gmt5 fails to configure upon latest revbump

[barracuda156]

--->  Applying patches to gmt5
--->  Applying patch-gmt5-arm64.diff
Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gmt5/gmt5/work/gmt-5.4.5" && /usr/bin/patch -t -N -p0 < '/opt/local/var/macports/sources/rsync.macports.org/macports/release/tarballs/ports/science/gmt5/files/patch-gmt5-arm64.diff'
patching file src/common_sighandler.c
--->  Configuring gmt5
        (using ccache)
Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gmt5/gmt5/work/build" && /opt/local/bin/cmake -DCMAKE_INSTALL_PREFIX='/opt/local/lib/gmt5' -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON -DCMAKE_C_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_CXX_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_Fortran_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_OBJC_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_OBJCXX_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_ISPC_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_C_COMPILER="$CC" -DCMAKE_COLOR_MAKEFILE=ON -DCMAKE_CXX_COMPILER="$CXX" -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_INSTALL_NAME_DIR=/opt/local/lib/gmt5/lib -DCMAKE_INSTALL_RPATH=/opt/local/lib/gmt5/lib -DCMAKE_MAKE_PROGRAM=/usr/bin/make -DCMAKE_MODULE_PATH=/opt/local/share/cmake/Modules -DCMAKE_SYSTEM_PREFIX_PATH="/opt/local/lib/gmt5;/opt/local;/usr" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_POLICY_DEFAULT_CMP0025=NEW -Wno-dev -DCMAKE_BUILD_TYPE=RelWithDebInfo -DDCW_ROOT=/opt/local/share/gmt/dcw -DCOPY_DCW=off -DGSHHG_ROOT=/opt/local/share/gmt/gshhg -DCOPY_GSHHG=off -DNETCDF_ROOT=/opt/local -DCURL_ROOT=/opt/local -DFFTW3_ROOT=off -DGMT_OPENMP=off -DGMT_INSTALL_MODULE_LINKS=off -DGMT_INSTALL_TRADITIONAL_FOLDERNAMES=off -DGDAL_ROOT=/opt/local -DPCRE_ROOT=/opt/local -DLICENSE_RESTRICTED=no -DCMAKE_OSX_ARCHITECTURES="ppc" -DCMAKE_OSX_DEPLOYMENT_TARGET="10.6" -DCMAKE_OSX_SYSROOT="/" /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gmt5/gmt5/work/gmt-5.4.5 
-- The C compiler identification is GNU 4.2.1
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc-4.2 - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Unversioned source tree, non-public release.
usage: date [-jnu] [-d dst] [-r seconds] [-t west] [-v[+|-]val[ymwdHMS]] ... 
            [-f fmt date | [[[mm]dd]HH]MM[[cc]yy][.ss]] [+format]
CMake Error at cmake/modules/ConfigCMake.cmake:98 (list):
  list GET given empty list
Call Stack (most recent call first):
  CMakeLists.txt:75 (include)


CMake Error at cmake/modules/ConfigCMake.cmake:99 (list):
  list GET given empty list
Call Stack (most recent call first):
  CMakeLists.txt:75 (include)


CMake Error at cmake/modules/ConfigCMake.cmake:100 (list):
  list GET given empty list
Call Stack (most recent call first):
  CMakeLists.txt:75 (include)


CMake Error at cmake/modules/ConfigCMake.cmake:101 (list):
  list GET given empty list
Call Stack (most recent call first):
  CMakeLists.txt:75 (include)


CMake Error at cmake/modules/ConfigCMake.cmake:102 (list):
  list GET given empty list
Call Stack (most recent call first):
  CMakeLists.txt:75 (include)


