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Old 01-04-2013, 05:50 AM   #1
ihelbig
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Location: Kiel, Germany

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Default samtools installation error "cannot find -lcurses"

Dear all,
I am trying to install samtools on OpenSuse and I have already added quite a few development packages that were required. However, it still gives me an error message because of "cannot find -lcurses"

Does anyone know what that means?

This is the entire error message

ih@kkkad007:~/samtools-0.1.18> make
make[1]: Entering directory `/home/ih/samtools-0.1.18'
make[2]: Entering directory `/home/ih/samtools-0.1.18'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/home/ih/samtools-0.1.18'
make[2]: Entering directory `/home/ih/samtools-0.1.18/bcftools'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/home/ih/samtools-0.1.18/bcftools'
make[2]: Entering directory `/home/ih/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/home/ih/samtools-0.1.18/misc'
gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
/usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lcurses
collect2: error: ld returned 1 exit status
make[1]: *** [samtools] Error 1
make[1]: Leaving directory `/home/ih/samtools-0.1.18'
make: *** [all-recur] Error 1
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Old 01-04-2013, 06:38 AM   #2
GenoMax
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You are missing the "ncurses" (and perhaps ncurses-devel) library. You can install it using your package manager.
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Old 01-04-2013, 07:29 AM   #3
maubp
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In general, the compiler message missing -lxxx means the library xxx is missing. In this case, ncurses.

In most Linux distributions libraries like this are split in two, the run time and development packages. This is done for space efficiency - if you're just using pre-compiled code, you don't need all the development files as well. The packages are normally called something like xxx and either xxx-dev or xxx-devel depending on the Linux distribution. (The naming can be more complicated, perhaps libxxx and either libxxx-dev or libxxx-devel in some cases, or with a version number in the name as well).

As GenoMax wrote, for OpenSuse you'll want "ncurses" and "ncurses-devel".
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Old 01-04-2013, 10:00 AM   #4
swbarnes2
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Yeah, on my system I had the same problem. Someone suggested I change that line in the Makefile to 'use lncurses' or something like that, and now it works.
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Old 01-04-2013, 11:02 AM   #5
ihelbig
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Location: Kiel, Germany

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Thank you for the answer. Through some other help page, I had received a similar idea. I just added a "n" in the Makefile to change lcurses to lncurses and then the installation worked.

Ingo
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Old 02-01-2013, 12:48 PM   #6
ECO
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On Ubuntu 11.10, this is from installing the package "libncurses5" with apt-get:

sudo apt-get install libncurses5

...getting there.
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