Makefile - samtools installation failed

Question

I'm trying to install samtools on openSUSE, I did this:

cd htslib-1.2.1
./configure
make install

Worked fine.

bcftools-1.2
./configure
make install

Worked fine.

And for samtools:

cd samtools-1.2
make install

Produces this output:

    /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libcurses.so when searching for -lcurses
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lcurses
collect2: error: ld returned 1 exit status
Makefile:125: recipe for target 'samtools' failed
make: *** [samtools] Error 1

I can't figure out why this won't work. I know how make tool work, but I'm newbie in linuxOS.

    # Makefile for samtools, utilities for the Sequence Alignment/Map format.
#
#    Copyright (C) 2008-2014 Genome Research Ltd.
#    Portions copyright (C) 2010-2012 Broad Institute.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.

CC       = gcc
CPPFLAGS = $(DFLAGS) $(INCLUDES)
CFLAGS   = -g -Wall -O2
LDFLAGS  =
LDLIBS   =
DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
            sam_header.o bam_plbuf.o
AOBJS=      bam_index.o bam_plcmd.o sam_view.o \
            bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o \
            bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
            bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
            cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \
            faidx.o stats.o stats_isize.o bam_flags.o bam_split.o \
            bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o
INCLUDES=   -I. -I$(HTSDIR)
LIBCURSES=  -lcurses # -lXCurses

prefix      = /usr/local
exec_prefix = $(prefix)
bindir      = $(exec_prefix)/bin
mandir      = $(prefix)/share/man
man1dir     = $(mandir)/man1

MKDIR_P = mkdir -p
INSTALL = install -p
INSTALL_PROGRAM = $(INSTALL)
INSTALL_DATA    = $(INSTALL) -m 644
INSTALL_DIR     = $(MKDIR_P) -m 755


PROGRAMS = samtools

BUILT_MISC_PROGRAMS = \
    misc/ace2sam misc/maq2sam-long misc/maq2sam-short \
    misc/md5fa misc/md5sum-lite misc/wgsim

MISC_PROGRAMS = \
    $(BUILT_MISC_PROGRAMS) \
    misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
    misc/interpolate_sam.pl misc/novo2sam.pl \
    misc/plot-bamstats misc/psl2sam.pl \
    misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl \
    misc/soap2sam.pl \
    misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl

BUILT_TEST_PROGRAMS = \
    test/merge/test_bam_translate \
    test/merge/test_pretty_header \
    test/merge/test_rtrans_build \
    test/merge/test_trans_tbl_init \
    test/split/test_count_rg \
    test/split/test_expand_format_string \
    test/split/test_filter_header_rg \
    test/split/test_parse_args \
    test/vcf-miniview

all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS)


# Adjust $(HTSDIR) to point to your top-level htslib directory
HTSDIR = htslib-1.2.1
include $(HTSDIR)/htslib.mk
HTSLIB = $(HTSDIR)/libhts.a
BGZIP  = $(HTSDIR)/bgzip


PACKAGE_VERSION = 1.2

# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git
# description of the working tree: either a release tag with the same value
# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag.
# $(shell), :=, etc are GNU Make-specific.  If you don't have GNU Make,
# comment out this conditional.
ifneq "$(wildcard .git)" ""
PACKAGE_VERSION := $(shell git describe --always --dirty)

# Force version.h to be remade if $(PACKAGE_VERSION) has changed.
version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force))
endif

# If you don't have GNU Make but are building from a Git repository, you may
# wish to replace this with a rule that always rebuilds version.h:
# version.h: force
#   echo '#define SAMTOOLS_VERSION "`git describe --always --dirty`"' > $@
version.h:
    echo '#define SAMTOOLS_VERSION "$(PACKAGE_VERSION)"' > $@


.SUFFIXES: .c .o

.c.o:
    $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $<


lib:libbam.a

libbam.a:$(LOBJS)
    $(AR) -csru $@ $(LOBJS)

samtools: $(AOBJS) libbam.a $(HTSLIB)
    $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz

bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h
bam_lpileup_h = bam_lpileup.h $(htslib_sam_h)
bam_plbuf_h = bam_plbuf.h $(htslib_sam_h)
bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h)
sam_h = sam.h $(htslib_sam_h) $(bam_h)
sample_h = sample.h $(HTSDIR)/htslib/kstring.h

bam.o: bam.c $(bam_h) sam_header.h
bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h
bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h
bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h
bam_aux.o: bam_aux.c
bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h)
bam_color.o: bam_color.c $(bam_h)
bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h
bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h
bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h
bam_mate.o: bam_mate.c $(bam_h)
bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kprobaln.h
bam_pileup.o: bam_pileup.c $(sam_h)
bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)
bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h)
bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h)
bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h
bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h
bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h)
bam_stat.o: bam_stat.c $(bam_h) samtools.h
bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h)
bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h)
bam_tview_html.o: bam_tview_html.c $(bam_tview_h)
bam_flags.o: bam_flags.c $(sam_h)
bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h
bamtk.o: bamtk.c $(htslib_hts_h) version.h samtools.h
bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h
bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h
cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h)
errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h
kprobaln.o: kprobaln.c kprobaln.h
padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h)
phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h
sam.o: sam.c $(htslib_faidx_h) $(sam_h)
sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h
sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h
sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h
stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h
stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h)


