[MacPorts] #43867: netcdf not building on snow leopard
#43867: netcdf not building on snow leopard -----------------------+-------------------------------- Reporter: gnurser@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Keywords: netcdf | Port: netcdf -----------------------+-------------------------------- Hi,[[BR]] netcdf-4.3.1.1_1+dap+gcc47+netcdf4+openmpi is failing to build for me. Problem seems to be missing symbol "_H5Pset_fapl_mpiposix" Cheers, George Nurser -- Ticket URL: <https://trac.macports.org/ticket/43867> MacPorts <http://www.macports.org/> Ports system for OS X
#43867: netcdf not building on snow leopard ------------------------+----------------------- Reporter: gnurser@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: netcdf | ------------------------+----------------------- Changes (by mf2k@…): * owner: macports-tickets@… => takeshi@… * keywords: netcdf => * cc: takeshi@… (removed) -- Ticket URL: <https://trac.macports.org/ticket/43867#comment:1> MacPorts <http://www.macports.org/> Ports system for OS X
#43867: netcdf not building on snow leopard ------------------------+----------------------- Reporter: gnurser@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: netcdf | ------------------------+----------------------- Comment (by ryandesign@…): netcdf was updated to 4.3.2 in r120562; please run "sudo port selfupdate" and try again with that version. -- Ticket URL: <https://trac.macports.org/ticket/43867#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X
#43867: netcdf not building on snow leopard ------------------------+----------------------- Reporter: gnurser@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: netcdf | ------------------------+----------------------- Comment (by gnurser@…): Replying to [comment:2 ryandesign@…]:
netcdf was updated to 4.3.2 in r120562; please run "sudo port selfupdate" and try again with that version.
Ok. Just tried that, but same result, it seems. -- Ticket URL: <https://trac.macports.org/ticket/43867#comment:3> MacPorts <http://www.macports.org/> Ports system for OS X
#43867: netcdf not building on snow leopard ------------------------+----------------------- Reporter: gnurser@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: netcdf | ------------------------+----------------------- Comment (by bjandre@…): It looks like hdf5 1.8.13 is not compatible with netcdf 4.3.2. See: https://github.com/Homebrew/homebrew-science/issues/911 -- Ticket URL: <https://trac.macports.org/ticket/43867#comment:4> MacPorts <http://www.macports.org/> Ports system for OS X
#43867: netcdf not building on snow leopard ------------------------+----------------------- Reporter: gnurser@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: netcdf | ------------------------+----------------------- Comment (by maximilian.behr@…): CC me -- Ticket URL: <https://trac.macports.org/ticket/43867#comment:6> MacPorts <http://www.macports.org/> Ports system for OS X
#43867: netcdf not building on snow leopard ------------------------+----------------------- Reporter: gnurser@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: netcdf | ------------------------+----------------------- Comment (by aruminat@…): Here, the same thing happens on Mavericks. {{{ $ sw_vers ProductName: Mac OS X ProductVersion: 10.9.3 BuildVersion: 13D65 }}} -- Ticket URL: <https://trac.macports.org/ticket/43867#comment:7> MacPorts <http://www.macports.org/> Ports system for OS X
#43867: netcdf not building on snow leopard ------------------------+----------------------- Reporter: gnurser@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: netcdf | ------------------------+----------------------- Comment (by smasson@…): cc me -- Ticket URL: <https://trac.macports.org/ticket/43867#comment:8> MacPorts <http://www.macports.org/> Ports system for OS X
#43867: netcdf not building on snow leopard ------------------------+----------------------- Reporter: gnurser@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: netcdf | ------------------------+----------------------- Comment (by gnurser@…): While waiting for the proper fix I found that[[BR]] (i) editing out occurrences of a/ & b/ from the patch referenced by homebrew above i.e.[[BR]] https://github.com/Unidata/netcdf-c/commit/435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8.diff[[BR]] (ii) saving as e.g. patch_netcdf.diff into the directory[[BR]] /opt/local/var/macports/sources/rsync.macports.org/release/ports/science/netcdf/files[[BR]] (iii) replacing line 35 in[[BR]] /opt/local/var/macports/sources/rsync.macports.org/release/ports/science/netcd/Portfile[[BR]] by[[BR]] patchfiles patch-configure.diff patch-netcdf.diff[[BR]] allowed netcdf to built satisfactorily. -- Ticket URL: <https://trac.macports.org/ticket/43867#comment:11> MacPorts <http://www.macports.org/> Ports system for OS X
