samtools compiling issues on Solaris 11

[BmoreHawk]

Hi all,

I'm quite new to the field and I'm having issues compiling samtools 0.1.19 from source. I'm using a SunOs Solaris 11 platform and this is the message displayed .... (I have installed zlib 1.2.3 and GNU ncurses 5.9 as indicated in the INSTALL file)...

am2bcf_indel.c: In function ‘bcf_call_gap_prep’:
bam2bcf_indel.c:408:3: warning: implicit declaration of function ‘alloca’
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
bam_tview_curses.c:7:2: warning: #warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
In file included from bam_tview.h:11:0,
from bam_tview_curses.c:19:
faidx.h:76:50: error: expected ‘;’, ‘,’ or ‘)’ before ‘register’
bam_tview_curses.c:287:2: warning: #warning "No curses library is available; tview with curses is disabled."
*** Error code 1
make: Fatal error: Command failed for target `bam_tview_curses.o'
Current working directory /home/username/samtools/samtools-0.1.19
*** Error code 1
The following command caused the error:
target=`echo all-recur | sed s/-recur//`; \
wdir=`pwd`; \
list='. bcftools misc'; for subdir in $list; do \
cd $subdir; \
make CC="gcc" DFLAGS="-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1" CFLAGS="-g -Wall -O2" \
INCLUDES="-I." LIBPATH="" $target || exit 1; \
cd $wdir; \
done;
make: Fatal error: Command failed for target `all-recur'


I tried to make clean and modify the Makefile as follows

`-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
comment out the line starting with `LIBCURSES='. as suggested in the INSTALL file

but I still get an error...

does anyone have an idea on what is going wrong ?

[GenoMax]

Have you tried appending the LD_LIBRARY_PATH variable with paths for ncurses and zlib?

[swbarnes2]

Random suggestion; at the suggestion of another informatics guy at my work, I altered the samtools Makefile so that it read

LIBCURSES=	-lncurses

And that made it work for me. So maybe a small tweak to that line of the Makefile will fix your problem.

[sridhar28]

Hi,
I face same problem as mentioned. i am installing samtools version0.19 .
The Error i am getting is
warning: #warning "No curses library is available; tview with curses is disabled."
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_tview_html.c -o bam_tview_html.o
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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lncurses -lm -lz -lpthread
phase.o: In function `loadpos':
/illumina/data/galaxy/apps/samtools/phase.c:475: undefined reference to `gzopen64'
bedcov.o: In function `main_bedcov':
/illumina/data/galaxy/apps/samtools/bedcov.c:69: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `__bam_get_lines':
/illumina/data/galaxy/apps/samtools/bam_import.c:76: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `sam_open':
/illumina/data/galaxy/apps/samtools/bam_import.c:472: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `sam_header_read2':
/illumina/data/galaxy/apps/samtools/bam_import.c:126: undefined reference to `gzopen64'
libbam.a(bedidx.o):/illumina/data/galaxy/apps/samtools/bedidx.c:107: more undefined references to `gzopen64' follow
collect2: ld returned 1 exit status
make[1]: *** [samtools] Error 1
make[1]: Leaving directory `/illumina/data/galaxy/apps/samtools'
make: *** [all-recur] Error 1

Even i tried to change "LIBCURSES= -lncurses" and try make. but again i am getting same error

please suggest..

Thanks
Sridhar

[GenoMax]

Hi,
I face same problem as mentioned. i am installing samtools version0.19 .
The Error i am getting is
warning: #warning "No curses library is available; tview with curses is disabled."
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_tview_html.c -o bam_tview_html.o
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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lncurses -lm -lz -lpthread
phase.o: In function `loadpos':
/illumina/data/galaxy/apps/samtools/phase.c:475: undefined reference to `gzopen64'
bedcov.o: In function `main_bedcov':
/illumina/data/galaxy/apps/samtools/bedcov.c:69: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `__bam_get_lines':
/illumina/data/galaxy/apps/samtools/bam_import.c:76: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `sam_open':
/illumina/data/galaxy/apps/samtools/bam_import.c:472: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `sam_header_read2':
/illumina/data/galaxy/apps/samtools/bam_import.c:126: undefined reference to `gzopen64'
libbam.a(bedidx.o):/illumina/data/galaxy/apps/samtools/bedidx.c:107: more undefined references to `gzopen64' follow
collect2: ld returned 1 exit status
make[1]: *** [samtools] Error 1
make[1]: Leaving directory `/illumina/data/galaxy/apps/samtools'
make: *** [all-recur] Error 1

Even i tried to change "LIBCURSES= -lncurses" and try make. but again i am getting same error

please suggest..

Thanks
Sridhar

Have you installed the Zlib and NCURSES libraries?

[sridhar28]

Hi geno,

Thank you for the reply.

I dint install those library.. could you please tell how to install it??

Thanks
Sridhar

[GenoMax]

Hi geno,

Thank you for the reply.

I dint install those library.. could you please tell how to install it??

Thanks
Sridhar

I am rusty on solaris so there may be other ways to get this:

http://zlib.net/

http://ftp.gnu.org/pub/gnu/ncurses/

Sunfreeware site: http://www.sunfreeware.com/source-list.html

[sridhar28]

Hi Geno,

Thanks for the links..

i am using redhat linux system..
after installing again i am facing same errors.. any thoughts??

samtools binary will be created only after installing the libraries??