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[netCDF #EPQ-640599]: make check failed



Hi Ben,

It looks like you used the wrong compile variables:

export CFLAG=-m64
export FFLAG=-m64

It should be CFLAGS and FFLAGS. For the CFLAGS, use -arch x86_64. Try 
rebuilding, but this time use this:

export CFLAGS="-arch x86_64"
export FFLAGS=-m64

Let me know how that works.

Sean

> Hi Sean,
> 
> Thanks again for your prompt response. I'm not sure if I'm using the
> gfortran compiler correctly. When I downloaded one of the simple test codes
> from the website and attempted to run it, I got this response (here I link
> the directory that contains the libraries, just in case):
> 
> gfortran -I /usr/bin/include -o simple_xy_wr.exe simple_xy_wr.f
> Undefined symbols for architecture x86_64:
> "_nf_create_", referenced from:
> _MAIN__ in ccVJvzkh.o
> "_nf_def_dim_", referenced from:
> _MAIN__ in ccVJvzkh.o
> "_nf_def_var_", referenced from:
> _MAIN__ in ccVJvzkh.o
> "_nf_enddef_", referenced from:
> _MAIN__ in ccVJvzkh.o
> "_nf_put_var_int_", referenced from:
> _MAIN__ in ccVJvzkh.o
> "_nf_close_", referenced from:
> _MAIN__ in ccVJvzkh.o
> "_nf_strerror_", referenced from:
> _handle_err_ in ccVJvzkh.o
> ld: symbol(s) not found for architecture x86_64
> collect2: ld returned 1 exit statu
> 
> Is this related to the same error?
> 
> Hope you're well,
> 
> Ben
> 
> address@hidden> wrote:
> 
> > Hi Ben,
> >
> > From the looks of you make_check.out file, everything compiled correctly
> > and is good. Now I see what happened. So you did a make check install first,
> > which will compile netCDF, check it for errors, and install it. When you ran
> > make check the second time, the code behind make check could not find the
> > compiled libraries under your source directories because they had already
> > been moved out of there to some other location on your disk (make check
> > specifically looks in some temporary folders for the compiled libraries -
> > once you make install, those libraries are taken out of the temp folders,
> > and so make check cannot find them).
> >
> > Things look good to me!
> >
> > Sean
> >
> > > Hi Sean,
> > >
> > > Thank you for your help with this. Here are the make.out and
> > make_check.out
> > > files.
> > >
> > > Hope you're well,
> > >
> > > Ben
> > >
> > > address@hidden> wrote:
> > >
> > > > Greetings Benjamin,
> > > >
> > > > Would you kindly send the full output from make and make check? First,
> > do
> > > >
> > > > make clean
> > > >
> > > > Then, re-run the configure script as you did previously. Next, do
> > > >
> > > > make &> make.out
> > > >
> > > > and after that, do
> > > >
> > > > make check &> make_check.out
> > > >
> > > > Then, would you mind sending the make.out and make_check.out files?
> > They
> > > > will be of much help. I looks like the apple gcc-4 is having issues
> > finding
> > > > the standard c libraries and header files, but the make and make check
> > logs
> > > > will tell us for sure.
> > > >
> > > > Thanks so much!
> > > >
> > > > Sean
> > > >
> > > > > Full Name: Benjamin Johnson
> > > > > Email Address: address@hidden
> > > > > Organization: University of Maryland-College Park
> > > > > Package Version: netcdf 4.1.3
> > > > > Operating System: Mac OS X Lion
> > > > > Hardware: Intel processor
> > > > > Description of problem: I am trying to configure netcdf to run on Mac
> > OS
> > > > X Lion's x86_64 architecture (my config.log is attached). Before
> > installing
> > > > I set my environment variables:
> > > > >
> > > > > export CFLAG=-m64
> > > > > export FFLAG=-m64
