Atlas upgrade failed with "command execution failed"

[serge.rykovanov@…]

I have exactly the same problem as in closed ticket "Ticket #39065"

I am running Mac OS X 10.7.5, XCode 4.5.2

Here is the log of what I was doing:

sergey$ sudo port clean atlas
--->  Cleaning atlas
sergey$ sudo port upgrade outdated
--->  Computing dependencies for atlas
--->  Fetching distfiles for atlas
--->  Verifying checksum(s) for atlas
--->  Extracting atlas
--->  Applying patches to atlas
--->  Configuring atlas
Selected C compiler: /opt/local/bin/clang-mp-3.3
Selected F77 compiler: gfortran46
--->  Building atlas
Error: org.macports.build for port atlas returned: command execution failed
Please see the log file for port atlas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log
Error: Unable to upgrade port: 1
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets

[larryv (Lawrence Velázquez)]

Please clean atlas and try installing again, and attach the log file after it fails.

[serge.rykovanov@…]

okay, now for unknown reason atlas is installing (although takes already more than 2 hours).

In the meanwhile I tried working with h5py using ipython and that caused the ipython to crash, so i decided to manually update h5py.

Here is what I did exactly:

sudo port clean atlas
--->  Cleaning atlas
Sergeys-MacBook-Pro-2:VDSR sergey$ sudo port upgrade outdated
--->  Computing dependencies for atlas
--->  Fetching distfiles for atlas
--->  Verifying checksum(s) for atlas
--->  Extracting atlas
--->  Applying patches to atlas
--->  Configuring atlas
Selected C compiler: /opt/local/bin/clang-mp-3.3
Selected F77 compiler: gfortran46
--->  Building atlas
Error: org.macports.build for port atlas returned: command execution failed
Please see the log file for port atlas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log
Error: Unable to upgrade port: 1
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Sergeys-MacBook-Pro-2:VDSR sergey$ ipython notebook --pylab inline
[NotebookApp] Using existing profile dir: u'/Users/sergey/.ipython/profile_default'
[NotebookApp] Serving notebooks from /Users/sergey/work/Patrack/RADIATION_PREPARATION/Test_Single/VDSR
[NotebookApp] The IPython Notebook is running at: http://127.0.0.1:8888/
[NotebookApp] Use Control-C to stop this server and shut down all kernels.
[NotebookApp] Using MathJax from CDN: http://cdn.mathjax.org/mathjax/latest/MathJax.js
[NotebookApp] Kernel started: a0c8ad21-0329-4236-8218-4d19824a424c
[NotebookApp] Connecting to: tcp://127.0.0.1:51464
[NotebookApp] Connecting to: tcp://127.0.0.1:51465
[NotebookApp] Connecting to: tcp://127.0.0.1:51467
[IPKernelApp] To connect another client to this kernel, use:
[IPKernelApp] --existing kernel-a0c8ad21-0329-4236-8218-4d19824a424c.json
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.8.9, library is 1.8.10
	    SUMMARY OF THE HDF5 CONFIGURATION
	    =================================

General Information:
-------------------
		   HDF5 Version: 1.8.10
		  Configured on: Mon Feb 18 08:10:07 PST 2013
		  Configured by: macports@tenseven-slave.macports.org
		 Configure mode: production
		    Host system: i386-apple-darwin11.4.2
	      Uname information: Darwin tenseven-slave.macports.org 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
		       Byte sex: little-endian
		      Libraries: 
	     Installation point: /opt/local

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/bin/clang
                         CFLAGS: -pipe -O2 
                      H5_CFLAGS:  
                      AM_CFLAGS: 
                       CPPFLAGS: -I/opt/local/include
                    H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS: 
               Shared C Library: yes
               Static C Library: yes
  Statically Linked Executables: no
                        LDFLAGS: -L/opt/local/lib 
                     H5_LDFLAGS: 
                     AM_LDFLAGS: 
 	 	Extra libraries:  -lz -lm 
 		       Archiver: ar
 		 	 Ranlib: ranlib
 	      Debugged Packages: 
		    API Tracing: no

