CentOS 5.x installation issues (lots of log files)

I download this:
https://codeload.github.com/mothur/mothur/zip/master

and try to run make:

-bash-3.2$ make
gfortran -c *.f
/bin/sh: gfortran: command not found
make: *** [fortranSource] Error 127

How do I fix this?

yum list gfortran

doesn’t seem to return anything. I’ve done some googling and haven’t come up with a clear answer yet. May try installing ubuntu.

-bash-3.2$ sudo yum list gfortran
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile

I installed these:

  • sudo yum install readline-devel ncurses-devel
  • sudo yum -y install openmpi openmpi-devel

Looks good. I install this

  • sudo yum groupinstall “Development Tools”

Total size: 88 M
Is this ok [y/N]: y
Downloading Packages:
Running rpm_check_debug
Running Transaction Test
Finished Transaction Test

but got this error

Transaction Check Error:
file /usr/share/man/man1/Xserver.1x.gz from install of
xorg-x11-server-Xvfb-1.1.1-48.101.0.1.el5.centos.3.x86_64 conflicts with file
from package xorg-x11-server-Xnest-1.1.1-48.52.el5.x86_64
file /usr/share/man/man1/Xserver.1x.gz from install of
xorg-x11-server-Xvfb-1.1.1-48.101.0.1.el5.centos.3.x86_64 conflicts with file
from package xorg-x11-server-Xorg-1.1.1-48.52.el5.x86_64

Error Summary

Alternative route:

I found this thread and this command works but I don’t know what’s next:

g++  -O3  -DUSE_READLINE sharedutilities.cpp -c -I. -o ./sharedutilities.o

-bash-3.2$ make
gfortran -c *.f
/bin/sh: gfortran: command not found
make: *** [fortranSource] Error 127

You need to install the fortran compiler

Based on what you’ve posted, I’m not really sure what you’re asking or where you’re stuck…

Sorry,
Pat

Yea that’s one of the things I was trying to do. I should of used yum search instead of yum list. I just got past that point and now I’m getting a C++ error?!??!?!

I’m just trying to install mothur on CentOS 5.5. Thansk for the help. Error is below:

-bash-3.2$
gfortran -c *.f
In file ddot.f:51

IF (INCX .EQ. INCY) IF (INCX-1) 5,20,60
1
Warning: Obsolete: arithmetic IF statement at (1)
g++ -O3 -DBIT_VERSION -DRELEASE_DATE="“2/12/2014"” -DVERSION="“1.33.0"” -DUSE_READLINE -I. -arch x86_64 -c -o abstractdecisiontree.o abstractdecisiontree.cpp
g++: x86_64: No such file or directory
cc1plus: error: unrecognized command line option “-arch”
make: *** [abstractdecisiontree.o] Error 1
-bash-3.2$ sudo yum install gcc-gfortran

Compiler versions below

-bash-3.2$
g++ (GCC) 4.1.2 20080704 (Red Hat 4.1.2-54)
Copyright © 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

===================

-bash-3.2$
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile

  • rpmforge: mirror.oscc.org.my
  • base: mirrors.adams.net
  • updates: lug.mtu.edu
  • addons: centosmirror.quintex.com
  • extras: yum.phx.singlehop.com
    Setting up Install Process
    Parsing package install arguments
    Package gcc-gfortran-4.1.2-54.el5.x86_64 already installed and latest version
    Nothing to do
    -bash-3.2$
    gcc-gfortran-4.1.2-54.el5
    libgfortran-4.1.2-54.el5
    libgfortran-4.1.2-54.el5