Cygwin compilation problems: -rdynamic unrecognised, expl(),logl() missing

[NicoleJohn]

Good day.

I am trying to install SAMTools 1.3 on Cygwin using my Windows8.1 64bit machine. I successfully ran the "./configure" command as shown below:
$ ./configure
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking location of HTSlib source tree... htslib-1.3
checking for NcursesW wide-character library... yes
checking for working ncursesw/curses.h... yes
checking for working ncursesw.h... no
checking for working ncurses.h... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
=== configuring in htslib-1.3 (/cygdrive/c/Users/NicoleJohnMagculia/Home/bin/sam tools-1.3/htslib-1.3)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/ local' --cache-file=/dev/null --srcdir=.
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk

config.status: creating config.h

However when I tried to perform "make" function, I encountered this problem:

$ make
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_index.o bam_index.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_plcmd.o bam_plcmd.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o sam_view.o sam_view.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_cat.o bam_cat.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_md.o bam_md.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_reheader.o bam_reheader.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_sort.o bam_sort.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bedidx.o bedidx.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o kprobaln.o kprobaln.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_rmdup.o bam_rmdup.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_rmdupse.o bam_rmdupse.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_mate.o bam_mate.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_stat.o bam_stat.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_color.o bam_color.c
echo '#define SAMTOOLS_VERSION "1.3"' > version.h
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bamtk.o bamtk.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o errmod.o errmod.c
errmod.c: In function ‘cal_coef’:
errmod.c:85:30: warning: incompatible implicit declaration of built-in function ‘expl’
sum = sum1 + expl(lC[n<<8|k] + k*le + (n-k)*le1);
^
errmod.c:86:43: warning: incompatible implicit declaration of built-in function ‘logl’
beta[k] = -10. / M_LN10 * logl(sum1 / sum);
^
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o sample.o sample.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o sam_opts.o sam_opts.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o cut_target.o cut_target.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o phase.o phase.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam2depth.o bam2depth.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o padding.o padding.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bedcov.o bedcov.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bamshuf.o bamshuf.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o faidx.o faidx.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o dict.o dict.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o stats.o stats.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o stats_isize.o stats_isize.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_flags.o bam_flags.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_split.o bam_split.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_tview.o bam_tview.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_tview_curses.o bam_tview_curses.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_tview_html.o bam_tview_html.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_lpileup.o bam_lpileup.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_quickcheck.o bam_quickcheck.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_addrprg.o bam_addrprg.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_aux.o bam_aux.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam.o bam.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_import.o bam_import.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o sam.o sam.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o sam_header.o sam_header.c
gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -Ihtslib-1.3 -c -o bam_plbuf.o bam_plbuf.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
cd htslib-1.3 && make lib-static
make[1]: Entering directory '/cygdrive/c/Users/NicoleJohnMagculia/Home/bin/samto ols-1.3/htslib-1.3'
gcc -g -O2 -I. -c -o kfunc.o kfunc.c
gcc -g -O2 -I. -c -o knetfile.o knetfile.c
gcc -g -O2 -I. -c -o kstring.o kstring.c
gcc -g -O2 -I. -c -o bgzf.o bgzf.c
gcc -g -O2 -I. -c -o faidx.o faidx.c
gcc -g -O2 -I. -c -o hfile.o hfile.c
gcc -g -O2 -I. -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.3"' > version.h
gcc -g -O2 -I. -c -o hts.o hts.c
gcc -g -O2 -I. -c -o md5.o md5.c
gcc -g -O2 -I. -c -o regidx.o regidx.c
gcc -g -O2 -I. -c -o sam.o sam.c
gcc -g -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -I. -c -o tbx.o tbx.c
gcc -g -O2 -I. -c -o vcf.o vcf.c
gcc -g -O2 -I. -c -o vcfutils.o vcfutils.c
gcc -g -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -I. -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -I. -c -o cram/files.o cram/files.c
gcc -g -O2 -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -O2 -I. -c -o cram/sam_header.o cram/sam_header.c
gcc -g -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -I. -c -o cram/thread_pool.o cram/thread_pool.c
gcc -g -O2 -I. -c -o cram/vlen.o cram/vlen.c
gcc -g -O2 -I. -c -o cram/zfio.o cram/zfio.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils. o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/fil es.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
make[1]: Leaving directory '/cygdrive/c/Users/NicoleJohnMagculia/Home/bin/samtoo ls-1.3/htslib-1.3'
gcc -pthread -rdynamic -o samtools 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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf. o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_t view_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o libb am.a htslib-1.3/libhts.a -lncursesw -lm -lz -ldl
gcc: error: unrecognized command line option ‘-rdynamic’
Makefile:139: recipe for target 'samtools' failed
make: *** [samtools] Error 1

---

How can I troubleshoot this problem? I am not a computer programmer and just relying on the information I read in your instructions. Your assistance is very much valuable to me.

Thanks.

Sincerely,

Nicole John

[jmarshall]

It seems the -rdynamic option is not accepted by Cygwin's GCC. Samtools needs it on most platforms to support HTSlib plugins, and its being present in the makefile always is temporary (see 3c15c88).

You haven't configured HTSlib to use plugins, so you don't need it. Remove the word -rdynamic from the ALL_LDFLAGS line in the Makefile and remove the word -ldl from the following ALL_LIBS line. Having removed -rdynamic/-ldl, you should be able to link samtools on Cygwin successfully.

Samtools et al are not heavily tested on Windows or Cygwin, as there are few people using them there. So it is in fact easier to compile them on Linux, other Unixes, or Mac OS X, if you have access to these platforms.

---

errmod.c:85:30: warning: incompatible implicit declaration of built-in function ‘expl’
errmod.c:86:43: warning: incompatible implicit declaration of built-in function ‘logl’

This is similar to samtools/bcftools#281 and can be fixed similarly if it causes trouble.

[NicoleJohn]

Thank you so much for your prompt reply. I successfully compiled and installed the samtools in cygwin.

Again, thanks!

All the best,

Nicole John

[jmarshall]

The missing expl() and logl() library functions also cause linking to fail. A quick hack to fix this is to add -Dexpl=exp -Dlogl=log to the ALL_CPPFLAGS line in the same part of the Makefile. (If you've already run make, delete errmod.o to ensure that it gets remade when you rerun make.)

[NicoleJohn]

Good day.

Now, I am trying to compile bcftools 1.3 again through Cygwin. I have removed -rdynamic from the makefile as I encountered the same error again. However, after doing this, another error occurred (see below):

[…snip… This bcftools plugin compilation failure on Cygwin is now samtools/bcftools#377.]