# test programs

# For tests that might use it, set $REF_PATH explicitly to use only reference
# areas within the test suite (or set it to ':' to use no reference areas).
# (regression.sh sets $REF_PATH to a subdirectory itself.)
check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS)
    REF_PATH=: test/test.pl --exec bgzip=$(BGZIP)
    test/merge/test_bam_translate test/merge/test_bam_translate.tmp
    test/merge/test_pretty_header
    test/merge/test_rtrans_build
    test/merge/test_trans_tbl_init
    cd test/mpileup && ./regression.sh
    test/split/test_count_rg
    test/split/test_expand_format_string
    test/split/test_filter_header_rg
    test/split/test_parse_args


test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB)
    $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) -lz

test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB)
    $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz

test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB)
    $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz

test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB)
    $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz

test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB)
    $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz

test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB)
    $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) -lz

test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB)
    $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz

test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB)
    $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) -lz

test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)
    $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz

test_test_h = test/test.h $(htslib_sam_h)

test/merge/test_bam_translate.o: test/merge/test_bam_translate.c $(test_test_h) bam_sort.o
test/merge/test_pretty_header.o: test/merge/test_pretty_header.c bam_sort.o
test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c bam_sort.o
test/merge/test_trans_tbl_init.o: test/merge/test_trans_tbl_init.c bam_sort.o
test/split/test_count_rg.o: test/split/test_count_rg.c bam_split.o $(test_test_h)
test/split/test_expand_format_string.o: test/split/test_expand_format_string.c bam_split.o $(test_test_h)
test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c bam_split.o $(test_test_h)
test/split/test_parse_args.o: test/split/test_parse_args.c bam_split.o $(test_test_h)
test/test.o: test/test.c $(htslib_sam_h) $(test_test_h)
test/vcf-miniview.o: test/vcf-miniview.c $(htslib_vcf_h)


# misc programs

misc/ace2sam: misc/ace2sam.o
    $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(LDLIBS) -lz

misc/maq2sam-short: misc/maq2sam-short.o
    $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(LDLIBS) -lz

misc/maq2sam-long: misc/maq2sam-long.o
    $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(LDLIBS) -lz

misc/md5fa: misc/md5fa.o misc/md5.o
    $(CC) $(LDFLAGS) -o $@ misc/md5fa.o misc/md5.o $(LDLIBS) -lz

misc/md5sum-lite: misc/md5sum-lite.o
    $(CC) $(LDFLAGS) -o $@ misc/md5sum-lite.o $(LDLIBS)

misc/wgsim: misc/wgsim.o
    $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz

misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h
misc/md5.o: misc/md5.c misc/md5.h
misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h
misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h

misc/maq2sam-short.o: misc/maq2sam.c
    $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c

misc/maq2sam-long.o: misc/maq2sam.c
    $(CC) $(CFLAGS) $(CPPFLAGS) -DMAQ_LONGREADS -c -o $@ misc/maq2sam.c

misc/md5sum-lite.o: misc/md5.c misc/md5.h
    $(CC) $(CFLAGS) $(CPPFLAGS) -DMD5SUM_MAIN -c -o $@ misc/md5.c


install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
    $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
    $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
    $(INSTALL_DATA) samtools.1 $(DESTDIR)$(man1dir)


testclean:
    -rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
    -cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out

mostlyclean: testclean
    -rm -f *.o misc/*.o test/*.o test/*/*.o version.h

clean: mostlyclean
    -rm -f $(PROGRAMS) libbam.a $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS)

distclean: clean
    -rm -f TAGS

clean-all: clean clean-htslib


tags:
    ctags -f TAGS *.[ch] misc/*.[ch]


force:


.PHONY: all check clean clean-all distclean force install
.PHONY: lib mostlyclean tags test testclean

You don't have an appropriate version of the curses library. You appear to have a 32bit version installed but not a 64bit version of the library. You need to fix that. — Etan Reisner, Nov 29 '15 at 15:54
What did you try? Did you manage to get the 64bit package for the curses library/libraries installed? — Etan Reisner, Nov 29 '15 at 16:16
No, I couldn't find right rpm file. All I found was this: http://rpmfind.net/linux/rpm2html/search.php?query=libcurses.so.1()(64bit) I intstalled termcap-2.0.8-1043.1.2.x86_64.rpm but that didn't fix anything. — Aleksandar Makragić, Nov 29 '15 at 16:28
Don't search online randomly. Use your distributions package tools to do this. YaST or whatever it is on SuSE. Ask it what packages provide the library you need. And you likely need the -devel package for the libraries for this. — Etan Reisner, Nov 29 '15 at 16:29
In SuSE, you would use yast2 (and zypper) to change packages. — Thomas Dickey, Nov 29 '15 at 16:30
Well I tried to search for libcurse with Yast but I haven't find anything. Can you tell me how to do it with Zypper? I honestly don't know what to do anymore. — Aleksandar Makragić, Nov 29 '15 at 16:54

score 2 · Accepted Answer · edited May 23 '17 at 12:08

2

On SUSE, you may need to link with -lncurses rather than -lcurses. See for example this answer to What's the difference between -lcurses and -lncurses….

So try make LIBCURSES=-lncurses.

Samtools may soon acquire a configure script which will detect what curses you have on your machine and use -lcurses/-lncurses/etc as appropriate.

edited May 23 '17 at 12:08

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answered Dec 02 '15 at 15:04

John Marshall

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Makefile - samtools installation failed

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