sage -upgrade from 6.2 error

[Robert McBroom]

sage -upgrade from 6.2 error on Fedora 19.  Running in a root window upgrade terminates with a permission error

Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-isl=/builddir/build/BUILD/gcc-4.8.3-20140911/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.3-20140911/obj-x86_64-redhat-linux/cloog-install --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.3 20140911 (Red Hat 4.8.3-7) (GCC)
****************************************************
sys:1: RuntimeWarning: not adding directory '/usr/local/sage-6.2-x86_64-Linux/local/var/tmp/sage/build/atlas-3.10.2' to sys.path since it's not owned by a trusted user.
Untrusted users could put files in this directory which might then be imported by your Python code. As a general precaution from similar exploits, you should not execute Python code from this directory
Traceback (most recent call last):
  File "./spkg-install", line 15, in <module>
    from configuration import conf, cp, ln, which, try_run, edit_in_place
ImportError: No module named configuration

real    0m0.026s
user    0m0.016s
sys     0m0.009s
************************************************************************
Error installing package atlas-3.10.2
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
  /usr/local/sage-6.2-x86_64-Linux/logs/pkgs/atlas-3.10.2.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/usr/local/sage-6.2-x86_64-Linux/local/var/tmp/sage/build/atlas-3.10.2 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
  (cd '/usr/local/sage-6.2-x86_64-Linux/local/var/tmp/sage/build/atlas-3.10.2' && '/usr/local/sage-6.2-x86_64-Linux/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
make[2]: *** [/usr/local/sage-6.2-x86_64-Linux/local/var/lib/sage/installed/atlas-3.10.2] Error 1
make[2]: Leaving directory `/usr/local/sage-6.2-x86_64-Linux/build'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/usr/local/sage-6.2-x86_64-Linux/build'

real    8m6.098s
user    5m1.192s
sys     0m49.701s
***************************************************************
Error building Sage.

The following package(s) may have failed to build:

package: atlas-3.10.2
***************************************************************
The log file contents are
***************************************************************
***************************************************************
sys:1: RuntimeWarning: not adding directory '' to sys.path since it's not owned by a trusted user.
Untrusted users could put files in this directory which might then be imported by your Python code. As a general precaution from similar exploits, you should not execute Python code from this directory
Found local metadata for atlas-3.10.2
Attempting to download package atlas-3.10.2
>>> Trying to download http://www.sagemath.org/packages/upstream/atlas/atlas-3.10.2.tar.bz2
[............................................................]
Checksum: 7d24b5f5213479bd55d997d03d187731be4013b6 vs 7d24b5f5213479bd55d997d03d187731be4013b6
atlas-3.10.2
====================================================
Setting up build directory for atlas-3.10.2
Finished set up
****************************************************
Host system:
Linux dv7t.launchmodem.com 3.14.23-100.fc19.x86_64 #1 SMP Thu Oct 30 18:36:00 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=/bin/gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.3/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-isl=/builddir/build/BUILD/gcc-4.8.3-20140911/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.3-20140911/obj-x86_64-redhat-linux/cloog-install --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.3 20140911 (Red Hat 4.8.3-7) (GCC)
****************************************************
sys:1: RuntimeWarning: not adding directory '/usr/local/sage-6.2-x86_64-Linux/local/var/tmp/sage/build/atlas-3.10.2' to sys.path since it's not owned by a trusted user.
Untrusted users could put files in this directory which might then be imported by your Python code. As a general precaution from similar exploits, you should not execute Python code from this directory
Traceback (most recent call last):
  File "./spkg-install", line 15, in <module>
    from configuration import conf, cp, ln, which, try_run, edit_in_place
ImportError: No module named configuration

real    0m0.026s
user    0m0.016s
sys    0m0.009s
************************************************************************
Error installing package atlas-3.10.2
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
  /usr/local/sage-6.2-x86_64-Linux/logs/pkgs/atlas-3.10.2.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/usr/local/sage-6.2-x86_64-Linux/local/var/tmp/sage/build/atlas-3.10.2 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
  (cd '/usr/local/sage-6.2-x86_64-Linux/local/var/tmp/sage/build/atlas-3.10.2' && '/usr/local/sage-6.2-x86_64-Linux/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************

[Volker Braun]

Sage requires that you build it as an unprivileged user.