build failure for paths with spaces

[ghost]

I'm not sure if this is the right place to be posting this, so apologies in advance if it is not.
Anyways, I am attempting to install Meep version 1.4.3 on a Windows 7 machine through Cygwin. Harminv and h5utils seem to have installed fine, but I run into an error when attempting to make libctl. Here is the output from the configure script:

$ ./configure
checking whether to enable maintainer-specific portions of Makefiles... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
configure: WARNING: Libtool does not cope well with whitespace in pwd
checking build system type... x86_64-unknown-cygwin
checking host system type... x86_64-unknown-cygwin
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/x86_64-pc-cygwin/bin/ld.exe
checking if the linker (/usr/x86_64-pc-cygwin/bin/ld.exe) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 8192
checking how to convert x86_64-unknown-cygwin file names to x86_64-unknown-cygwin format... func_convert_file_noop
checking how to convert x86_64-unknown-cygwin file names to toolchain format... func_convert_file_noop
checking for /usr/x86_64-pc-cygwin/bin/ld.exe option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... file_magic ^x86 archive import|^x86 DLL
checking for dlltool... dlltool
checking how to associate runtime and link libraries... func_cygming_dll_for_implib
checking for ar... ar
checking for archiver @file support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -DDLL_EXPORT -DPIC
checking if gcc PIC flag -DDLL_EXPORT -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/x86_64-pc-cygwin/bin/ld.exe) supports shared libraries... yes
checking dynamic linker characteristics... Win32 ld.exe
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking for indent... indent
checking for ANSI C header files... (cached) yes
checking for guile... guile
checking for sqrt in -lm... yes
checking for guile-config... guile-config
checking if linking to guile works... yes
checking libguile.h usability... yes
checking libguile.h presence... yes
checking for libguile.h... yes
checking guile/gh.h usability... no
checking guile/gh.h presence... no
checking for guile/gh.h... no
######################### yes ##############################
checking for modern non-gh interface... yes
checking for gh_enter... no
checking for gh_eval_str... no
checking for gh_load... no
checking for gh_bool2scm... no
checking for gh_vector_ref... no
checking for gh_list_ref... no
checking for gh_length... no
checking for scm_flush_all_ports... yes
checking for scm_make_complex... yes
checking for scm_c_make_rectangular... yes
checking for scm_variable_set_x... yes
checking for scm_c_lookup... yes
checking for scm_c_make_vector... yes
checking for scm_variable_ref... yes
checking for SCM_COMPLEXP... yes
checking whether gh_lookup works properly... no
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -DDLL_EXPORT
checking if gfortran PIC flag -DDLL_EXPORT works... yes
checking if gfortran static flag -static works... no
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/x86_64-pc-cygwin/bin/ld.exe) supports shared libraries... yes
checking dynamic linker characteristics... Win32 ld.exe
checking how to hardcode library paths into programs... immediate
checking how to get verbose linking output from gfortran... -v
checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-pc-cygwin/6.4.0 -L/usr/lib/gcc/x86_64-pc-cygwin/6.4.0/../../../../x86_64-pc-cygwin/lib/../lib -L/usr/lib/gcc/x86_64-pc-cygwin/6.4.0/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-cygwin/6.4.0/../../../../x86_64-pc-cygwin/lib -L/usr/lib/gcc/x86_64-pc-cygwin/6.4.0/../../.. -lm -lgfortran -lquadmath -lcygwin -ladvapi32 -lshell32 -luser32
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for C complex keyword... complex
checking for egrep... (cached) /usr/bin/grep -E
checking nlopt.h usability... no
checking nlopt.h presence... no
checking for nlopt.h... no
checking for basename in -lgen... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating utils/Makefile
config.status: creating examples/Makefile
config.status: creating examples/example.scm
config.status: creating utils/gen-ctl-io
config.status: creating config.h
config.status: config.h is unchanged
config.status: creating src/ctl.h
config.status: src/ctl.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands

And here is what comes up when I run make:
$ make
make all-recursive
make[1]: Entering directory '/cygdrive/c/Users/Xiao Research1/Downloads/libctl-4.0.1/libctl-4.0.1'
Making all in src
make[2]: Entering directory '/cygdrive/c/Users/Xiao Research1/Downloads/libctl-4.0.1/libctl-4.0.1/src'
make all-am
make[3]: Entering directory '/cygdrive/c/Users/Xiao Research1/Downloads/libctl-4.0.1/libctl-4.0.1/src'
make[3]: Leaving directory '/cygdrive/c/Users/Xiao Research1/Downloads/libctl-4.0.1/libctl-4.0.1/src'
make[2]: Leaving directory '/cygdrive/c/Users/Xiao Research1/Downloads/libctl-4.0.1/libctl-4.0.1/src'
Making all in utils
make[2]: Entering directory '/cygdrive/c/Users/Xiao Research1/Downloads/libctl-4.0.1/libctl-4.0.1/utils'
make[2]: *** No rule to make target '/cygdrive/c/Users/Xiao', needed by 'ctl-io.c'. Stop.
make[2]: Leaving directory '/cygdrive/c/Users/Xiao Research1/Downloads/libctl-4.0.1/libctl-4.0.1/utils'
make[1]: *** [Makefile:470: all-recursive] Error 1
make[1]: Leaving directory '/cygdrive/c/Users/Xiao Research1/Downloads/libctl-4.0.1/libctl-4.0.1'
make: *** [Makefile:378: all] Error 2

I haven't been able to find a similar issue online thus far, so I'm not quite sure what's wrong. It appears as though it is truncating the directory 'Xiao Research1' at the whitespace and is attempting to find path/to/directory/Xiao, which is not a directory. Any idea what's wrong here?