#43867: netcdf not building on snow leopard ------------------------+----------------------- Reporter: gnurser@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: netcdf | ------------------------+----------------------- Comment (by smasson@…): The directory {{{ /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/netcdf/files }}} is not existing... I guess it is {{{ /opt/local/var/macports/sources/rsync.macports.org/release/ports/science/netcdf/files }}} I am right?[[BR]] I also think the the file as to be saved as patch-netcdf.diff and not patch_netcdf.diff[[BR]] I tried with netcdf-4.3.2_0+dap+gcc48+netcdf4+openmpi which has the same error : {{{ :info:build Undefined symbols for architecture x86_64: :info:build "_H5Pset_fapl_mpiposix", referenced from: :info:build import-atom in libnetcdf.dylib :info:build ld: symbol(s) not found for architecture x86_64 :info:build collect2: error: ld returned 1 exit status }}} With the modifications given in (i), (ii) and (iii), I get this new error message in the main.log file: {{{ :info:patch patching file configure :info:patch ---> Applying patch-netcdf.diff :debug:patch Environment: CC_PRINT_OPTIONS='YES' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_netcdf/netcdf/work/.CC_PRINT_OPTIONS' CPATH='/opt/local/include' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.9' :debug:patch Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_netcdf/netcdf/work/netcdf-c-4.3.2" && /usr/bin/patch -p0' :debug:patch Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_netcdf/netcdf/work/netcdf-c-4.3.2" && /usr/bin/patch -p0 < '/opt/local/var/macports/sources/rsync.macports.org/release/ports/science/netcdf/files /patch-netcdf.diff' :info:patch can't find file to patch at input line 5 :info:patch Perhaps you used the wrong -p or --strip option? :info:patch The text leading up to this was: :info:patch -------------------------- :info:patch |diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md :info:patch |index 27f228c..1a69d17 100644 :info:patch |--- a/RELEASE_NOTES.md :info:patch |+++ b/RELEASE_NOTES.md :info:patch -------------------------- :info:patch File to patch: :info:patch Skip this patch? [y] :info:patch Skipping patch. :info:patch 1 out of 1 hunk ignored :info:patch can't find file to patch at input line 18 :info:patch Perhaps you used the wrong -p or --strip option? :info:patch The text leading up to this was: :info:patch -------------------------- :info:patch |diff --git a/libsrc4/nc4file.c b/libsrc4/nc4file.c :info:patch |index ec3bb0c..5c957be 100644 :info:patch |--- a/libsrc4/nc4file.c :info:patch |+++ b/libsrc4/nc4file.c :info:patch -------------------------- :info:patch File to patch: :info:patch Skip this patch? [y] :info:patch Skipping patch. :info:patch 4 out of 4 hunks ignored :info:patch can't find file to patch at input line 102 :info:patch Perhaps you used the wrong -p or --strip option? :info:patch The text leading up to this was: :info:patch -------------------------- :info:patch |diff --git a/nc_test4/tst_nc4perf.c b/nc_test4/tst_nc4perf.c :info:patch |index 47af70e..3528b82 100644 :info:patch |--- a/nc_test4/tst_nc4perf.c :info:patch |+++ b/nc_test4/tst_nc4perf.c :info:patch -------------------------- :info:patch File to patch: :info:patch Skip this patch? [y] :info:patch Skipping patch. :info:patch 1 out of 1 hunk ignored :info:patch can't find file to patch at input line 118 :info:patch Perhaps you used the wrong -p or --strip option? :info:patch The text leading up to this was: :info:patch -------------------------- :info:patch |diff --git a/nc_test4/tst_parallel3.c b/nc_test4/tst_parallel3.c :info:patch |index 27f9c98..9fa534f 100644 :info:patch |--- a/nc_test4/tst_parallel3.c :info:patch |+++ b/nc_test4/tst_parallel3.c :info:patch -------------------------- :info:patch File to patch: :info:patch Skip this patch? [y] :info:patch Skipping patch. :info:patch 1 out of 1 hunk ignored :info:patch Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_netcdf/netcdf/work/netcdf-c-4.3.2" && /usr/bin/patch -p0 < '/opt/local/var/macports/sources/rsync.macports.org/release/ports/science/netcdf/files /patch-netcdf.diff' :info:patch Exit code: 1 :error:patch org.macports.patch for port netcdf returned: command execution failed :debug:patch Error code: CHILDSTATUS 