Languages:
----------
                        Fortran: no

                            C++: yes
                   C++ Compiler: /usr/bin/clang++
                      C++ Flags: -pipe -O2 
                   H5 C++ Flags:  
                   AM C++ Flags: 
             Shared C++ Library: yes
             Static C++ Library: yes

Features:
---------
                  Parallel HDF5: no
             High Level library: yes
                   Threadsafety: no
            Default API Mapping: v18
 With Deprecated Public Symbols: yes
         I/O filters (external): deflate(zlib)
         I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
                            MPE: no
                     Direct VFD: no
                        dmalloc: no
Clear file buffers before write: yes
           Using memory checker: no
         Function Stack Tracing: no
                           GPFS: no
      Strict File Format Checks: no
   Optimization Instrumentation: no
       Large File Support (LFS): yes
Bye...
[NotebookApp] Kernel a0c8ad21-0329-4236-8218-4d19824a424c failed to respond to heartbeat
^CShutdown Notebook Server (y/[n])? y
[NotebookApp] Shutdown confirmed
[NotebookApp] Shutting down kernels
[NotebookApp] Kernel shutdown: a0c8ad21-0329-4236-8218-4d19824a424c
Sergeys-MacBook-Pro-2:VDSR sergey$ sudo port upgrade py27-h5py
Password:
--->  Computing dependencies for py27-distribute
--->  Fetching archive for py27-distribute
--->  Attempting to fetch py27-distribute-0.6.43_0.darwin_11.noarch.tbz2 from http://packages.macports.org/py27-distribute
--->  Attempting to fetch py27-distribute-0.6.43_0.darwin_11.noarch.tbz2.rmd160 from http://packages.macports.org/py27-distribute
--->  Installing py27-distribute @0.6.43_0
--->  Cleaning py27-distribute
--->  Computing dependencies for py27-distribute
--->  Deactivating py27-distribute @0.6.39_0
--->  Cleaning py27-distribute
--->  Activating py27-distribute @0.6.43_0
--->  Cleaning py27-distribute
--->  Computing dependencies for py27-h5py
--->  Fetching archive for py27-h5py
--->  Attempting to fetch py27-h5py-2.1.3_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/py27-h5py
--->  Attempting to fetch py27-h5py-2.1.3_0.darwin_11.x86_64.tbz2.rmd160 from http://packages.macports.org/py27-h5py
--->  Installing py27-h5py @2.1.3_0
--->  Cleaning py27-h5py
--->  Computing dependencies for py27-h5py
--->  Deactivating py27-h5py @2.0.1_3
--->  Cleaning py27-h5py
--->  Activating py27-h5py @2.1.3_0
--->  Cleaning py27-h5py
--->  Updating database of binaries: 100.0%
--->  Scanning binaries for linking errors: 100.0%
--->  Found 103 broken file(s), matching files to ports
--->  Found 5 broken port(s), determining rebuild order
--->  Rebuilding in order
     py27-pil @1.1.7 
     py27-rpy2 @2.2.1 
     arpack @3.1.2 +accelerate+gcc45+openmpi
     octave @3.2.4 +atlas+gcc45
     gcc46 @4.6.3 
--->  Computing dependencies for py27-pil
--->  Cleaning py27-pil
--->  Computing dependencies for py27-rpy2
--->  Cleaning py27-rpy2
--->  Computing dependencies for arpack
--->  Cleaning arpack
Portfile changed since last build; discarding previous state.
--->  Computing dependencies for octave
--->  Fetching archive for octave
--->  Attempting to fetch octave-3.2.4_13+atlas+gcc45.darwin_11.x86_64.tbz2 from http://packages.macports.org/octave
--->  Attempting to fetch octave-3.2.4_13+atlas+gcc45.darwin_11.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/octave
--->  Attempting to fetch octave-3.2.4_13+atlas+gcc45.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/octave
--->  Fetching distfiles for octave
--->  Verifying checksum(s) for octave
--->  Extracting octave
--->  Applying patches to octave
--->  Configuring octave
--->  Building octave
--->  Staging octave into destroot
--->  Installing octave @3.2.4_13+atlas+gcc45
--->  Cleaning octave
--->  Computing dependencies for octave
--->  Deactivating octave @3.2.4_10+atlas+gcc45
--->  Cleaning octave
--->  Activating octave @3.2.4_13+atlas+gcc45
--->  Cleaning octave
--->  Computing dependencies for gcc46
--->  Fetching archive for gcc46
--->  Attempting to fetch gcc46-4.6.4_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/gcc46
--->  Attempting to fetch gcc46-4.6.4_0.darwin_11.x86_64.tbz2.rmd160 from http://packages.macports.org/gcc46
