netcdf-4.4.0_3+dap+gcc6+hdf4+netcdf4 upgrade/build error

[jml1@…]

Netcdf-4.4.0_3 fails to build on Mac OSX 10.11 (Xcode 7.3.1). Initially, the error occurred upgrading to netcdf-4.4.0_3+dap+gcc49+hdf4+netcdf4+openmpi, but I simplified to the headline config with a fresh install (i.e. after "sudo port -f uninstall installed") and I still get the same problem

The failure occurs during linking of the C shared library "libnetcdf.dylib" with the following error:

:info:build Undefined symbols for architecture x86_64:
:info:build   "_jpeg_CreateCompress", referenced from:
:info:build       _DFCIjpeg in libdf.a(dfjpeg.o)
:info:build   "_jpeg_CreateDecompress", referenced from:
:info:build       _DFCIunjpeg in libdf.a(dfunjpeg.o)
:info:build   "_jpeg_destroy_compress", referenced from:
:info:build       _DFCIjpeg in libdf.a(dfjpeg.o)
:info:build   "_jpeg_destroy_decompress", referenced from:
:info:build       _DFCIunjpeg in libdf.a(dfunjpeg.o)
:info:build   "_jpeg_finish_compress", referenced from:
:info:build       _DFCIjpeg in libdf.a(dfjpeg.o)
:info:build   "_jpeg_finish_decompress", referenced from:
:info:build       _DFCIunjpeg in libdf.a(dfunjpeg.o)
:info:build   "_jpeg_read_header", referenced from:
:info:build       _DFCIunjpeg in libdf.a(dfunjpeg.o)
:info:build   "_jpeg_read_scanlines", referenced from:
:info:build       _DFCIunjpeg in libdf.a(dfunjpeg.o)
:info:build   "_jpeg_resync_to_restart", referenced from:
:info:build       _jpeg_HDF_src in libdf.a(dfunjpeg.o)
:info:build       _DFCIunjpeg in libdf.a(dfunjpeg.o)
:info:build   "_jpeg_set_defaults", referenced from:
:info:build       _DFCIjpeg in libdf.a(dfjpeg.o)
:info:build   "_jpeg_set_quality", referenced from:
:info:build       _DFCIjpeg in libdf.a(dfjpeg.o)
:info:build   "_jpeg_start_compress", referenced from:
:info:build       _DFCIjpeg in libdf.a(dfjpeg.o)
:info:build   "_jpeg_start_decompress", referenced from:
:info:build       _DFCIunjpeg in libdf.a(dfunjpeg.o)
:info:build   "_jpeg_std_error", referenced from:
:info:build       _DFCIjpeg in libdf.a(dfjpeg.o)
:info:build       _DFCIunjpeg in libdf.a(dfunjpeg.o)
:info:build   "_jpeg_write_scanlines", referenced from:
:info:build       _DFCIjpeg in libdf.a(dfjpeg.o)
:info:build ld: symbol(s) not found for architecture x86_64
:info:build collect2: error: ld returned 1 exit status
:info:build make[2]: *** [liblib/libnetcdf.11.0.0.dylib] Error 1

Furthermore:

/o/l/lib> port installed jpeg
The following ports are currently installed:
  jpeg @9a_1 (active)

and, for example:

/o/l/lib> nm "libdf.a(dfjpeg.o)"

libdf.a(dfjpeg.o):
0000000000000260 T _DFCIjpeg
0000000000000510 s _DFCIjpeg.FUNC
                 U _HEpush
                 U _Hendaccess
                 U _Hstartaccess
                 U _Hstartwrite
                 U _Hwrite
                 U ___stack_chk_fail
                 U ___stack_chk_guard
                 U _calloc
                 U _free
00000000000000c0 T _hdf_empty_output_buffer
0000000000000000 T _hdf_init_destination
0000000000000110 T _hdf_term_destination
                 U _jpeg_CreateCompress
0000000000000180 T _jpeg_HDF_dest
0000000000000502 s _jpeg_HDF_dest.FUNC
0000000000000240 T _jpeg_HDF_dest_term
                 U _jpeg_destroy_compress
                 U _jpeg_finish_compress
0000000000000708 S _jpeg_message_handler
                 U _jpeg_set_defaults
                 U _jpeg_set_quality
                 U _jpeg_start_compress
                 U _jpeg_std_error
                 U _jpeg_write_scanlines
                 U _malloc

[mf2k (Frank Schima)]

In the future, please fill in the Port field and Cc the port maintainers (port info --maintainers netcdf), if any.

[jml1@…]

Sorry, first ticket...!

Replying to mf2k@…:

In the future, please fill in the Port field and Cc the port maintainers (port info --maintainers netcdf), if any.

[tenomoto (Takeshi Enomoto)]

libjpeg is looked for and found, but not added to the list of libraries for linking. Fixed in r149569. Thanks for reporting.