8234 1 :debug:patch Backtrace: command execution failed while executing "system $fullcmdstring" ("eval" body line 1) invoked from within "eval system $notty $nice \$fullcmdstring" invoked from within "command_exec patch "" "< '$patch'"" (procedure "portpatch::patch_main" line 35) invoked from within "portpatch::patch_main org.macports.patch" ("eval" body line 1) invoked from within "eval $procedure $targetname" :info:patch Warning: targets not executed for netcdf: org.macports.install org.macports.patch org.macports.configure org.macports.build org.macports.destroot :notice:patch Please see the log file for port netcdf for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_netcdf/netcdf/main.log }}} -- Ticket URL: <https://trac.macports.org/ticket/43867#comment:15> MacPorts <http://www.macports.org/> Ports system for OS X
#43867: netcdf not building on snow leopard ------------------------+----------------------- Reporter: gnurser@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: netcdf | ------------------------+----------------------- Comment (by gnurser@…): Replying to [comment:15 smasson@…]:
The directory {{{
/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/netcdf/files
}}} is not existing... I guess it is {{{
/opt/local/var/macports/sources/rsync.macports.org/release/ports/science/netcdf/files
}}}[[BR]]
I needed the /tarballs this time (though not the last time I tried this kind of thing), but a better way to get to it is cd $(port dir netcdf)
I am right?[[BR]] I also think the the file as to be saved as patch-netcdf.diff and not patch_netcdf.diff[[BR]]
Careless of me. Yes.
I tried with netcdf-4.3.2_0+dap+gcc48+netcdf4+openmpi which has the same
error :
{{{ :info:build Undefined symbols for architecture x86_64: :info:build "_H5Pset_fapl_mpiposix", referenced from: :info:build import-atom in libnetcdf.dylib :info:build ld: symbol(s) not found for architecture x86_64 :info:build collect2: error: ld returned 1 exit status }}}
With the modifications given in (i), (ii) and (iii), I get this new error message in the main.log file:
{{{ :info:patch patching file configure :info:patch ---> Applying patch-netcdf.diff :debug:patch Environment: CC_PRINT_OPTIONS='YES'
CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_netcdf/netcdf/work/.CC_PRINT_OPTIONS'
CPATH='/opt/local/include' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.9' :debug:patch Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_netcdf/netcdf/work/netcdf-c-4.3.2" && /usr/bin/patch -p0' :debug:patch Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_netcdf/netcdf/work/netcdf-c-4.3.2" && /usr/bin/patch -p0 < '/opt/local/var/macports/sources/rsync.macports.org/release/ports/science/netcdf/files /patch-netcdf.diff' :info:patch can't find file to patch at input line 5 :info:patch Perhaps you used the wrong -p or --strip option? :info:patch The text leading up to this was: :info:patch -------------------------- :info:patch |diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md :info:patch |index 27f228c..1a69d17 100644 :info:patch |--- a/RELEASE_NOTES.md :info:patch |+++ b/RELEASE_NOTES.md
You need to do in (i) a global removal of a/ and b/ so e.g. the above 2 lines become
:info:patch {{{|---}}} RELEASE_NOTES.md[[BR]]
:info:patch |+++ RELEASE_NOTES.md
-- Ticket URL: <https://trac.macports.org/ticket/43867#comment:16> MacPorts <http://www.macports.org/> Ports system for OS X
#43867: netcdf not building on snow leopard ------------------------+----------------------- Reporter: gnurser@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: | Keywords: Port: netcdf | ------------------------+----------------------- Comment (by smasson@…): Hi George, happy to find you here! [[BR]] After a "port selfupdate" and a clean removal of all the "a/" and "b/" from the patch file, your fix works perfectly.[[BR]] Seb -- Ticket URL: <https://trac.macports.org/ticket/43867#comment:17> MacPorts <http://www.macports.org/> Ports system for OS X
#43867: netcdf not building on snow leopard ------------------------+----------------------- Reporter: gnurser@… | Owner: takeshi@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.0 Resolution: fixed | Keywords: Port: netcdf | ------------------------+----------------------- Changes (by sean@…): * status: new => closed * resolution: => fixed Comment: Sorry about the delay in patching this. I added the patch in r121070. -- Ticket URL: <https://trac.macports.org/ticket/43867#comment:18> MacPorts <http://www.macports.org/> Ports system for OS X
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