--->  Installing gcc46 @4.6.4_0
--->  Cleaning gcc46
--->  Computing dependencies for gcc46
--->  Deactivating gcc46 @4.6.3_8
--->  Cleaning gcc46
--->  Activating gcc46 @4.6.4_0
--->  Cleaning gcc46
--->  Updating database of binaries: 100.0%
--->  Scanning binaries for linking errors: 100.0%
--->  Found 14 broken file(s), matching files to ports
--->  Found 3 broken port(s), determining rebuild order
--->  Rebuilding in order
     py27-pil @1.1.7 
     py27-rpy2 @2.2.1 
     arpack @3.1.2 +accelerate+gcc45+openmpi
--->  Computing dependencies for py27-pil
--->  Cleaning py27-pil
--->  Unable to uninstall py27-pil @1.1.7_6, the following ports depend on it:
--->  	py27-opengl @3.0.1_0
Warning: Uninstall forced.  Proceeding despite dependencies.
--->  Deactivating py27-pil @1.1.7_6
--->  Unable to deactivate py27-pil @1.1.7_6, the following ports depend on it:
--->  	py27-opengl @3.0.1_0
Warning: Deactivate forced.  Proceeding despite dependencies.
--->  Cleaning py27-pil
--->  Uninstalling py27-pil @1.1.7_6
--->  Cleaning py27-pil
--->  Computing dependencies for py27-pil
--->  Fetching distfiles for py27-pil
--->  Attempting to fetch Imaging-1.1.7.tar.gz from http://distfiles.macports.org/py-pil
--->  Verifying checksum(s) for py27-pil
--->  Extracting py27-pil
--->  Applying patches to py27-pil
--->  Configuring py27-pil
--->  Building py27-pil
--->  Staging py27-pil into destroot
--->  Installing py27-pil @1.1.7_6
--->  Activating py27-pil @1.1.7_6
--->  Cleaning py27-pil
--->  Computing dependencies for py27-rpy2
--->  Cleaning py27-rpy2
--->  Deactivating py27-rpy2 @2.2.1_0
--->  Cleaning py27-rpy2
--->  Uninstalling py27-rpy2 @2.2.1_0
--->  Cleaning py27-rpy2
--->  Computing dependencies for py27-rpy2
--->  Fetching distfiles for py27-rpy2
--->  Attempting to fetch rpy2-2.2.1.tar.gz from http://distfiles.macports.org/py-rpy2
--->  Verifying checksum(s) for py27-rpy2
--->  Extracting py27-rpy2
--->  Configuring py27-rpy2
--->  Building py27-rpy2
--->  Staging py27-rpy2 into destroot
--->  Installing py27-rpy2 @2.2.1_0
--->  Activating py27-rpy2 @2.2.1_0
--->  Cleaning py27-rpy2
--->  Computing dependencies for arpack
--->  Cleaning arpack
--->  Unable to uninstall arpack @3.1.2_1+accelerate+gcc45+openmpi, the following ports depend on it:
--->  	octave @3.2.4_7+atlas+gcc45
--->  	octave @3.2.4_8+atlas+gcc45
--->  	octave @3.2.4_9+atlas+gcc45
--->  	octave @3.2.4_10+atlas+gcc45
--->  	octave @3.2.4_13+atlas+gcc45
Warning: Uninstall forced.  Proceeding despite dependencies.
--->  Deactivating arpack @3.1.2_1+accelerate+gcc45+openmpi
--->  Unable to deactivate arpack @3.1.2_1+accelerate+gcc45+openmpi, the following ports depend on it:
--->  	octave @3.2.4_13+atlas+gcc45
Warning: Deactivate forced.  Proceeding despite dependencies.
--->  Cleaning arpack
--->  Uninstalling arpack @3.1.2_1+accelerate+gcc45+openmpi
--->  Cleaning arpack
--->  Computing dependencies for arpack
--->  Fetching distfiles for arpack
--->  Attempting to fetch get from http://distfiles.macports.org/arpack/3.1.2
--->  Verifying checksum(s) for arpack
--->  Extracting arpack
--->  Applying patches to arpack
--->  Configuring arpack
--->  Building arpack
--->  Staging arpack into destroot
--->  Installing arpack @3.1.2_1+accelerate+gcc45+openmpi
--->  Activating arpack @3.1.2_1+accelerate+gcc45+openmpi
--->  Cleaning arpack
--->  Updating database of binaries: 100.0%
--->  Scanning binaries for linking errors: 100.0%
--->  No broken files found.
Sergeys-MacBook-Pro-2:VDSR sergey$ sudo port upgrade outdated
Password:
--->  Computing dependencies for atlas
--->  Building atlas
Error: org.macports.build for port atlas returned: command execution failed
Please see the log file for port atlas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log
Error: Unable to upgrade port: 1
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Sergeys-MacBook-Pro-2:VDSR sergey$ sudo port clean atlas
--->  Cleaning atlas
Sergeys-MacBook-Pro-2:VDSR sergey$ sudo port upgrade outdated
--->  Computing dependencies for atlas
--->  Fetching distfiles for atlas
--->  Verifying checksum(s) for atlas
--->  Extracting atlas
--->  Applying patches to atlas
--->  Configuring atlas
Selected C compiler: /opt/local/bin/clang-mp-3.3
Selected F77 compiler: gfortran46
--->  Building atlas