> > > > >
> > > > > Then ran:
> > > > >
> > > > > sudo ./configure --prefix=/lib --disable-netcdf-4 --enable-shared
> > > > > sudo make check install
> > > > > sudo make check
> > > > >
> > > > > Running the last command produced the following:
> > > > >
> > > > > make check
> > > > > Making check in include
> > > > > make[1]: Nothing to be done for `check'.
> > > > > Making check in libdispatch
> > > > > make[1]: Nothing to be done for `check'.
> > > > > Making check in oc
> > > > > make[1]: Nothing to be done for `check'.
> > > > > Making check in libsrc
> > > > > make[1]: Nothing to be done for `check'.
> > > > > Making check in libdap2
> > > > > make[1]: Nothing to be done for `check'.
> > > > > Making check in liblib
> > > > > make[1]: Nothing to be done for `check'.
> > > > > Making check in nctest
> > > > > make  nctest tst_rename
> > > > > make[2]: `nctest' is up to date.
> > > > > make[2]: `tst_rename' is up to date.
> > > > > make  check-TESTS
> > > > > Testing V2 API with 2 different netCDF formats.
> > > > >
> > > > >
> > > > > Switching to netCDF classic format.
> > > > > *** Testing nccreate ...        *** test_nccreate: nccreate failed to
> > > > NC_CLOBBER
> > > > > *** Testing ncopen ...          *** could not create temp file
> > > > > *** Testing ncredef ...         *** test_ncredef: ncopen failed
> > > > > *** Testing ncendef ...         *** test_ncendef: ncopen failed
> > > > > *** Testing ncclose ...         *** test_ncclose: ncopen failed
> > > > > *** Testing ncinquire ...       *** test_ncinquire: ncopen failed
> > > > > *** Testing ncsync ...          *** test_ncsync: ncopen in NC_WRITE
> > mode
> > > > failed
> > > > > *** Testing ncabort ...         *** test_ncabort: ncopen failed
> > > > > *** Testing ncdimdef ...        *** test_ncdimdef: ncopen failed
> > > > > *** Testing ncdimid ...         *** test_ncdimid: ncopen failed
> > > > > *** Testing ncdiminq ...        *** test_ncdiminq: ncopen failed
> > > > > *** Testing ncdimrename ...     *** test_ncdimrename: ncopen failed
> > > > > *** Testing ncvardef ...        *** test_ncvardef: ncopen failed
> > > > > *** Testing ncvarid ...         *** test_ncvarid: ncopen failed
> > > > > *** Testing ncvarinq ...        *** test_ncvarinq: ncopen failed
> > > > > *** Testing ncvarput1 ...       *** test_ncvarput1: ncopen failed
> > > > > *** Testing ncvarget1 ...       *** test_ncvarget1: ncopen failed
> > > > > *** Testing ncvarput ...        *** test_ncvarput: ncopen failed
> > > > > *** Testing ncvarget ...        *** test_ncvarget: ncopen failed
> > > > > *** Testing ncvarputg ...       *** test_ncvarputg: ncopen failed
> > > > > *** Testing ncvargetg ...       *** test_ncvargetg: ncopen failed
> > > > > *** Testing ncrecinq ...        *** test_ncrecinq: ncopen failed
> > > > > *** Testing ncrecput ...        *** test_ncrecput: ncopen failed
> > > > > *** Testing ncattput ...        *** test_ncattput: ncopen failed
> > > > > *** Testing ncattinq ...        *** test_ncattinq: ncopen failed
> > > > > *** Testing ncattget ...        *** test_ncattget: ncopen failed
> > > > > *** Testing ncattcopy ...       *** test_ncattcopy: ncopen failed
> > > > > *** Testing ncattname ...       *** test_ncattname: ncopen failed
> > > > > *** Testing ncattrename ...     *** test_ncattrename: ncopen failed
> > > > > *** Testing ncattdel ...        *** test_ncattdel: ncopen failed
> > > > > *** Testing nctypelen ...       ok ***
> > > > >
> > > > >
> > > > > Switching to 64-bit offset format.
> > > > > *** Testing nccreate ...        *** test_nccreate: nccreate failed to
