Error for samtools, `ZLIB_1.2.3.3` not found

[bakerwm]

That's version 1.2.3, which is < 1.2.3.3.

Thanks, the error was fixed when I replaced the 1.2.3 version by 1.2.8.

[bakerwm]

Looks like your executable is correctly linked (same libraries as I see).

Are there files in your /usr/local/lib? On my server that directory is empty. I wonder if there are duplicate copies of "libz.*" there.

Oh, Yeah, It's done, Samtools works. Thanks GenoMax for the help.

Here are what I did last night:
1. Replace " -D_CURSES_LIB=1" by " -D_CURSES_LIB=0" in line 4 of Makefile

2. Comment out "#LIBCURSES= -lcurses # -lXCurses" in Makefile.

3. I do have duplicate of "libz*" in /usr/local/lib/. And then replace the "/lib64/libz.so.1.2.3" by "/usr/local/bin/libz.so.1.2.8". Keep the /lib64/lib and /usr/local/lib/ directory like this.

$ls -l /usr/local/lib/libz*
-rw-r--r-- 1 root root 126318 Dec 18 12:47 /usr/local/lib/libz.a
lrwxrwxrwx 1 root root     13 Dec 18 12:47 /usr/local/lib/libz.so.1 -> libz.so.1.2.8
-rwxr-xr-x 1 root root  99184 Dec 18 12:47 /usr/local/lib/libz.so.1.2.8
$ls -l  /lib64/libz*
lrwxrwxrwx 1 root root    13 Dec 19 09:42 /lib64/libz.so.1 -> libz.so.1.2.8
-rwxr-xr-x 1 root root 99184 Dec 19 09:41 /lib64/libz.so.1.2.8

[bakerwm]

Looks like your executable is correctly linked (same libraries as I see).

Are there files in your /usr/local/lib? On my server that directory is empty. I wonder if there are duplicate copies of "libz.*" there.

thanks so much ,i will try your suggestion and report how is going?

[GenoMax]

Looks like your executable is correctly linked (same libraries as I see).

Are there files in your /usr/local/lib? On my server that directory is empty. I wonder if there are duplicate copies of "libz.*" there.

[bakerwm]

Samtools is working for me (albeit on RH 6.5 which is probably not fully identical to CentOS).

Can you try to use only your mod #2 (i.e. do not use #1) along with commenting the LIBCURSES line out?

Post the output of

$ ldd samtools

#2 + commenting LIBCURSES line, error reported as following when "make"

make[1]: *** [samtools] Error 1
make[1]: Leaving directory `/home/wangming/Documents/samtools-0.1.19'
make: *** [all-recur] Error 1

at least using #2 and “-L/usr/local/lib" of #1, then compile is OK.

$ldd samtools
./samtools: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by ./samtools)
        linux-vdso.so.1 =>  (0x00007fffd0ef8000)
        libm.so.6 => /lib64/libm.so.6 (0x0000003b1a400000)
        libz.so.1 => /lib64/libz.so.1 (0x0000003547000000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003b1ac00000)
        libc.so.6 => /lib64/libc.so.6 (0x0000003b1a000000)
        /lib64/ld-linux-x86-64.so.2 (0x0000003b19c00000)

[GenoMax]

Samtools is working for me (albeit on RH 6.5 which is probably not fully identical to CentOS).

Can you try to use only your mod #2 (i.e. do not use #1) along with commenting the LIBCURSES line out?

Post the output of

$ ldd samtools

[bakerwm]

I was able to compile on RedHat 6.5 by doing the following.

Keep your #2 modification.

Comment out "#LIBCURSES= -lcurses # -lXCurses" in Makefile.

"ncurses" library files are in /lib64 in my case. I also have libz.so.1.2.3.

I did comment out "LIBCURSES= -lcurses # -lXCurses", and keep #1 & #2 modifications together.
compile is OK, but still report the error:

$./samtools 
./samtools: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by ./samtools)

[bakerwm]

That's version 1.2.3, which is < 1.2.3.3.

Sorry, I cannot fix this error/ the libz is already the latest version.

[GenoMax]

I was able to compile on RedHat 6.5 by doing the following.

Keep your #2 modification.

Comment out "#LIBCURSES= -lcurses # -lXCurses" in Makefile.

