install error

[yupingz]

Hi,

I keep getting the following error when run ./configure

./configure: line 5240: syntax error near unexpected token 2.2' ./configure: line 5240:LT_PREREQ(2.2)'

And I checked my config.log, the error occurred from here

gcc version 9.1.0 (Ubuntu 9.1.0-2ubuntu2~16.04) configure:3112: $? = 0 configure:3101: g++ -V >&5 g++: error: unrecognized command line option '-V' g++: fatal error: no input files compilation terminated. configure:3112: $? = 1 configure:3101: g++ -qversion >&5 g++: error: unrecognized command line option '-qversion'; did you mean '--version'? g++: fatal error: no input files compilation terminated.

Could you help figure what might be the reason? Thanks.

[hyunminkang]

I think you need to install libtool.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Fri, Jun 7, 2019 at 10:24 AM yzz207 notifications@github.com wrote:

Hi,

I keep getting the following error when run ./configure

./configure: line 5240: syntax error near unexpected token 2.2' ./configure: line 5240: LT_PREREQ(2.2)'

And I checked my config.log, the error occurred from here

gcc version 9.1.0 (Ubuntu 9.1.0-2ubuntu2~16.04) configure:3112: $? = 0 configure:3101: g++ -V >&5 g++: error: unrecognized command line option '-V' g++: fatal error: no input files compilation terminated. configure:3112: $? = 1 configure:3101: g++ -qversion >&5 g++: error: unrecognized command line option '-qversion'; did you mean '--version'? g++: fatal error: no input files compilation terminated.

Could you help figure what might be the reason? Thanks.

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[davidaknowles]

I'm having the same issue. I got libtool to compile fine as far as I can tell, do I just to need to have it on my path after that? (I don't have admin rights on the cluster so I can't using apt-get or make install).

[welchr]

Does which libtoolize show that it's on your PATH? If so, does re-running autoreconf -vfi and then ./configure work?

[davidaknowles]

I was being dumb: I added the libtool bin to my PATH definition in my .bash_profile but never sourced it. Works fine now. You might want to add something about this to the install instructions since it doesn't seem to be a super standard dependency.

Thanks for the help.

[silviamorins]

Hi, I am trying to install demuxlet and get the following when running ./configure:

./configure: line 5195: syntax error near unexpected token `2.2'
./configure: line 5195: `LT_PREREQ(2.2)'

I have installed libtools, which libtoolize gives ~/.conda/envs/demuxlet_test/bin/libtoolize and in my config.log I get following errors:

$ grep "error" config.log
x86_64-conda_cos6-linux-gnu-c++: error: unrecognized command line option '-V'
x86_64-conda_cos6-linux-gnu-c++: fatal error: no input files
x86_64-conda_cos6-linux-gnu-c++: error: unrecognized command line option '-qversion'; did you mean '--version'?
x86_64-conda_cos6-linux-gnu-c++: fatal error: no input files
x86_64-conda_cos6-linux-gnu-c++: error: unrecognized command line option '-V'
x86_64-conda_cos6-linux-gnu-c++: fatal error: no input files
x86_64-conda_cos6-linux-gnu-c++: error: unrecognized command line option '-qversion'; did you mean '--version'?
x86_64-conda_cos6-linux-gnu-c++: fatal error: no input files
conftest.cpp:11:10: fatal error: ac_nonexistent.h: No such file or directory
conftest.cpp:11:10: fatal error: ac_nonexistent.h: No such file or directory
conftest.cpp:30:15: error: expected unqualified-id before string constant
               "error: bool is not defined"
conftest.cpp:48:48: error: 's' does not name a type
conftest.cpp:58:28: error: 's' was not declared in this scope
conftest.cpp:76:24: error: 's' was not declared in this scope
conftest.cpp:80:63: error: 'i' was not declared in this scope
|               "error: bool is not defined"
|               "error: false is not defined"
|               "error: false is not 0"
|               "error: true is not defined"
|               "error: true is not 1"
|               "error: __bool_true_false_are_defined is not defined"
conftest.cpp:63:13: error: '_Bool' was not declared in this scope
conftest.cpp:65:58: error: size of array 'test_array' is negative
conftest.cpp:65:58: error: size of array 'test_array' is negative
conftest.cpp:64:20: error: expected primary-expression before ')' token
conftest.cpp:64:23: error: expected primary-expression before ')' token
configure:4719: checking for error_at_line
ac_cv_lib_error_at_line=yes

What should I do? Thank you in advance for your help!

[Puriney]

I found popscle's docker container makes life smooth. https://github.com/statgen/popscle

[skchronicles]

Solution

For anyone else running into this issue, I found that installing libtool fixes the problem.

Here is a basic sent of instructions that you can follow to install htslib and demuxlet:

# Step 1. Install and build HTSlib 1.10 (required by demuxlet)
# Needs to be a sibling directory to demuxlet install,
# the name of the htslib directory must be called htslib
wget https://github.com/samtools/htslib/releases/download/1.10/htslib-1.10.tar.bz2 \
    && tar -vxjf htslib-1.10.tar.bz2 \
    && rm htslib-1.10.tar.bz2 \
    && cd htslib-1.10 \
    && autoreconf -i \
    && ./configure \
    && make \
    && make install \
    && ln -s /opt2/htslib-1.10 /opt2/htslib \
    && cd ..

# Step 2. Install and build demuxlet, the ./configure command 
# needs libtool installed first   
DEBIAN_FRONTEND=noninteractive apt-get install -y libtool \
    && git clone https://github.com/statgen/demuxlet.git \
    && cd demuxlet \
    && autoreconf -vfi \
    && ./configure \
    && make \
    && make install

I hope this helps!

Best Regards, @skchronicles