Install errors

[hepcat72]

Making in my account on:

uname -a
Linux gen-comp1 2.6.32-754.6.3.el6.x86_64 #1 SMP Wed Oct 10 18:28:26 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux

Got over the first hurdle:

make
configure.ac:26: error: possibly undefined macro: m4_esyscmd_s
      If this token and others are legitimate, please use m4_pattern_allow.
      See the Autoconf documentation.
autoreconf: /usr/bin/autoconf failed with exit status: 1
cd lib/htslib && \
./configure --disable-bz2 --disable-lzma --enable-libcurl
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
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 for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type... plain .so
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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 getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking whether fdatasync(int) is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: error: cannot find input file: config.h.in
make: *** [Makefile:75: htslib] Error 1

by doing:

cd lib/htslib
autoreconf -i
cd -
make

But now I'm getting:

make

...

  * linking lumpy
../../obj//gzstream.o: In function `gzstreambuf::open(char const*, int)':
gzstream.C:(.text+0x2a2): undefined reference to `gzopen64'
collect2: ld returned 1 exit status
make[1]: *** [Makefile:57: lumpy] Error 1
make: *** [Makefile:53: lumpy] Error 2

Any suggestions?

[hepcat72]

OK. I think this is probably a dupe of #106.

[hepcat72]

I updated to zlib-1.2.11 and it solved the issue.