atlas build failure

[bertagna@…]

hello, I'm trying to install a bioinformatics software program on my MacBook (Snow Lepord, 10.6.4) called STAMP (Statistical Analysis of Metagenomics Profiles). One of the installations required is py26-numpy. I entered the following;

c-67-170-178-177:~ anthonybertagnolli$ sudo port install py26-numpy
Password:
--->  Computing dependencies for py26-numpy
--->  Dependencies to be installed: atlas fftw-3 py26-nose
--->  Building atlas
Error: Target org.macports.build returned: shell command failed
Log for atlas is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/main.log
Error: The following dependencies failed to build: atlas fftw-3 py26-nose
Error: Status 1 encountered during processing.
To report a bug, see <http://guide.macports.org/#project.tickets>

Not sure what the appropriate action is at this point, would appreciate any help in getting past a shell command failure. I have been using X11 for most of my installation work, tried to install numpy using the terminal, but I got the same the result. Not sure if this even matters, just a piece of information that i thought might be useful. Thanks,

-Anthony

[fracai]

The "shell command failed" is a somewhat generic error that occurs when the build failed. Please upload the log file indicated in your output. /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/main.log

Also, try updating your Portfiles ( port selfupdate ) as atlas was having problems about a week ago that have since been cleared up.

[jmroot (Joshua Root)]

As per the ticket guidelines linked from the New Ticket page, please fill in the Port field and cc the maintainer, remember to preview and use WikiFormatting, and don't set the Milestone field.

[bertagna@…]

log file

[bertagna@…]

Hi, thanks for the suggestions, i have attached the main-log. I looked into updating the ports, however, this failed as well, below is the text;

Last login: Sat Jul 10 10:55:12 on ttys001 c-67-170-178-177:~ anthonybertagnolli$ port self update Unrecognized action "self" c-67-170-178-177:~ anthonybertagnolli$ port selfupdate ---> Updating the ports tree Error: Synchronization of the local ports tree failed doing rsync Error: /opt/local/bin/port: port selfupdate failed: Couldn't sync the ports tree: Synchronization of 1 source(s) failed c-67-170-178-177:~ anthonybertagnolli$

thanks,

-anthony bertagnolli

[bertagna@…]

HI, I was able to perform a port selfupdate using the following line;

sudo port -fvds selfupdate

the last line after this ran was this; The ports tree has been updated. To upgrade your installed ports, you should run

port upgrade outdated

i ran port upgrade outdated, and got this response; No ports mached given expression.

Either way, I tried to instal py26-numpy once again, and yet again recieved the same error as previously. Still not sure how to fix this. Thanks,

-anthony

[jmroot (Joshua Root)]

Please review the FAQ on selfupdate failures and check that port info atlas shows the current version, "atlas @3.8.3, Revision 4". The ticket guidelines specify that the port version should be included in the summary line to avoid uncertainty like this.

[bertagna@…]

Replying to jmr@…:

Please review the FAQ on selfupdate failures and check that port info atlas shows the current version, "atlas @3.8.3, Revision 4". The ticket guidelines specify that the port version should be included in the summary line to avoid uncertainty like this.

Port version atlas@3.8.3 Revision 4 (math).

[shawathome@…]

mainlog from michael shaw

[shawathome@…]

main.log from michael shaw (gedit)

[shawathome@…]

atlas install work from michael shaw

[shawathome@…]

I am a new person having the same issue with installing/building atlas. I am new to Mac and have had my iMac two days. I wanted to install gedit for command line editor and the process went OK until atlas. It froze during the atlas building. I have attached the log file for the atlas and gedit install attempts as well as my command line work for your reference. I reviewed and followed all the recommendations on tickets #24869 and #25619 to no avail. I have used linux for years but am new to mac. Can you please provide a solution. I appreciate your effort.

Thanks in advance, Mike Shaw

iMac - snow leopard 10.6.4 kernel - Darwin 10.4.0 MacPorts base - 1.9.1 Port version atlas - 3.8.3

[kwkelly@…]

Cc Me!

[kwkelly@…]

I got that error, then did

$ sudo port clean --all atlas

then tried reinstalling it and it worked just fine.

[ssn34@…]

Cc Me!

[ssn34@…]

Replying to kwkelly@…:

I got that error, then did

$ sudo port clean --all atlas

then tried reinstalling it and it worked just fine.

I have the same problem. The clean didn't work for me, I'm still getting the same error. Running mac os x 10.4, and updated macports and all ports. It keeps complaining about libmpfr.1.dylib. I'm attaching my log.

[ssn34@…]

ssn34 main.log

[skymoo (Adam Mercer)]

the mpfr port provides /opt/local/lib/libmpfr.4.dylib not /opt/local/lib/libmpfr.1.dylib, so I imagine you need to force a rebuild of gcc44 so get it to link with the correct mpfr library

[ssn34@…]

Did a port -f uninstall gcc44, then reinstalled it and then reinstalled atlas. It seemed to work at first but then .. another error.. this one is more cryptic to me. Any help is greatly appreciated. Attaching the huge log file.

[ssn34@…]

attempt to install atlas after gcc44 rebuild

[shawathome@…]

FYI, I also was able to fix my atlas install/build problem by following this (force clean all):

~snip

Last login: Wed Jul 28 09:37:18 on console mike:~ michaelshaw$ sudo port clean --all atlas Password: ---> Cleaning atlas Warning: Distfiles directory '/opt/local/var/macports/distfiles/atlas/3.8.3_4' may contain distfiles needed for other ports, use the -f flag to force removal mike:~ michaelshaw$ sudo port clean --all -f atlas ---> Cleaning atlas mike:~ michaelshaw$ sudo port install atlas ---> Computing dependencies for atlas ---> Fetching atlas ---> Attempting to fetch atlas3.8.3.tar.bz2 from ​http://distfiles.macports.org/atlas/3.8.3_4 ---> Attempting to fetch lapack.tgz from ​http://distfiles.macports.org/atlas/3.8.3_4 ---> Verifying checksum(s) for atlas ---> Extracting atlas ---> Applying patches to atlas ---> Configuring atlas ---> Building atlas ---> Staging atlas into destroot ---> Installing atlas @3.8.3_4+gcc44 ---> Activating atlas @3.8.3_4+gcc44 ---> Cleaning atlas mike:~ michaelshaw$

~end snip

FYI, it took a long time to perform the build (~approx. 1.5 hrs). I was able to make sure the build was actually processing by viewing the log file during the build and thereby ensuring that changes were happening. I think I just gave up the last time I tried to do the build because I thought it had stalled. The trick is to verify what's going on by viewing the file in real time. The build file is located in /var/macports/logs.

Thanks for all the comments, suggestions and help.

[andrew@…]

Cc Me!

[andrew@…]

I noticed that I was running Xcode 3.2.2 and updated it to Xcode 3.2.3, following which I managed to build atlas @3.8.3.

@shawathorne & kwkelly: Not sure if this may have had an impact on your perceived successes above re: clean & reinstall, as I tried that previously and it did not help. Could it have been a passing of time, during which you allowed Software Update to update Xcode? It may have been a completely unrelated issue, but I still believe it is worth asking the question.

[jameskyle@…]

This build does take a while, if you'd like to "see things happening" to ensure that it's not stalled, use the -v switch:

$ sudo port install -v atlas

Lots of interesting text going by. :)

If I understand this post, it looks like some changes in the gcc44 build was effecting the atlas build. By removing and cleaning the gcc port, then rebuilding the issues went away?

As such, I'm closing as "fixed", but please reopen if my interpretation is incorrect.