Forgot to copy the list on this email. On Mon, Sep 23, 2013 at 9:32 AM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
On Fri, Sep 20, 2013 at 6:12 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Hi Carlos,
Can you try again? Also the new unstable version if you can. Thanks for the help! ATLAS is a beast :(
Sorry for the delayed response. Busy weekend.
Trying to install package_atlas_3_10 on Ubuntu 13.04:
STDERR It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information #############################################
I think this is the other relevant part in the log:
# try to disable cpu throttling if hash cpufreq-selector 2>/dev/null; then cpufreq-selector -g performance elif hash cpupower 2>/dev/null; then cpupower frequency-set -g performance else echo 'Please deactivate CPU throttling by your own, or install cpufreq-selector' exit fi
STDERR Error calling SetGovernor: Caller is not authorized
I had to install 'cpufreq-selector' to get here, not installed by default. I can confirm I get the same error when trying to run this command directly: $ cpufreq-selector -g performance Error calling SetGovernor: Caller is not authorized
package_atlas_3_11 fails in exactly the same way in this box.
Somehow this is also a silent failing and numpy, biopython and ngs-tools(my tool package depending on biopython) get "Installed"(Green)
Yes that is correct. I designed it (in theory) in that way, that if ATLAS crashes (due to CPU throttling enabled) every other package can be installed without problem. Every other behaviour is a bug.
while lapack, atlas and split_by_barcode(my actual tool wrapper depending on ngs-tools package) get "Installed, missing tool dependencies"(Grey). This means if I try to use my wrapper in this state I get this error: /bin/sh: 1: ngs-tools: not found
On Ubuntu it gets installed without errors. Everything is green :)
However, if I do a "Repair repository" on split_by_barcode it goes into "Installed"(Green) and everything seems to work from then on.
Mh, thats seems to be a bug. I will try to reproduce on a computer where ATLAS is crashing.
Thanks for testing this. I also believe this might be a bug. --Carlos