Hi all,

I've downloaded the latest 64bit linux Ugene (ugene-1.10.4-x86-full.tar.gz), unpacked it and when I tried to launch it I got the following errors:

Code:

$ ./ugene -ui /mnt/ris-fas1a/linux_users2/hzen/bin/software/ugene/ugene-1.10.4/ugeneui: /usr/lib64/libz.so.1: no version information available (required by /mnt/ris-fas1a/linux_users2/hzen/bin/software/ugene/ugene-1.10.4/libU2Core.so.1) /mnt/ris-fas1a/linux_users2/hzen/bin/software/ugene/ugene-1.10.4/ugeneui: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /mnt/ris-fas1a/linux_users2/hzen/bin/software/ugene/ugene-1.10.4/libU2Core.so.1) /mnt/ris-fas1a/linux_users2/hzen/bin/software/ugene/ugene-1.10.4/ugeneui: /lib64/libc.so.6: version `GLIBC_2.9' not found (required by /mnt/ris-fas1a/linux_users2/hzen/bin/software/ugene/ugene-1.10.4/libQtGui.so.4) /mnt/ris-fas1a/linux_users2/hzen/bin/software/ugene/ugene-1.10.4/ugeneui: /lib64/libc.so.6: version `GLIBC_2.9' not found (required by /mnt/ris-fas1a/linux_users2/hzen/bin/software/ugene/ugene-1.10.4/libQtCore.so.4)

Following are the information of the above lib64 files:


Code:

$ file /usr/lib64/libz.so.1 /usr/lib64/libz.so.1: symbolic link to `libz.so.1.2.3' $ file /usr/lib64/libstdc++.so.6 /usr/lib64/libstdc++.so.6: symbolic link to `libstdc++.so.6.0.8' $ file /lib64/libc.so.6 /lib64/libc.so.6: symbolic link to `libc-2.5.so'

I've tried to google around for these error but it is getting me nowhere.

I'm running scientific linux which is basically a redhat linux. And unfortunately I'm not exactly a linux guru either  :-[ Any help will be greatly appreciated. Thank you.

Rosz, could you tell us please what operating system you use? Probably, we know what is the problem, but we need to be sure.

I'm running scientific linux 5.4 which is based on redhat.

Thank you.

I have 16GB of RAM

Hi, Rosz.

Did you have an older version working? I ask you that because I had a similar problem in ubuntu, and the solution was to delete all the files in the previous version before extracting the new files to that folder.
So, if your working ugene is in
/mnt/ris-fas1a/linux_users2/hzen/bin/software/ugene/
Then try deleting everything in that folder and then extract the new files (directly to the ugene folder and not creating a subfolder like 'ugene-1.10.4').

Hello,

I'm having nearly the same problem.
The OS is CentOS 5.2 (redhat-based) with kernel 2.6.18.
I used ugene-1.11.0 and it is installed for the first time.

when I start ugene I get the following message:

Code:

$ ./ugene -ui /ugene-1.11.0/ugeneui: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /ugene-1.11.0/libU2Core.so.1) /ugene-1.11.0/ugeneui: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /ugene-1.11.0/libU2Core.so.1) /ugene-1.11.0/ugeneui: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /ugene-1.11.0/libU2Algorithm.so.1) /ugene-1.11.0/ugeneui: /lib64/libc.so.6: version `GLIBC_2.9' not found (required by /ugene-1.11.0/libQtGui.so.4) /ugene-1.11.0/ugeneui: /lib64/libc.so.6: version `GLIBC_2.11' not found (required by /ugene-1.11.0/libQtGui.so.4) /ugene-1.11.0/ugeneui: /lib64/libc.so.6: version `GLIBC_2.10' not found (required by /ugene-1.11.0/libQtNetwork.so.4) /ugene-1.11.0/ugeneui: /lib64/libc.so.6: version `GLIBC_2.9' not found (required by /ugene-1.11.0/libQtCore.so.4)

libstdc++:

Code:

$ strings /usr/lib64/libstdc++.so.6 | grep GLIBCXX GLIBCXX_3.4 GLIBCXX_3.4.1 GLIBCXX_3.4.2 GLIBCXX_3.4.3 GLIBCXX_3.4.4 GLIBCXX_3.4.5 GLIBCXX_3.4.6 GLIBCXX_3.4.7 GLIBCXX_3.4.8 GLIBCXX_FORCE_NEW

libc:

Code:

$ strings /lib64/libc.so.6  | grep GLIBC   GLIBC_2.2.5 GLIBC_2.2.6 GLIBC_2.3 GLIBC_2.3.2 GLIBC_2.3.3 GLIBC_2.3.4 GLIBC_2.4 GLIBC_2.5 GLIBC_PRIVATE

So the 'universal binary package' does not work.

So I compiled it on Ubuntu and copied it to CentOS 5.2 but it didn't work because of:

Code:

$ ./ugene -ui myUgene/ugeneui: error while loading shared libraries: myUgene/libU2Core.so.1: ELF file OS ABI invalid $ readelf -h libU2Core.so ELF Header:  Magic:   7f 45 4c 46 02 01 01 03 00 00 00 00 00 00 00 00  Class:                             ELF64  Data:                              2's complement, little endian  Version:                           1 (current)  OS/ABI:                            UNIX - Linux  ABI Version:                       0  Type:                              DYN (Shared object file)  Machine:                           Advanced Micro Devices X86-64  Version:                           0x1  Entry point address:               0x7f6c0  Start of program headers:          64 (bytes into file)  Start of section headers:          1930840 (bytes into file)  Flags:                             0x0  Size of this header:               64 (bytes)  Size of program headers:           56 (bytes)  Number of program headers:         7  Size of section headers:           64 (bytes)  Number of section headers:         31  Section header string table index: 28

maybe I could change the spec for the QT-Project to compile it for CentOS where I need OS/ABI: UNIX - System V instead of OS/ABI:UNIX - Linux.

any help would be appreciated.

I found a solution to compile ugene for CentOS 5.1:

Install CentOS 5.1 in a virtual machine i.e. virtualbox.

Start CentOS in virtualbox and install new Qt-dev packages [http ://joseph.freivald.com/linux/2010/02/25/qt-4-6-2-packages-for-centos-5-4/] (please remove the <space> after http, because I'm not allowed to post links):

Code:

$ rpm -ivh http ://software.freivald.com/centos/software.freivald.com-1.0.0-1.noarch.rpm $ export PATH=$PATH:/usr/lib64/qt4/bin/

Download, unpack, configure and compile ugene:

Code:

$ cd ~/ugene $ wget http ://ugene.unipro.ru/downloads/ugene-1.11.0.tar.gz $ tar xfv ugene-1.11.0.tar.gz $ cd ~/ugene/ugene-1.11.0 $ qmake CONFIG+=x64 -r $ make

Copy some Qt-libs to ~/ugene/ugene-1.11.0/src/_release
(libQtWebKit.so.4, libQtCore.so.4, libQtGui.so.4, libQtNetwork.so.4, libQtOpenGL.so.4, libQtScript.so.4, libQtSvg.so.4, libQtXmlPatterns.so.4, libQtXml.so.4)

Now you can use the folder _release and copy it to desired CentOS and start ugene...