[ChristopherHogan]

The easiest thing to try would be to use a build directory that doesn't have any spaces in the path.

[stevengj]

Yes, paths with spaces will break a lot of Unixy scripts and Makefiles unless they are written very defensively. Even if we fix this for libctl, it is likely that compiling other things will break too.

[ghost]

Thank you, that seems to have resolved that issue. I ran make once, and make check only had near2far fail. I downloaded the gsl-devel package, which was missing before, and make check then had all 19 fail. After running make again, I got this:

$ make
make all-recursive
make[1]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3'
Making all in src
make[2]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/src'
make all-am
make[3]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/src'
make[3]: Nothing to be done for 'all-am'.
make[3]: Leaving directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/src'
make[2]: Leaving directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/src'
Making all in tests
make[2]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/tests'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/tests'
Making all in examples
make[2]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/examples'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/examples'
Making all in libctl
make[2]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/libctl'
make all-am
make[3]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/libctl'
CXX meep.o
CXX structure.o
CXX meep_wrap.o
meep_wrap.c
*** Warning: This system cannot link to static lib archive /usr/local/lib/libharminv.la.
*** I have the capability to make that library automatically link in when
*** you link to this library. But I can only do this if you have a
*** shared version of the library, which you do not appear to have.
libtool: warning: undefined symbols not allowed in x86_64-unknown-cygwin shared libraries; building static only
make[2]: *** [Makefile:705: libmeepgeom.la] Interrupt
make[1]: *** [Makefile:506: all-recursive] Interrupt
make: *** [Makefile:415: all] Interrupt

[ChristopherHogan]

Looks like you need to add the --enable-shared flag when running configure for harminv.

[ghost]

I re-configured harminv with your suggestion, as well as re-ran make and make install. When I run make for meep, it finishes, but with the same warning about libtool. Make check gives the following:

$ make check
Making check in src
make[1]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/src'
make  check-am
make[2]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/src'
make[2]: Nothing to be done for 'check-am'.
make[2]: Leaving directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/src'
make[1]: Leaving directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/src'
Making check in tests
make[1]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/tests'
make  aniso_disp.exe bench.exe bragg_transmission.exe convergence_cyl_waveguide.exe cylindrical.exe flux.exe harmonics.exe integrate.exe known_results.exe near2far.exe one_dimensional.exe physical.exe stress_tensor.exe symmetry.exe three_d.exe two_dimensional.exe 2D_convergence.exe h5test.exe pml.exe
make[2]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/tests'
make[2]: 'aniso_disp.exe' is up to date.
make[2]: 'bench.exe' is up to date.
make[2]: 'bragg_transmission.exe' is up to date.
make[2]: 'convergence_cyl_waveguide.exe' is up to date.
make[2]: 'cylindrical.exe' is up to date.
make[2]: 'flux.exe' is up to date.
make[2]: 'harmonics.exe' is up to date.
make[2]: 'integrate.exe' is up to date.
make[2]: 'known_results.exe' is up to date.
make[2]: 'near2far.exe' is up to date.
make[2]: 'one_dimensional.exe' is up to date.
make[2]: 'physical.exe' is up to date.
make[2]: 'stress_tensor.exe' is up to date.
make[2]: 'symmetry.exe' is up to date.
make[2]: 'three_d.exe' is up to date.
make[2]: 'two_dimensional.exe' is up to date.
make[2]: '2D_convergence.exe' is up to date.
make[2]: 'h5test.exe' is up to date.
make[2]: 'pml.exe' is up to date.
make[2]: Leaving directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/tests'
make  check-TESTS
make[2]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/tests'
make[3]: Entering directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/tests'
FAIL: aniso_disp.exe
FAIL: bench.exe
FAIL: bragg_transmission.exe
FAIL: convergence_cyl_waveguide.exe
FAIL: cylindrical.exe
FAIL: flux.exe
FAIL: harmonics.exe
FAIL: integrate.exe
FAIL: known_results.exe
FAIL: near2far.exe
FAIL: one_dimensional.exe
FAIL: physical.exe
FAIL: stress_tensor.exe
FAIL: symmetry.exe
FAIL: three_d.exe
FAIL: two_dimensional.exe
FAIL: 2D_convergence.exe
FAIL: h5test.exe
FAIL: pml.exe
============================================================================
Testsuite summary for meep 1.4.3
============================================================================
# TOTAL: 19
# PASS:  0
# SKIP:  0
# XFAIL: 0
# FAIL:  19
# XPASS: 0
# ERROR: 0
============================================================================
See tests/test-suite.log
Please report to [email protected]
============================================================================
make[3]: *** [Makefile:922: test-suite.log] Error 1
make[3]: Leaving directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/tests'
make[2]: *** [Makefile:1030: check-TESTS] Error 2
make[2]: Leaving directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/tests'
make[1]: *** [Makefile:1227: check-am] Error 2
make[1]: Leaving directory '/cygdrive/c/meep-1.4.3/meep-1.4.3/tests'
make: *** [Makefile:506: check-recursive] Error 1

[ChristopherHogan]

What errors do you see in tests/test-suite.log?

[ghost]

They all appear to have the same error, of this form:
C:/meep-1.4.3/meep-1.4.3/tests/.libs/h5test.exe: error while loading shared libraries: cygstdc++-6.dll: cannot open shared object file: No such file or directory
FAIL h5test.exe (exit status: 127)

But for each file being tested.

Edit: This seems to be some kind of missing library/incorrect path issue. Apparently in Cygwin usr/bin is just a link to /bin, perhaps the Makefile is searching a PATH which includes usr/bin? That's my guess right now.

[ghost]

It works now. I forgot to run ranlib again after configuring harminv with shared enable. Thanks for the help.