#25619: atlas build failure ------------------------------------+--------------------------------------- Reporter: bertagna@… | Owner: jameskyle@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.1 Keywords: | Port: atlas ------------------------------------+--------------------------------------- Changes (by jmr@…): * owner: macports-tickets@… => jameskyle@… * port: => atlas * milestone: MacPorts 2.0.0 => Old description:

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

New description: 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 -- Comment: 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. Please attach the log mentioned in the output. -- Ticket URL: <http://trac.macports.org/ticket/25619#comment:2> MacPorts <http://www.macports.org/> Ports system for Mac OS

#25619: atlas build failure ------------------------------------+--------------------------------------- Reporter: bertagna@… | Owner: jameskyle@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.1 Keywords: | Port: atlas ------------------------------------+--------------------------------------- Comment(by 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 -- Ticket URL: <http://trac.macports.org/ticket/25619#comment:4> MacPorts <http://www.macports.org/> Ports system for Mac OS

#25619: atlas build failure ------------------------------------+--------------------------------------- Reporter: bertagna@… | Owner: jameskyle@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.1 Keywords: | Port: atlas ------------------------------------+--------------------------------------- Comment(by bertagna@…): Replying to [comment:5 jmr@…]:

Please review the [wiki:FAQ#selfupdatefails 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). -- Ticket URL: <http://trac.macports.org/ticket/25619#comment:6> MacPorts <http://www.macports.org/> Ports system for Mac OS

#25619: atlas build failure ------------------------------------+--------------------------------------- Reporter: bertagna@… | Owner: jameskyle@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.1 Keywords: | Port: atlas ------------------------------------+--------------------------------------- Comment(by kwkelly@…): I got that error, then did $ sudo port clean --all atlas then tried reinstalling it and it worked just fine. -- Ticket URL: <http://trac.macports.org/ticket/25619#comment:9> MacPorts <http://www.macports.org/> Ports system for Mac OS

#25619: atlas build failure ------------------------------------+--------------------------------------- Reporter: bertagna@… | Owner: jameskyle@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.1 Keywords: | Port: atlas ------------------------------------+--------------------------------------- Comment(by ram@…): 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 -- Ticket URL: <http://trac.macports.org/ticket/25619#comment:12> MacPorts <http://www.macports.org/> Ports system for Mac OS

#25619: atlas build failure ------------------------------------+--------------------------------------- Reporter: bertagna@… | Owner: jameskyle@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.1 Keywords: | Port: atlas ------------------------------------+--------------------------------------- Comment(by 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. -- Ticket URL: <http://trac.macports.org/ticket/25619#comment:14> MacPorts <http://www.macports.org/> Ports system for Mac OS

#25619: atlas build failure -------------------------------------+-------------------------------------- Reporter: bertagna@… | Owner: jameskyle@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 1.9.1 Resolution: fixed | Keywords: Port: atlas | -------------------------------------+-------------------------------------- Changes (by jameskyle@…): * status: new => closed * resolution: => fixed Comment: 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. -- Ticket URL: <http://trac.macports.org/ticket/25619#comment:17> MacPorts <http://www.macports.org/> Ports system for Mac OS