C++ 11 features, any idea ?

[polikuo]

I'm trying to compile something I don't really need.
It's for my bioinformatic course I'm taking at the moment.
We have an educational CentOS server for the course.
I can do my homework on that, so it doesn't really matter porting it.

./configure stuck at the very beginning.
Does anybody more experienced know what this means ?

configure: loading site script ./src/build-system/config.site
configure: creating cache config.cache
checking TeamCity build number... none
checking Subversion revision... unknown
checking NCBI stable components' version... unknown
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
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 how to run the C preprocessor... gcc -E
checking for gcc... gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
adjusted C   compiler: /usr/local/bin/gcc
adjusted C++ compiler: /usr/local/bin/g++
checking whether /usr/local/bin/gcc  has an option to export all symbols... no
checking whether /usr/local/bin/gcc  supports -Wl,--{en,dis}able-new-dtags... no
checking whether _LIBCPP_VERSION is declared... no
checking how to enable C++ '11 features in /usr/local/bin/g++ ... no

The program we're using.
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST/

[curaga]

Whenever configure fails, look in config.log for the failing line.

[polikuo]

I find out these lines in config.log

conftest.c:9:28: fatal error: ac_nonexistent.h: No such file or directory
g++: error: libgomp.spec: No such file or directory

ac_nonexistent.h can't be found anywhere, but I've heard that this is the expected behavior.
libgomp.spec is in gcc_libs-dev.tcz which is automatically loaded with compiletc.

I've attached the log for those who is interested.

[Juanito]

Try this:

Code: [Select]

$ sudo ln -s /usr/local/lib/libgomp.spec /usr/lib/libgomp.spec

[polikuo]

Try this:

Code: [Select]

$ sudo ln -s /usr/local/lib/libgomp.spec /usr/lib/libgomp.spec

Hmm, how come I've never thought of that.

configure pass the compiler check

After numerous dependency checks and get stuck at

configure: trying to build the NCBI SRA/VDB Toolkit from GitHub
configure: error: SRA/VDB build failed status 1

... but git is already installed. 
config.log has 18717 lines.
This is gonna take a while. 
Homework first, I'll just use the server.
Will come back here when I have time for it.