> > > > NC_CLOBBER
> > > > > *** Testing ncopen ...          *** could not create temp file
> > > > > *** Testing ncredef ...         *** test_ncredef: ncopen failed
> > > > > *** Testing ncendef ...         *** test_ncendef: ncopen failed
> > > > > *** Testing ncclose ...         *** test_ncclose: ncopen failed
> > > > > *** Testing ncinquire ...       *** test_ncinquire: ncopen failed
> > > > > *** Testing ncsync ...          *** test_ncsync: ncopen in NC_WRITE
> > mode
> > > > failed
> > > > > *** Testing ncabort ...         *** test_ncabort: ncopen failed
> > > > > *** Testing ncdimdef ...        *** test_ncdimdef: ncopen failed
> > > > > *** Testing ncdimid ...         *** test_ncdimid: ncopen failed
> > > > > *** Testing ncdiminq ...        *** test_ncdiminq: ncopen failed
> > > > > *** Testing ncdimrename ...     *** test_ncdimrename: ncopen failed
> > > > > *** Testing ncvardef ...        *** test_ncvardef: ncopen failed
> > > > > *** Testing ncvarid ...         *** test_ncvarid: ncopen failed
> > > > > *** Testing ncvarinq ...        *** test_ncvarinq: ncopen failed
> > > > > *** Testing ncvarput1 ...       *** test_ncvarput1: ncopen failed
> > > > > *** Testing ncvarget1 ...       *** test_ncvarget1: ncopen failed
> > > > > *** Testing ncvarput ...        *** test_ncvarput: ncopen failed
> > > > > *** Testing ncvarget ...        *** test_ncvarget: ncopen failed
> > > > > *** Testing ncvarputg ...       *** test_ncvarputg: ncopen failed
> > > > > *** Testing ncvargetg ...       *** test_ncvargetg: ncopen failed
> > > > > *** Testing ncrecinq ...        *** test_ncrecinq: ncopen failed
> > > > > *** Testing ncrecput ...        *** test_ncrecput: ncopen failed
> > > > > *** Testing ncrecget ...        *** test_ncrecget: ncopen failed
> > > > > *** Testing ncvarrename ...     *** test_ncvarrename: ncopen failed
> > > > > *** Testing ncattput ...        *** test_ncattput: ncopen failed
> > > > > *** Testing ncattinq ...        *** test_ncattinq: ncopen failed
> > > > > *** Testing ncattget ...        *** test_ncattget: ncopen failed
> > > > > *** Testing ncattcopy ...       *** test_ncattcopy: ncopen failed
> > > > > *** Testing ncattname ...       *** test_ncattname: ncopen failed
> > > > > *** Testing ncattrename ...     *** test_ncattrename: ncopen failed
> > > > > *** Testing ncattdel ...        *** test_ncattdel: ncopen failed
> > > > > *** Testing nctypelen ...       ok ***
> > > > >
> > > > > Total number of failures: 64
> > > > > nctest FAILURE!!!
> > > > > FAIL: nctest
> > > > >
> > > > > *** Testing v3/v4 API versions of some v2 tests.
> > > > > *** testing simple dim rename...Sorry! Unexpected result,
> > tst_rename.c,
> > > > line: 219
> > > > > FAIL: tst_rename
> > > > > PASS: compare_test_files.sh
> > > > > ================================================
> > > > > 2 of 3 tests failed
> > > > > Please report to address@hidden
> > > > > ================================================
> > > > > make[2]: *** [check-TESTS] Error 1
> > > > > make[1]: *** [check-am] Error 2
> > > > > make: *** [check-recursive] Error 1
> > > > >
> > > > >
> > > >
> > > >
> > > > Ticket Details
> > > > ===================
> > > > Ticket ID: EPQ-640599
> > > > Department: Support netCDF
> > > > Priority: Normal
> > > > Status: Open
> > > >
> > > >
> > >
> > >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: EPQ-640599
> > Department: Support netCDF
> > Priority: Normal
> > Status: Open
> >
> >
> 
> 


Ticket Details
===================
Ticket ID: EPQ-640599
Department: Support netCDF
Priority: Normal
Status: Open