Install failure Failed to build gem native extension. /usr/bin/ruby extconf.rb

Looking forward to trying sequenceserver , but could not find my around a glitch during installation (call and error message at the bottom of this post). Anyone have suggestions?

Environment and versions:

CentOS Linux release 7.5.1804 (Core)

ruby -v
ruby 2.0.0p648 (2015-12-16) [x86_64-linux]

gem -v
2.0.14.1

gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
Configured with: …/configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-28) (GCC)

List of installed and available ruby packages. Note that ruby-devel is installed.

sudo yum list ruby*
Loaded plugins: fastestmirror, langpacks, rhnplugin
There was an error communicating with RHN.
Red Hat Satellite or RHN Classic support will be disabled.
rhn-plugin: Error communicating with server. The message was:
Internal Server Error
Loading mirror speeds from cached hostfile

  • base: repo.ialab.dsu.edu
  • extras: ftpmirror.your.org
  • updates: mirror.sesp.northwestern.edu
    Installed Packages
    ruby.x86_64 2.0.0.648-33.el7_4 @base
    ruby-devel.x86_64 2.0.0.648-33.el7_4 @base
    ruby-irb.noarch 2.0.0.648-33.el7_4 @base
    ruby-libs.x86_64 2.0.0.648-33.el7_4 @base
    rubygem-bigdecimal.x86_64 1.2.0-33.el7_4 @base
    rubygem-io-console.x86_64 0.4.2-33.el7_4 @base
    rubygem-json.x86_64 1.7.7-33.el7_4 @base
    rubygem-psych.x86_64 2.0.0-33.el7_4 @base
    rubygem-rdoc.noarch 4.0.0-33.el7_4 @base
    rubygems.noarch 2.0.14.1-33.el7_4 @base
    Available Packages
    ruby-doc.noarch 2.0.0.648-33.el7_4 base
    ruby-hivex.x86_64 1.3.10-6.9.el7 base
    ruby-libguestfs.x86_64 1:1.36.10-6.el7_5.2 updates
    ruby-libs.i686 2.0.0.648-33.el7_4 base
    ruby-saslwrapper.x86_64 0.16-5.el7 extras
    ruby-tcltk.x86_64 2.0.0.648-33.el7_4 base
    rubygem-abrt.noarch 0.3.0-1.el7 base
    rubygem-abrt-doc.noarch 0.3.0-1.el7 base
    rubygem-bundler.noarch 1.7.8-3.el7 base
    rubygem-bundler-doc.noarch 1.7.8-3.el7 base
    rubygem-minitest.noarch 4.3.2-33.el7_4 base
    rubygem-net-http-persistent.noarch 2.8-5.el7 base
    rubygem-net-http-persistent-doc.noarch 2.8-5.el7 base
    rubygem-rake.noarch 0.9.6-33.el7_4 base
    rubygem-thor.noarch 0.19.1-1.el7 base
    rubygem-thor-doc.noarch 0.19.1-1.el7 base
    rubygems-devel.noarch 2.0.14.1-33.el7_4

Installation call and error message:

sudo gem install sequenceserver
Building native extensions. This could take a while…
ERROR: Error installing sequenceserver:
ERROR: Failed to build gem native extension.

/usr/bin/ruby extconf.rb

Creating Makefile for ruby version 2.0.0 on x86_64-linux <<<<<
creating Makefile

make “DESTDIR=”
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o base64.o -c base64.c
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o builder.o -c builder.c
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o cache.o -c cache.c
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o cache8.o -c cache8.c
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o dump.o -c dump.c
dump.c: In function ‘dump_obj’:
dump.c:813:6: warning: implicit declaration of function ‘RSTRUCT_GET’ [-Wimplicit-function-declaration]
VALUE beg = RSTRUCT_GET(obj, 0);
^
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o err.o -c err.c
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o gen_load.o -c gen_load.c
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o hash_load.o -c hash_load.c
hash_load.c: In function ‘add_element’:
hash_load.c:77:3: warning: implicit declaration of function ‘rb_id2sym’ [-Wimplicit-function-declaration]
key = rb_id2sym(rb_intern(attrs->name));
^
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o obj_load.o -c obj_load.c
obj_load.c: In function ‘end_element’:
obj_load.c:771:7: warning: implicit declaration of function ‘RSTRUCT_SET’ [-Wimplicit-function-declaration]
RSTRUCT_SET(ph->obj, 0, h->obj);
^
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o ox.o -c ox.c
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o parse.o -c parse.c
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o sax.o -c sax.c
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o sax_as.o -c sax_as.c
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o sax_buf.o -c sax_buf.c
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o sax_hint.o -c sax_hint.c
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I. -DRUBY_TYPE=ruby -DRUBY_RUBY -DRUBY_VERSION=2.0.0 -DRUBY_VERSION_MAJOR=2 -DRUBY_VERSION_MINOR=0 -DRUBY_VERSION_MICRO=0 -DHAS_RB_TIME_TIMESPEC=0 -DHAS_TM_GMTOFF=0 -DHAS_ENCODING_SUPPORT=1 -DHAS_ONIG=1 -DHAS_PRIVATE_ENCODING=0 -DHAS_NANO_TIME=1 -DHAS_RSTRUCT=1 -DHAS_IVAR_HELPERS=1 -DHAS_PROC_WITH_BLOCK=1 -DHAS_GC_GUARD=1 -DHAS_BIGDECIMAL=1 -DHAS_TOP_LEVEL_ST_H=0 -DNEEDS_UIO=1 -DHAS_DATA_OBJECT_WRAP=0 -DUNIFY_FIXNUM_AND_BIGNUM=0 -Wall -fPIC -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -mtune=generic -fPIC -m64 -o special.o -c special.c
rm -f ox.so
gcc -shared -o ox.so base64.o builder.o cache.o cache8.o dump.o err.o gen_load.o hash_load.o obj_load.o ox.o parse.o sax.o sax_as.o sax_buf.o sax_hint.o special.o -L. -L/usr/lib64 -L. -Wl,-z,relro -fstack-protector -rdynamic -Wl,-export-dynamic -m64 -lruby -lpthread -lrt -ldl -lcrypt -lm -lc

make “DESTDIR=” install
/usr/bin/mkdir -p ./.gem.20180918-2329-19nlq0m
exit > .RUBYARCHDIR.time
/usr/bin/install -c -m 0755 ox.so ./.gem.20180918-2329-19nlq0m

Gem files will remain installed in /usr/local/share/gems/gems/ox-2.10.0 for inspection.
Results logged to /usr/local/share/gems/gems/ox-2.10.0/ext/ox/gem_make.out

The error is being raised by a dependency, the ox gem, which we use for parsing BLAST’s XML. The problem could simply be that we are using a >3 year old version of the ox gem. Could you try running ‘sudo gem install ox’ on your system and see if that works? This will try to install the latest version of ox. If that works then we can update the dependency accordingly.

Priyam