SAMTool install error about curses

[NicolaLosito]

On an Ubuntu box all you will need is:

sudo apt-get install libncurses5 libncurses5-dev

to solve the missing curses.h file not found error

[kausikmhg]

do yum install ncurses-devel , i hpe it will solve th issue

recommended for Centos , RHEL

Same problem faced and solved
Kausik Bhattacharyya
Delhi University

[dakl]

Not sure this is the appropriate thread for this problem.

Anyhow, it looks like you're missing zlib. Did you try installing zlib-devel. If you're on RedHat/Fedora/CentOS, try

sudo yum install zlib-devel

//D

[ngadewal]

I am getting following error while installing samtools
The update version of zlib and ncurses are installed.
I tried to look posts but cold not find answer to "bgzf error"

*********************************************************************************
make[1]: Entering directory `/root/samtools-0.1.18'
make[2]: Entering directory `/root/samtools-0.1.18'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
In file included from bgzf.c:36:
bgzf.h:29:18: error: zlib.h: No such file or directory
bgzf.c: In function ‘open_write’:
bgzf.c:186: error: ‘Z_DEFAULT_COMPRESSION’ undeclared (first use in this function)
bgzf.c:186: error: (Each undeclared identifier is reported only once
bgzf.c:186: error: for each function it appears in.)
bgzf.c: In function ‘deflate_block’:
bgzf.c:297: error: ‘z_stream’ undeclared (first use in this function)
bgzf.c:297: error: expected ‘;’ before ‘zs’
bgzf.c:298: error: ‘zs’ undeclared (first use in this function)
bgzf.c:305: warning: implicit declaration of function ‘deflateInit2’
bgzf.c:305: error: ‘Z_DEFLATED’ undeclared (first use in this function)
bgzf.c:306: error: ‘Z_DEFAULT_STRATEGY’ undeclared (first use in this function)
bgzf.c:307: error: ‘Z_OK’ undeclared (first use in this function)
bgzf.c:311: warning: implicit declaration of function ‘deflate’
bgzf.c:311: error: ‘Z_FINISH’ undeclared (first use in this function)
bgzf.c:312: error: ‘Z_STREAM_END’ undeclared (first use in this function)
bgzf.c:313: warning: implicit declaration of function ‘deflateEnd’
bgzf.c:345: warning: implicit declaration of function ‘crc32’
bgzf.c: In function ‘inflate_block’:
bgzf.c:371: error: ‘z_stream’ undeclared (first use in this function)
bgzf.c:371: error: expected ‘;’ before ‘zs’
bgzf.c:373: error: ‘zs’ undeclared (first use in this function)
bgzf.c:380: warning: implicit declaration of function ‘inflateInit2’
bgzf.c:381: error: ‘Z_OK’ undeclared (first use in this function)
bgzf.c:385: warning: implicit declaration of function ‘inflate’
bgzf.c:385: error: ‘Z_FINISH’ undeclared (first use in this function)
bgzf.c:386: error: ‘Z_STREAM_END’ undeclared (first use in this function)
bgzf.c:387: warning: implicit declaration of function ‘inflateEnd’
bgzf.c: In function ‘check_header’:
bgzf.c:405: error: ‘Z_DEFLATED’ undeclared (first use in this function)
make[2]: *** [bgzf.o] Error 1
make[2]: Leaving directory `/root/samtools-0.1.18'
make[1]: *** [lib-recur] Error 1
make[1]: Leaving directory `/root/samtools-0.1.18'
make: *** [all-recur] Error 1
*****************************************************************************

Please help
-Nikhil

[dakl]

I had to install ncurses-devel to make this work. I also changed the Makefile as suggested above.

cheers
Daniel

[satoshi936]

thank you, RockChalkJayhawk. I had a same problem and your answer solved the problem.

Open SUSE 11.3
samtools 0.1.18
=======================================
$ pwd
/opt/utillities/samtools/samtools-0.1.18
$ vi Makefile
- change a line in "Makefile" as follows
-------------------------------------------------
original: LIBCURSES= -lcurses # -lXCurses
changed: LIBCURSES= -lncurses # -lXCurses
--------------------------------------------------
$ make
- compile worked well
========================================

[chaz81]

Thanks RCJ, just found your post and had been struggling with that!

[RockChalkJayhawk]

Problem Solved

I ran into this problem as well. To get around it, change the makefile from

LIBCURSES= -lcurses

to

LIBCURSES= -lncurses

That should fix the problem.

[RockChalkJayhawk]

Hi all,
When I install SAMTool 0.1.8 on linux, I got error: cannot find -lcurses
collect2: ld returned 1 exit status
But I have libncurses.so installed under /usr/lib.
After run rpm -qa | grep ncurses, I got:
ncurses-devel-5.5-18.11
ncurses-5.5-18.11
yast2-ncurses-2.13.68-0.3
ncurses-devel-32bit-5.5-18.11
ncurses-32bit-5.5-18.11
It seemed I've installed dependencies.
Did I miss something? Thanks.

Did you get this problem fixed?

[xinwu]

Hi all,
When I install SAMTool 0.1.8 on linux, I got error: cannot find -lcurses
collect2: ld returned 1 exit status
But I have libncurses.so installed under /usr/lib.
After run rpm -qa | grep ncurses, I got:
ncurses-devel-5.5-18.11
ncurses-5.5-18.11
yast2-ncurses-2.13.68-0.3
ncurses-devel-32bit-5.5-18.11
ncurses-32bit-5.5-18.11
It seemed I've installed dependencies.
Did I miss something? Thanks.