Before doing all that I made sure I did "port selfupdate" and "port upgrade outdated". So I do not know what steps to take when this happens again? (and similar things happen every time I do selfupdate). Shouldn't the "h5py" be upgraded anyway? Why do I need to pick it manually? Why after upgrading it, the atlas out of the sudden starts building? Does it mean something is wrong with the queue of installation?

What are general ideas to avoid this problem in future? How is the self-update and upgrade outdated process should be properly done (maybe I am doing something wrong??? )?

Thanks a lot.

[ryandesign (Ryan Carsten Schmidt)]

You have a lot of questions that I don't know how to answer. All I can say is if a port fails to build, and you've cleaned and tried again, then file a bug report and attach the main.log file so that the maintainer can take a look. Remember to fill in the Port field and to Cc the port's maintainer. If atlas fails to build again, attach the main.log file here. Otherwise, if it finishes the installation successfully, let us know so we can close this ticket. If you have further questions about how to use MacPorts, ask on the macports-users mailing list.

[Veence (Vincent)]

Since I see no followup to the message of Ryan, I dare consider this issue as somehow fixed.

[serge.rykovanov@…]

Replying to vince@…:

Since I see no followup to the message of Ryan, I dare consider this issue as somehow fixed.

Atlas is now installed. Next stop was vtk - exactly the same story :) After that I deleted everything. I guess this ticket is closed. Thanks a lot for your help

[Veence (Vincent)]

My pleasure.