Error When Install Samtools, Version `Zlib_1.2.3.3` Not Found
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8.6 years ago
wm ▴ 540

samtools info: samtools-0.1.19 when I run the samtools, it comes out this error. I've installed zlib and ncurses before compile samtools.

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.

  1. system info: CentOS 6.3

    $head -n 1 /etc/issue CentOS release 6.3 (Final) $uname -a Linux bilijunlab 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 reported for the first time to compile

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 #
  1. 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
samtools linux • 8.3k views
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1
Entering edit mode

Thanks, Under the help of GenoMax, I fix the errors.

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/.

replace the "/lib64/libz.so.1.2.3" by "/usr/local/bin/libz.so.1.2.8".

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0
Entering edit mode

Worked for me too. I have put libz.so.1.2.8 file in "/usr/local/bin/". Although " -D_CURSES_LIB=1" was not there in my file, i have put " -D_CURSES_LIB=0" in line 4 of Makefile

EDIT: I tried changing the symbolic links of libz files. While doing so, I lost all the functionalities including SUDO. Whole system halted. Please never do this.

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Entering edit mode
8.6 years ago
cts ★ 1.7k

It may be that your LD_LIBRARY_PATH environmental variable is not set to include the directory containing zlib. Looks like zlib is installed in /lib64/ so try:

$ export LD_LIBRARY_PATH="/lib64/:$LD_LIBRARY_PATH"
$ samtools

and see if the error persists

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0
Entering edit mode

Sorry, the error still there.

I also tried to create a softlink of zlib to /lib64/, it does not work.

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