[wolfpack14]

When it comes to running packages like samtools, bedtools or any other kind of bioinformatics solution on a Windows box, you're better off getting VMWare and installing Ubuntu. Trying to compile things from source with Cygwin is asking for trouble.

[seqie]

there are installation instructions in the file "INSTALL":
The text-based viewer (tview) requires the GNU ncurses library
<http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and most of
the modern Linux/Unix distributions. If you do not have this library installed,
you can still compile the rest of SAMtools by manually changing:
`-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
comment out the line starting with `LIBCURSES='.

Worked for me (Ubuntu 12.04)

[NicolaLosito]

CFLAGS should be on the second line of the make file (Makefile)...

Makefile should be modified like this ...
CFLAGS= -g -Wall -O2 -I/usr/include/ncurses

On an Ubuntu box if you install the libncurses5 and libncurses5-dev the -I parameter is useless…

[Philcolson]

Thanks, NRP! I'll pass that onto anyone having a similar problem!

[NRP]

I was having the same problem running make in Ubuntu 12.04 lts, with errors resulting from problems with both zlib and curses. Ultimately the solution was to do this:

sudo apt-get update
sudo apt-get install zlib1g-dev libncurses5-dev
sudo make clean
sudo make

[Philcolson]

Figured it out! I put in, from somewhere I found online, the -Dexpl=exp -Dlogl=log line in DFLAGS. Got rid of that and it worked! Thanks!

[Philcolson]

I don't quite know what's important, so there's all of it.

[Philcolson]

phil@phil:~/Desktop/samtools-0.1.18$ make
make[1]: Entering directory `/home/phil/Desktop/samtools-0.1.18'
make[2]: Entering directory `/home/phil/Desktop/samtools-0.1.18'
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bgzf.c -o bgzf.o
bgzf.c: In function ‘bgzf_close’:
bgzf.c:630:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. kstring.c -o kstring.o
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_aux.c -o bam_aux.o
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam.c -o bam.o
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_import.c -o bam_import.o
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. sam.c -o sam.o
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_index.c -o bam_index.o
bam_index.c: In function ‘bam_index_load_core’:
bam_index.c:330:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:337:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:350:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:353:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:357:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:361:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:371:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:375:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_pileup.c -o bam_pileup.o
bam_pileup.c: In function ‘resolve_cigar2’:
bam_pileup.c:75:9: warning: variable ‘is_head’ set but not used [-Wunused-but-set-variable]
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_md.c -o bam_md.o
In file included from /usr/include/math.h:146:0,
from bam_md.c:5:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:101:1: error: conflicting types for ‘exp’
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:110:1: error: conflicting types for ‘log’
make[2]: *** [bam_md.o] Error 1
make[2]: Leaving directory `/home/phil/Desktop/samtools-0.1.18'
make[1]: *** [lib-recur] Error 1
make[1]: Leaving directory `/home/phil/Desktop/samtools-0.1.18'
make: *** [all-recur] Error 1

[Richard Finney]

Is the conflicting types a warning or an error ?
Can you display the full message?

If it's just a warning, don't worry about it.

[Philcolson]

If anyone has solved the error: conflicting types for 'exp' or the equivalent for 'log', I'd be incredibly grateful.

[dalia12]

daliya

I'm also using cygwin and followed the advices above (changed the Makefile, installed ncurses, zlib), but still got the error:

bgzf.h:29:18: 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 functio n)
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: parse error before "zs"
bgzf.c:298: error: `zs' undeclared (first use in this function)
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: error: `Z_FINISH' undeclared (first use in this function)
bgzf.c:312: error: `Z_STREAM_END' undeclared (first use in this function)
bgzf.c: In function `inflate_block':
bgzf.c:371: error: `z_stream' undeclared (first use in this function)
bgzf.c:371: error: parse error before "zs"
bgzf.c:373: error: `zs' undeclared (first use in this function)
bgzf.c:381: error: `Z_OK' undeclared (first use in this function)
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: In function `check_header':
bgzf.c:405: error: `Z_DEFLATED' undeclared (first use in this function)
Makefile:22: recipe for target `bgzf.o' failed
make[2]: *** [bgzf.o] Error 1
make[2]: Leaving directory `/samtools-0.1.18'
Makefile:25: recipe for target `lib-recur' failed
make[1]: *** [lib-recur] Error 1
make[1]: Leaving directory `/samtools-0.1.18'
Makefile:25: recipe for target `all-recur' failed
make: *** [all-recur] Error 1

I installed everything with the name zlib, but cannot get further

[pag]

may have solved this one
sudo ln -s /lib/x86_64-linux-gnu/libncurses.so.5 /lib/x86_64-linux-gnu/libncurses.so

CFLAGS= -g -Wall -O2 -I/usr/include/ncurses #-m64 #-arch ppc
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
LIBCURSES= -lncurses # -lXCurses


I also installed libcurses-perl and zlib-bin via ubuntu software center prior to getting this to work

note that
$ make test
make: *** No rule to make target `test'. Stop.
$ make check
make: *** No rule to make target `check'. Stop.
$ make install
make: *** No rule to make target `install'. Stop.

so, just the "make" itself is enough to install it?

[pag]

I followed this advice, but I get
In file included from /usr/include/math.h:146:0,
from bam_md.c:5:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:101:1: error: conflicting types for ‘exp’
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:110:1: error: conflicting types for ‘log’

Linux *** 3.2.0-26-generic-tuxonice #41~ppa3-Ubuntu SMP Wed Jul 11 19:04:21 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

[snakesgun]

I find another solution of this problem. Before compiling samtools, we can fix the 16th line of Makefile like this"LIBCURSES= -lncurses # -lXCurses". P.S. My operating system is openSUSE.

[Brian E]

I had a similar problem with getting samtools to work on Cygwin, only my error was:

bam_tview.c:5:20: fatal error: curses.h: No such file or directory

The fix was modifying the makefiles as Richard Finney suggested.
Thanks Richard.