./configure: line 16192: syntax error near unexpected token `BOOST_REQUIRE'

[shendurelab]

./configure: line 16192: syntax error near unexpected token `BOOST_REQUIRE'

[teedeedubya]

@chaijinchao ,
@SchwarzEM ,

Edit again (updating to account for road bumps encountered during "make")
I got it to configure!!

This is exactly what i did, in this order.

1. Did a fresh Centos 7 minimal install
2. download the following RPM and copy it to your box:
   ftp://rpmfind.net/linux/centos/7.3.1611/os/x86_64/Packages/boost-devel-1.53.0-26.el7.x86_64.rpm
3. download epel 7 repository configuration
   https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
4. install boos-devel:
   yum --nogpgcheck localinstall boost-devel-1.53.0-26.el7.x86_64.rpm
5. install the epel repository
   yum --nogpgcheck localinstall epel-release-latest-7.noarch.rpm
6. install samtools-devel and zlib-devel:
   yum install samtools-devel
   yum install zlib-devel
7. install some more crap:
   yum install gcc
   yum install unzip
   yum install automake
   yum install make
   yum install gcc-c++
8. unpack Lachesis and copy in a couple of needed files:
   unzip LACHESIS-master.zip
   cp /usr/share/automake-1.13/config.guess /root/LACHESIS-master/
   cp /usr/share/automake-1.13/config.sub /root/LACHESIS-master/
   cp /usr/share/automake-1.13/depcomp /root/LACHESIS-master/
9. export samtools(I didn't have to export boost)
   export LACHESIS_SAMTOOLS_DIR=/usr/include/samtools/
10. configure it
    ./configure --with-samtools=/usr/include/samtools/
11. delete artifacts left over in the repository
    source: https://github.com/shendurelab/LACHESIS/issues/28
    thanks @llinsson
    for i in find /root/LACHESIS-master/ -name "*.[ao]"; do echo -e "Removing ${i}"; rm ${i} ; done;
12. if for whatever reason, it's unable to find sam.h in SAMStepper.h and SAMStepper.cc,
    Modify ./src/include/gtools/SAMStepper.h and ./src/include/gtools/SAMStepper.cc
    from:
    #include <sam.h>
    to:
    #include "/usr/include/samtools/sam.h"
13. install it
    make
    make install
    Cheers,
    Tony

[teedeedubya]

Howdy, I'm having the same problem. I'm running on RHEL 6.8 64bit.

It's worth mentioning that this is actually failing on AX_LIB_SAMTOOLS(), you can confirm this by throwing an echo after it and it will just throw a syntax error on the echo. BOOST_REQUIRE(1.52.0) also fails.

We currently have 1.52.0 and 1.61.0 of boost installed multiple ways and samtools 0.1.19 installed multiple ways.
I set up a for loop for procedurally try to configure this thing with every possible boost directory. I've tried BOOST_ROOT, LACHESIS_BOOST_DIR, BOOST_LIB, BOOST_LIBRARIES and a few others.

I'll post if I find a work around,

Cheers,
Tony

[chaijingchao123]

i have the same problem. Do you know how to solve it?
thank you!

[teedeedubya]

Howdy Chaijinchao,
Still trying to get this puppy to configure. Someone came up with another work around in #30 to a similarish issue. It didn't work for me but it might for you :). If anyone has figured this out, please let us know.

[shenscore]

What's the version of your autoreconf?
I use autoreconf (GNU Autoconf) 2.69 and get these warning many times:

configure.ac:12: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body

then I try to run configure, I get the same error:

./configure: line 14730: syntax error near unexpected token `BOOST_REQUIRE'
./configure: line 14730: `BOOST_REQUIRE(1.52.0)'

I guess there is something wrong previously...
still try to figure out....

[WenchaoLin]

@shenscore
libtool-2.4.6 needed and
copy config.guess config.sub depcomp to /root/LACHESIS-master/