[Samtools-help] compile help

[James LaGasse]

Hello,



Linux newbie here attempting to compile Samtools on 32 bit Debian system.



When I use make, I got many lines indicating compilation was proceeding
smoothly, then it halted with:



gcc -g -Wall -O2 -I. -Ihtslib-1.4 -c -o bam_tview_curses.o
bam_tview_curses.c

bam_tview_curses.c:41:20: fatal error: curses.h: No such file or directory

#include <curses.h>

^

compilation terminated.

Makefile:133: recipe for target 'bam_tview_curses.o' failed

make: *** [bam_tview_curses.o] Error 1



How do I install curses? From what I can tell (from the Synaptic Package
Manager) curses in all its flavors is installed. How can I check further?
Where is curses.h supposed to be?



Thanks for any clues you can throw my way,



-Jim LaGasse

[Peter Cock]

Hi James,

Debian splits libraries into two packages, libXXX and libXXX-dev
(RedHat does the same but would typically append -devel not -dev).
The development package include the headers (*.h files) etc which
are only needed if compiling code to use the library.

In this case from memory I would try:

sudo apt-get install libncurses-dev

Peter

Post by James LaGasse
Hello,
Linux newbie here attempting to compile Samtools on 32 bit Debian system.
When I use make, I got many lines indicating compilation was proceeding
gcc -g -Wall -O2 -I. -Ihtslib-1.4 -c -o bam_tview_curses.o
bam_tview_curses.c
bam_tview_curses.c:41:20: fatal error: curses.h: No such file or directory
#include <curses.h>
^
compilation terminated.
Makefile:133: recipe for target 'bam_tview_curses.o' failed
make: *** [bam_tview_curses.o] Error 1
How do I install curses? From what I can tell (from the Synaptic Package
Manager) curses in all its flavors is installed. How can I check further?
Where is curses.h supposed to be?
Thanks for any clues you can throw my way,
-Jim LaGasse
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[James LaGasse]

Thanks Peter, that was a big help. Got through the curses problem, then applied the same tactic when it complained that it was missing bzlib.h (apt-get install libghc-bzlib-dev), and with no additional errors I was rewarded with a 2.7 MB executable called samtools.


-----Original Message-----
From: Peter Cock [mailto:***@googlemail.com]
Sent: Thursday, April 6, 2017 2:27 PM
To: James LaGasse <***@soundpharma.com>
Cc: samtools-***@lists.sourceforge.net
Subject: Re: [Samtools-help] compile help

Hi James,

Debian splits libraries into two packages, libXXX and libXXX-dev (RedHat does the same but would typically append -devel not -dev).
The development package include the headers (*.h files) etc which are only needed if compiling code to use the library.

In this case from memory I would try:

sudo apt-get install libncurses-dev

Peter

Post by James LaGasse
Hello,
Linux newbie here attempting to compile Samtools on 32 bit Debian system.
When I use make, I got many lines indicating compilation was
gcc -g -Wall -O2 -I. -Ihtslib-1.4 -c -o bam_tview_curses.o
bam_tview_curses.c
bam_tview_curses.c:41:20: fatal error: curses.h: No such file or directory
#include <curses.h>
^
compilation terminated.
Makefile:133: recipe for target 'bam_tview_curses.o' failed
make: *** [bam_tview_curses.o] Error 1
How do I install curses? From what I can tell (from the Synaptic Package
Manager) curses in all its flavors is installed. How can I check further?
Where is curses.h supposed to be?
Thanks for any clues you can throw my way,
-Jim LaGasse
----------------------------------------------------------------------
-------- Check out the vibrant tech community on one of the world's
most engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Samtools-help mailing list
https://lists.sourceforge.net/lists/listinfo/samtools-help

[Marcel Martin]

Post by James LaGasse
How do I install curses? From what I can tell (from the Synaptic
Package Manager) curses in all its flavors is installed. How can I
check further? Where is curses.h supposed to be?

It seems to be part of "libncurses-dev" (which seems to be an alias for
"libncurses5-dev").

Depending on your use case, perhaps you may want to consider miniconda
or anaconda. Then you could install a current samtools (or thousands of
other packages) with a single command from the "bioconda" channel, see
<https://bioconda.github.io/>.

Regards,
Marcel