#39268: Atlas upgrade failed with "command execution failed" --------------------------------+-------------------------------- Reporter: serge.rykovanov@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: | --------------------------------+-------------------------------- Comment (by 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 Cleaning atlas Sergeys-MacBook-Pro-2:VDSR sergey$ sudo port upgrade outdated ---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. -- Ticket URL: <https://trac.macports.org/ticket/39268#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X

#39268: Atlas upgrade failed with "command execution failed" --------------------------------+--------------------- Reporter: serge.rykovanov@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: invalid | Keywords: Port: atlas | --------------------------------+--------------------- Changes (by vince@…): * status: new => closed * resolution: => invalid Comment: Since I see no followup to the message of Ryan, I dare consider this issue as somehow fixed. -- Ticket URL: <https://trac.macports.org/ticket/39268#comment:4> MacPorts <http://www.macports.org/> Ports system for OS X

#39268: Atlas upgrade failed with "command execution failed" --------------------------------+--------------------- Reporter: serge.rykovanov@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: invalid | Keywords: Port: atlas | --------------------------------+--------------------- Comment (by vince@…): My pleasure. -- Ticket URL: <https://trac.macports.org/ticket/39268#comment:6> MacPorts <http://www.macports.org/> Ports system for OS X