[MacPorts] #49198: netcdf @4.3.3.1_2 +dap +netcdf4 +gcc49/+gcc5 test fails
#49198: netcdf @4.3.3.1_2 +dap +netcdf4 +gcc49/+gcc5 test fails ------------------------+----------------------- Reporter: dstrubbe@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Keywords: | Port: netcdf ------------------------+----------------------- Extracts from the log below. This is with XCode 6.4, OSX Yosemite 10.10.5. With +gcc49, using hdf5 @1.8.15-patch1_0+cxx+gcc49: {{{ :info:test PASS: t_nc :info:test PASS: tst_small :info:test ../test-driver: line 107: 33547 Segmentation fault: 11 "$@" > $log_file 2>&1 :info:test FAIL: nc_test :info:test PASS: tst_misc :info:test PASS: tst_norm :info:test PASS: tst_names :info:test PASS: tst_nofill :info:test PASS: tst_nofill2 :info:test PASS: tst_nofill3 :info:test ../test-driver: line 107: 33684 Segmentation fault: 11 "$@" > $log_file 2>&1 :info:test FAIL: tst_atts3 :info:test PASS: tst_meta :info:test PASS: tst_atts :info:test PASS: run_diskless.sh :info:test make[4]: Nothing to be done for `all'. :info:test ============================================================================ :info:test Testsuite summary for netCDF 4.3.3.1 :info:test ============================================================================ :info:test # TOTAL: 13 :info:test # PASS: 11 :info:test # SKIP: 0 :info:test # XFAIL: 0 :info:test # FAIL: 2 :info:test # XPASS: 0 :info:test # ERROR: 0 :info:test ============================================================================ :info:test See nc_test/test-suite.log :info:test Please report to support-netcdf@unidata.ucar.edu :info:test ============================================================================ :info:test make[3]: *** [test-suite.log] Error 1 }}} with +gcc5, using hdf5 @1.8.15-patch1_0+cxx+gcc5: {{{ info:test Making check in ncgen3 :info:test /Applications/Xcode.app/Contents/Developer/usr/bin/make check- TESTS :info:test FAIL: run_tests.sh :info:test FAIL: run_nc4_tests.sh :info:test make[4]: Nothing to be done for `all'. :info:test ============================================================================ :info:test Testsuite summary for netCDF 4.3.3.1 :info:test ============================================================================ :info:test # TOTAL: 2 :info:test # PASS: 0 :info:test # SKIP: 0 :info:test # XFAIL: 0 :info:test # FAIL: 2 :info:test # XPASS: 0 :info:test # ERROR: 0 :info:test ============================================================================ :info:test See ncgen3/test-suite.log :info:test Please report to support-netcdf@unidata.ucar.edu :info:test ============================================================================ :info:test make[3]: *** [test-suite.log] Error 1 :info:test make[2]: *** [check-TESTS] Error 2 :info:test make[1]: *** [check-am] Error 2 :info:test make: *** [check-recursive] Error 1 :info:test Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_netcdf/netcdf/work/netcdf-c-4.3.3.1" && /usr/bin/make check =========================================== netCDF 4.3.3.1: ncgen3/test-suite.log =========================================== # TOTAL: 2 # PASS: 0 # SKIP: 0 # XFAIL: 0 # FAIL: 2 # XPASS: 0 # ERROR: 0 .. contents:: :depth: 2 FAIL: run_tests.sh ================== *** Testing ncgen3. *** creating classic file c0.nc from c0.cdl... ./run_tests.sh: line 8: 76145 Segmentation fault: 11 ./ncgen3 -b -o c0.nc $srcdir/c0.cdl FAIL: run_nc4_tests.sh ====================== *** Testing ncgen3 for netCDF-4. *** creating netCDF-4 file c0_4.nc from c0.cdl... ./run_nc4_tests.sh: line 8: 76166 Segmentation fault: 11 ./ncgen3 -k3 -b -o c0_4.nc $srcdir/c0.cdl }}} -- Ticket URL: <https://trac.macports.org/ticket/49198> MacPorts <https://www.macports.org/> Ports system for OS X
#49198: netcdf @4.3.3.1_2 +dap +netcdf4 +gcc49/+gcc5 test fails -------------------------+----------------------- Reporter: dstrubbe@… | Owner: takeshi@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: netcdf | -------------------------+----------------------- Comment (by piergiuseppe.fogli@…): I have a similar problem with netcdf @4.3.3.1_4+dap+gcc5+netcdf4 using MacPorts 2.3.4 on El Capitan (10.11.1). The installation process seems OK, but I have problems running ncdump or other software using the netcdf library (nco, cdo, ncview, ...). [[BR]] gdb gives the following error: {{{ sudo gdb --args ncdump -h foo.nc Reading symbols from ncdump...(no debugging symbols found)...done. (gdb) run Starting program: /opt/local/bin/ncdump -h foo.nc netcdf foo { dimensions: time = UNLIMITED ; // (120 currently) latitude = 180 ; longitude = 360 ; nv = 2 ; variables: Program received signal SIGSEGV, Segmentation fault. 0x00007fff909c12da in stack_not_16_byte_aligned_error () from /usr/lib/system/libdyld.dylib (gdb) where #0 0x00007fff909c12da in stack_not_16_byte_aligned_error () from /usr/lib/system/libdyld.dylib #1 0x000000000000001c in ?? () #2 0x00000001000b31e8 in ?? () from /opt/local/lib/libnetcdf.7.dylib #3 0x0000000000000bbe in ?? () #4 0x0000000100020990 in utf8proc_reencode () from /opt/local/lib/libnetcdf.7.dylib #5 0x0000000100020a2c in utf8proc_map () from /opt/local/lib/libnetcdf.7.dylib #6 0x0000000100020a98 in utf8proc_NFC () from /opt/local/lib/libnetcdf.7.dylib #7 0x000000010002fde2 in NC_finddim () from /opt/local/lib/libnetcdf.7.dylib #8 0x000000010003027c in NC3_inq_dimid () from /opt/local/lib/libnetcdf.7.dylib #9 0x000000010001a0e2 in nc_inq_dimid () from /opt/local/lib/libnetcdf.7.dylib #10 0x0000000100004c25 in do_ncdump_rec.isra () #11 0x000000010000aecb in main () }}} This problem does not happen if netcdf is compiled without the gcc5 variant or with the clang37 variant (I have not tested other versions). Might the stack_not_16_byte_aligned_error error be related to the [[https://trac.macports.org/ticket/44596#comment:35|Libtool MACOSX_DEPLOYMENT_TARGET bug]] happening on El Capitan (10.11)? -- Ticket URL: <https://trac.macports.org/ticket/49198#comment:2> MacPorts <https://www.macports.org/> Ports system for OS X
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