found by listing the content of usr/lib/. There is no '.' in front of the name, so I don't think it's a hidden file. But somehow it might be invisible to my programs. Hmmmm?
 
Old 01-08-2008, 02:55 AM   #24
jay73
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As long as the package was installed in rpm format, it should have been registered by the rpm package manager (yum is essentially just a font-end to rpm). However, yum is not very refined. It often fails see the contents of a package in detail. If you ask me, that's just what is happening . The most straightforward way of settling this questions is ldd again. Just run ldd /usr/bin/mysql and check whether it lists libmysqlclient. If it does, it is really there and it is functional.
 
Old 01-12-2008, 08:46 PM   #25
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Sorry, I did not answer so long, my weeks are crazy.

I tried ldd, and (of course) I have libmysqlclient.so.14, also 10, 12 and 15.
I finally decided to cave in, i.e. I will run GENtle under Windows in a virtual box, let's see whether I can make that work.

Thanks, again for all your help, even if I can't run GENtle in Fedora, I sure learned a lot about my system. THANKS!
 
Old 01-16-2008, 02:20 PM   #26
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Yup, under windows I have the program running.
Too bad I had to cheat and can't pull it off under Fedora, but at least I can use the program.


MANY THANKS again to everybody who answered any of my questions!!!!
 
  


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