Trinity installation error

[JManuelMonroyKuhn]

Hello! I want to run Trinity on a cluster. I typed 'make' and I got at the end the following errors. Could anyone help me and orient me? Thanks

lib/misc.cc: In function 'std::string jellyfish::quote_arg(const std::string&)':
lib/misc.cc:86: error: 'all_of' is not a member of 'std'
make[3]: *** [lib/misc.lo] Error 1
make[3]: Leaving directory `/home/hpc/uj502/di29kiz/trinityrnaseq_r20140717/trinity-plugins/jellyfish-2.1.3'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/hpc/uj502/di29kiz/trinityrnaseq_r20140717/trinity-plugins/jellyfish-2.1.3'
make[1]: *** [jellyfish] Error 2
make[1]: Leaving directory `/home/hpc/uj502/di29kiz/trinityrnaseq_r20140717/trinity-plugins'
make: *** [plugins] Error 2

[GenoMax]

See if this is applicable: https://www.biostars.org/p/105334/

What version of GCC are you using?

[JManuelMonroyKuhn]

More errors

It worked!! Because I am working in a Cluster I had to module load gcc/4.9 but now I have this errors. Do you know what could be the problem?
Thanks

/usr/bin/ld: cannot find -lcurses
collect2: error: ld returned 1 exit status
make[3]: *** [samtools] Error 1
make[3]: Leaving directory `/home/hpc/uj502/di29kiz/trinityrnaseq_r20140717/trinity-plugins/rsem-1.2.15/sam'
make[2]: *** [sam/libbam.a] Error 2
make[2]: Leaving directory `/home/hpc/uj502/di29kiz/trinityrnaseq_r20140717/trinity-plugins/rsem-1.2.15'
make[1]: *** [rsem] Error 2
make[1]: Leaving directory `/home/hpc/uj502/di29kiz/trinityrnaseq_r20140717/trinity-plugins'
make: *** [plugins] Error 2

[GenoMax]

You are missing the ncurses library. Check to see if there is a module for it.

If you are planning to run this on a cluster then I would advise asking your cluster administrators to build a module for Trinity. That way they can take care of the dependencies and when you actually run your job there will be no issues with nodes not finding things, if your home directory is not available on all compute nodes.

[JManuelMonroyKuhn]

Hi!
I asked the cluster administrators about a module for ncurses and this was his answer:

You can find ncurses (lib, include) with

module load os_extension/devel
module show os_extension/devel

echo $DEVEL_LIB_PATH
echo $DEVEL_INC_PATH
echo $DEVEL_INC

So actually ncurses is in that module but I get the same error even after
module load os_extension/devel

[GenoMax]

Did you load the new GCC module along with the os_externsion/devel before compiling? What OS is your cluster using?

Do you know if *curses-dev library is installed in that module?

Try this code and you should see where it is trying to load curses from and if there are any errors:

$ ld -lcurses --verbose

[JManuelMonroyKuhn]

This is what I got:

attempt to open /usr/x86_64-suse-linux/lib64/libcurses.so failed
attempt to open /usr/x86_64-suse-linux/lib64/libcurses.a failed
attempt to open /usr/local/lib64/libcurses.so failed
attempt to open /usr/local/lib64/libcurses.a failed
attempt to open /lib64/libcurses.so failed
attempt to open /lib64/libcurses.a failed
attempt to open /usr/lib64/libcurses.so failed
attempt to open /usr/lib64/libcurses.a failed
attempt to open /usr/x86_64-suse-linux/lib/libcurses.so failed
attempt to open /usr/x86_64-suse-linux/lib/libcurses.a failed
attempt to open /usr/lib64/libcurses.so failed
attempt to open /usr/lib64/libcurses.a failed
attempt to open /usr/local/lib/libcurses.so failed
attempt to open /usr/local/lib/libcurses.a failed
attempt to open /lib/libcurses.so failed
attempt to open /lib/libcurses.a failed
attempt to open /usr/lib/libcurses.so failed
attempt to open /usr/lib/libcurses.a failed
ld: cannot find -lcurses

I loaded both modules. As for my OS

LSB Version: core-2.0-noarch:core-3.2-noarch:core-4.0-noarch:core-2.0-x86_64:core-3.2-x86_64:core-4.0-x86_64:desktop-4.0-amd64:desktop-4.0-noarch:graphics-2.0-amd64:graphics-2.0-noarch:graphics-3.2-amd64:graphics-3.2-noarch:graphics-4.0-amd64:graphics-4.0-noarch
Distributor ID: SUSE LINUX
Description: SUSE Linux Enterprise Server 11 (x86_64)
Release: 11
Codename: n/a

Linux lxa191 3.0.101-0.35-default #1 SMP Wed Jul 9 11:43:04 UTC 2014 (c36987d) x86_64 x86_64 x86_64 GNU/Linux

[JManuelMonroyKuhn]

I just solved my problem.
I modify the Makefile in
trinityrnaseq_r20140717/trinity-plugins/rsem-1.2.15/sam

I change the two lines:
LIBPATH= -L/lrz/sys/os_extension/SLES11SP3/devel_03Jul2014/usr/lib64
LIBCURSES= -lncurses

Thank you for all the help!!!