hdf5: broken file found by rev-upgrade

[steeves@…]

Starting from fresh install, running "port install hdf5" fails with

Error: Port hdf5 is still broken after rebuiling it more than 3 times.
Error: Please run port -d -y rev-upgrade and use the output to report a bug.
Port hdf5 still broken after rebuilding 3 time(s)
    while executing
"error "Port $portname still broken after rebuilding [expr $broken_port_counts($portname) - 1] time(s)""
    (procedure "revupgrade_scanandrebuild" line 240)
    invoked from within
"revupgrade_scanandrebuild broken_port_counts $opts"
    (procedure "macports::revupgrade" line 5)
    invoked from within
"macports::revupgrade $opts"
    (procedure "action_revupgrade" line 2)
    invoked from within
"action_revupgrade $action $portlist $opts"
    (procedure "action_target" line 94)
    invoked from within
"$action_proc $action $portlist [array get global_options]"
    (procedure "process_cmd" line 95)
    invoked from within
"process_cmd $remaining_args"
    invoked from within
"if { [llength $remaining_args] > 0 } {

    # If there are remaining arguments, process those as a command
    set exit_status [process_cmd $remaining..."
    (file "/opt/local/bin/port" line 4784)

[steevmi1@phusca-l24500][20:27]
[~/] % sudo port -d -y rev-upgrade
Password: 
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/bugpoint
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llc
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/lli
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-ar
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-as
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-bcanalyzer
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-cov
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-diff
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-dis
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-dwarfdump
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-extract
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-ld
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-link
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-mc
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-nm
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-objdump
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-prof
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-ranlib
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-rtdyld
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/llvm-size
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/macho-dump
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-3.0/bin/opt
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/ld64/ld
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/bugpoint
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llc
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/lli
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-ar
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-as
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-bcanalyzer
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-diff
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-dis
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-extract
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-ld
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-link
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-mc
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-nm
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-objdump
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-prof
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvm-ranlib
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/llvmc
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/macho-dump
DEBUG: Ignoring loadcommand containing @executable_path in /opt/local/libexec/llvm-2.9/bin/opt
--->  Scanning binaries for linking errors
Could not open /opt/local/lib/libh5test.0.dylib: Error opening or reading file (referenced from /opt/local/bin/h5perf)
DEBUG: Marking /opt/local/bin/h5perf as broken

--->  Found 1 broken file(s), matching files to ports
--->  Found 1 broken port(s), determining rebuild order
DEBUG: Processing port hdf5 @0:1.6.9_1  
--->  Rebuilding in order
     hdf5 @1.6.9 
DEBUG: epoch: in tree: 0 installed: 0
DEBUG: hdf5 1.6.9_1 exists in the ports tree
DEBUG: hdf5 1.6.9_1  is the latest installed
DEBUG: hdf5 1.6.9_1  is active
DEBUG: Merging existing variants '' into variants
DEBUG: new fully merged portvariants: 
DEBUG: Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/hdf5
DEBUG: OS darwin/10.8.0 (Mac OS X 10.6) arch i386
DEBUG: org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
DEBUG: org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
DEBUG: org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
DEBUG: universal_variant is false, so not adding the default universal variant
DEBUG: Not following dependencies
Skipping deactivate hdf5 @1.6.9_1 (dry run)
Skipping activate hdf5 @1.6.9_1 (dry run)
DEBUG: Rebuilding port hdf5 finished with status 0
Warning: If this was no dry run, rev-upgrade would now run the checks again to find unresolved and newly created problems

[ryandesign (Ryan Carsten Schmidt)]

Please use WikiFormatting when writing in Trac.

[asnedden@…]

Cc Me!

[ryandesign (Ryan Carsten Schmidt)]

Has duplicate #34683.

[asnedden@…]

This issue is quite aggravating because it seems that when I try installing other ports, macports searches for 'broken files' and now always finds this hdf5 issue and it appears that it is preventing the installation of other programs. I tried building fftw@2.1.5 via macports I got the identical message as described here ​https://trac.macports.org/ticket/34591. I checked for the libraries that should have been installed from fftw2.1.5. It appears that none of them were installed in /opt/local/lib as would be expected. Is there a way around this? Thanks.

[perutaca@…]

This issue is still unresolved. I have the exact same problem and same error messages. Ideas on working around it?

[perutaca@…]

Cc Me!

[neverpanic (Clemens Lang)]

Where does the hdf5 port install /opt/local/lib/libh5test.0.dylib? Check with port contents hdf5 | grep dylib.

[perutaca@…]

Replying to cal@…:

Where does the hdf5 port install /opt/local/lib/libh5test.0.dylib? Check with port contents hdf5 | grep dylib.

Here is the output of port contents hdf5 | grep dylib

/opt/local/lib/libhdf5.0.0.0.dylib /opt/local/lib/libhdf5.0.dylib /opt/local/lib/libhdf5.dylib /opt/local/lib/libhdf5_hl.0.0.0.dylib /opt/local/lib/libhdf5_hl.0.dylib /opt/local/lib/libhdf5_hl.dylib

[neverpanic (Clemens Lang)]

It seems libh5test.dylib only contains code used in testcases. While I could install libh5test.dylib, it is intended for installation.

Also, the binary causing this, h5perf doesn't do anything other than printing

:) clemens@cSchlepptop:[..]/destroot/opt/local/bin$ DYLD_LIBRARY_PATH=../lib/:../../../../hdf5-1.6.9/test/.libs/ ./h5perf 
No parallel IO performance because parallel is not configured

I think we can just remove the binary in question to fix this. I've done this in r95095. Please let me know if you think this was inappropriate.

[neverpanic (Clemens Lang)]

Replying to cal@…:

While I could install libh5test.dylib, it is intended for installation.

That should have read: "[…] it is not intended for installation."

[neverpanic (Clemens Lang)]

Also note there's a newer version of hdf5 available in the hdf5-18 port.