[Samtools-help] Problem installing samtools-0.1.7a on Solaris 10.

[Royden C. <ra...@vi...>]

Greetings.

When trying to install samtools-0.1.7a  on a Solaris 10 box I ran into  
the following error:

gcc -g -Wall -O2 -o samtools bam_tview.o bam_maqcns.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 -lm  -lcurses -lz -L. -lbam
Undefined                       first referenced
  symbol                             in file
socket                              ./libbam.a(knetfile.o)
setsockopt                          ./libbam.a(knetfile.o)
connect                             ./libbam.a(knetfile.o)
getaddrinfo                         ./libbam.a(knetfile.o)
freeaddrinfo                        ./libbam.a(knetfile.o)
ld: fatal: Symbol referencing errors. No output written to samtools
collect2: ld returned 1 exit status
*** Error code 1
make: Fatal error: Command failed for target `samtools'
Current working directory /root/downloads/samtools-0.1.7a
*** Error code 1
The following command caused the error:
target=`echo all-recur | sed s/-recur//`; \
         wdir=`pwd`; \
         list='. misc'; for subdir in $list; do \
                 cd $subdir; \
                 make CC="gcc" DFLAGS="-D_FILE_OFFSET_BITS=64 - 
D_USE_KNETFILE -D_CURSES_LIB=1" CFLAGS="-g -Wall -O2" \
                         INCLUDES="" LIBPATH="" $target || exit 1; \
                 cd $wdir; \
         done;
make: Fatal error: Command failed for target `all-recur'


I modified the Makefile
as follows
From
samtools:lib $(AOBJS)
                 $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $ 
(LIBCURSES) -lz -L. -lbam

to
samtools:lib $(AOBJS)
                 $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $ 
(LIBCURSES) -lz -L. -lbam -lsocket

And was able to get past this error..I hope this doesnt break any  
functionality.

Thank you
Royden Clark