"ncurses" library files are in /lib64 in my case. I also have libz.so.1.2.3.

[dpryan]

That's version 1.2.3, which is < 1.2.3.3.

[bakerwm]

Yes, here are the content in /lib64/

$ll /lib64/libz*
lrwxrwxrwx 1 root root    13 Dec 17 23:39 /lib64/libz.so.1 -> libz.so.1.2.3
-rwxrwxrwx 1 root root 91096 Feb 22  2013 /lib64/libz.so.1.2.3

[GenoMax]

Do you have /lib64/libz.so.1? Is that readable by "all"?

[bakerwm]

If you do not have "zlib" installed then you would need to install that but if you do have zlib installed then it may be just be a matter of creating a soft-link for the library in /lib64:

Make sure zlib is installed

$ rpm -qa | grep zlib

Create the softlink (adjust names/paths according to your system)

$ ln -s /lib64/libz.so.1 /usr/lib/libz.so.1

Unfortunately, the problem still there.

$rpm -qa |grep zlib
zlib-devel-1.2.3-29.el6.x86_64
zlib-1.2.3-29.el6.x86_64

$file /usr/lib/libz.so.1    
/usr/lib/libz.so.1: symbolic link to `/lib64/libz.so.1' 

$./samtools 
./samtools: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by ./samtools)

[GenoMax]

If you do not have "zlib" installed then you would need to install that but if you do have zlib installed then it may be just be a matter of creating a soft-link for the library in /lib64:

Make sure zlib is installed

$ rpm -qa | grep zlib

Create the softlink (adjust names/paths according to your system)

$ ln -s /lib64/libz.so.1 /usr/lib/libz.so.1

[bakerwm]

Error:

 $./samtools: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by ./samtools)

I've install zlib and ncurses at first.
=========================
Thanks GenoMax for the help, samtools on my server is working.

Here are what I did.
1. Replace " -D_CURSES_LIB=1" by " -D_CURSES_LIB=0" in line 4 of Makefile
2. Comment out "#LIBCURSES= -lcurses # -lXCurses" in Makefile.
3. Delete the duplicate of "libz*" in /usr/local/lib/.

I replace the "/lib64/libz.so.1.2.3" by "/usr/local/bin/libz.so.1.2.8". Then result of /lib64/lib and /usr/local/lib/ directory like this:

$ls -l /usr/local/lib/libz*
-rw-r--r-- 1 root root 126318 Dec 18 12:47 /usr/local/lib/libz.a
lrwxrwxrwx 1 root root     13 Dec 18 12:47 /usr/local/lib/libz.so.1 -> libz.so.1.2.8
-rwxr-xr-x 1 root root  99184 Dec 18 12:47 /usr/local/lib/libz.so.1.2.8
$ls -l  /lib64/libz*
lrwxrwxrwx 1 root root    13 Dec 19 09:42 /lib64/libz.so.1 -> libz.so.1.2.8
-rwxr-xr-x 1 root root 99184 Dec 19 09:41 /lib64/libz.so.1.2.8

=========================


system info: CentOS 6.3

$head -n 1 /etc/issue CentOS release 6.3 (Final) 
$uname -a Linux ***** 2.6.32-279.19.1.el6.x86_64 #1 SMP Wed Dec 19 07:05:20 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

when I download samtools source file "samtools-0.1.19.tar.bz2" from sourceforge.net. The following errors were reported for the first time to compile samtools.

Error 1:

$make
....
collect2: ld returned 1 exit status
make[1]: *** [samtools] Error 1
make[1]: Leaving directory `/home/wangming/Documents/samtools-0.1.19'
make: *** [all-recur] Error 1

According to suggestions from online searches. It can be compiled finally after a few changes to the file "Makefile"

1. Add the "-L/usr/local/lib -I/usr/include/ncurses" to end of line-2 of Makefile under directory of /samtools-0.1.19.
before:

CFLAGS=     -g -Wall -O2

after:

CFLAGS=         -g -Wall -O2  -L/usr/local/lib -I/usr/include/ncurses #

2. change the "-D_CURSES_LIB=1" to "-D_CURSES_LIB=0" in the line-4
before

DFLAGS=        -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1

after

DFLAGS=        -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0