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

mothur bugs
1

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
2

-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

3

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 (C) 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