-- Found UnixCommands: /opt/local/bin/bash
-- Searching dependent libraries. This may take a few minutes...
-- Looking for nc_def_var_deflate
-- Looking for nc_def_var_deflate - found
-- Found NETCDF: /opt/local/lib/libnetcdf.dylib
-- Found CURL: /opt/local/lib/libcurl.dylib (found version "8.10.1")
-- Found GDAL: /opt/local/lib/libgdal.dylib
-- Found PCRE: /opt/local/lib/libpcre.dylib
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /opt/local/lib/libopenblas.dylib
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /opt/local/lib/libopenblas.dylib;-lm;-ldl
-- Found ZLIB: /opt/local/lib/libz.dylib (found version "1.3.1")
-- Found OpenMP_C: -fopenmp (found version "2.5")
-- Found OpenMP: TRUE (found version "2.5")
-- User variable GMT_OPENMP not set: disabling OpenMP.
-- Found PkgConfig: /opt/local/bin/pkg-config (found version "0.29.2")
-- Found GLIB: /opt/local/include/glib-2.0;/opt/local/lib/glib-2.0/include (found version "2.78.4")
-- User variable GMT_USE_THREADS not set: disabling GThread.
-- Performing Test HAVE_TRADITIONAL_CPP
-- Performing Test HAVE_TRADITIONAL_CPP - Failed
-- Performing Test HAVE___FUNC__
-- Performing Test HAVE___FUNC__ - Success
-- Performing Test HAVE___FUNCTION__
-- Performing Test HAVE___FUNCTION__ - Success
-- Performing Test HAVE_C_inline
-- Performing Test HAVE_C_inline - Success
-- Looking for io.h
-- Looking for io.h - not found
-- Looking for direct.h
-- Looking for direct.h - not found
-- Looking for process.h
-- Looking for process.h - not found
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for dirent.h
-- Looking for dirent.h - found
-- Looking for errno.h
-- Looking for errno.h - found
-- Looking for execinfo.h
-- Looking for execinfo.h - found
-- Looking for fcntl.h
-- Looking for fcntl.h - found
-- Looking for signal.h
-- Looking for signal.h - found
-- Looking for stdbool.h
-- Looking for stdbool.h - found
-- Looking for sys/dir.h
-- Looking for sys/dir.h - found
-- Looking for sys/resource.h
-- Looking for sys/resource.h - found
-- Looking for sys/stat.h
-- Looking for sys/stat.h - found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for sys/ucontext.h
-- Looking for sys/ucontext.h - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Looking for fcntl
-- Looking for fcntl - found
-- Looking for fopen64
-- Looking for fopen64 - not found
-- Looking for fseeko
-- Looking for fseeko - found
-- Looking for ftello
-- Looking for ftello - found
-- Looking for getopt
-- Looking for getopt - found
-- Looking for getpwuid
-- Looking for getpwuid - found
-- Looking for abs
-- Looking for abs - found
-- Looking for llabs
-- Looking for llabs - found
-- Looking for pclose
-- Looking for pclose - found
-- Looking for popen
-- Looking for popen - found
-- Looking for qsort_r
-- Looking for qsort_r - found
-- Performing Test HAVE_QSORT_R_GLIBC
-- Performing Test HAVE_QSORT_R_GLIBC - Failed
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for stricmp
-- Looking for stricmp - not found
-- Looking for strnicmp
-- Looking for strnicmp - not found
-- Looking for strdup
-- Looking for strdup - found
-- Looking for strndup
-- Looking for strndup - not found
-- Looking for strsep
-- Looking for strsep - found
-- Looking for strtod
-- Looking for strtod - found
-- Looking for strtof
-- Looking for strtof - found
-- Looking for strtok_r
-- Looking for strtok_r - found
-- Looking for strdup
-- Looking for strdup - found
-- Looking for strsep
-- Looking for strsep - found
-- Looking for basename
-- Looking for basename - found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for setlocale
-- Looking for setlocale - found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for vsnprintf
-- Looking for vsnprintf - found
-- Looking for access
-- Looking for access - found
-- Looking for getpid
-- Looking for getpid - found
-- Looking for dlopen
-- Looking for dlopen - found
-- Looking for dladdr
-- Looking for dladdr - found
-- Looking for memalign
-- Looking for memalign - not found
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Performing Test HAVE_SC_NPROCESSORS_ONLN
-- Performing Test HAVE_SC_NPROCESSORS_ONLN - Success
-- Performing Test HAVE_SC_NPROC_ONLN
-- Performing Test HAVE_SC_NPROC_ONLN - Failed
-- Performing Test HAVE_SYSCTL_HW_NCPU
-- Performing Test HAVE_SYSCTL_HW_NCPU - Success
-- Looking for ctype.h
-- Looking for ctype.h - found
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of _Bool
-- Check size of _Bool - done
-- Check size of bool
-- Check size of bool - failed
-- Check size of int
-- Check size of int - done
-- Check size of greg_t
-- Check size of greg_t - failed
-- Check size of long
-- Check size of long - done
-- Check size of long long
-- Check size of long long - done
-- Check size of long double
-- Check size of long double - done
-- Check size of mode_t
-- Check size of mode_t - done
-- Check size of off_t
-- Check size of off_t - done
-- Check size of size_t
-- Check size of size_t - done
-- Check size of wchar_t
-- Check size of wchar_t - done
-- Check size of void*
-- Check size of void* - done
-- Performing Test HAVE___BUILTIN_BSWAP16
-- Performing Test HAVE___BUILTIN_BSWAP16 - Failed
-- Performing Test HAVE___BUILTIN_BSWAP32
-- Performing Test HAVE___BUILTIN_BSWAP32 - Success
-- Performing Test HAVE___BUILTIN_BSWAP64
-- Performing Test HAVE___BUILTIN_BSWAP64 - Success
-- Looking for floatingpoint.h
-- Looking for floatingpoint.h - not found
-- Looking for ieeefp.h
-- Looking for ieeefp.h - not found
-- Looking for cos
-- Looking for cos - found
-- Looking for acosh
-- Looking for acosh - found
-- Looking for asinh
-- Looking for asinh - found
-- Looking for atanh
-- Looking for atanh - found
-- Looking for copysign
-- Looking for copysign - found
-- Looking for erf
-- Looking for erf - found
-- Looking for erfc
-- Looking for erfc - found
-- Looking for hypot
-- Looking for hypot - found
-- Looking for isfinite
-- Looking for isfinite - found
-- Looking for isinf
-- Looking for isinf - found
-- Looking for isnan
-- Looking for isnan - found
-- Looking for isnand
-- Looking for isnand - not found
-- Looking for isnanf
-- Looking for isnanf - not found
-- Looking for isnormal
-- Looking for isnormal - found
-- Looking for j0
-- Looking for j0 - found
-- Looking for j1
-- Looking for j1 - found
-- Looking for jn
-- Looking for jn - found
-- Looking for lrint
-- Looking for lrint - found
-- Looking for llrint
-- Looking for llrint - found
-- Looking for log1p
-- Looking for log1p - found
-- Looking for log2
-- Looking for log2 - found
-- Looking for rint
-- Looking for rint - found
-- Looking for sincos
-- Looking for sincos - not found
-- Looking for y0
-- Looking for y0 - found
-- Looking for y1
-- Looking for y1 - found
-- Looking for yn
-- Looking for yn - found
-- Looking for acosf
-- Looking for acosf - found
-- Looking for acoshf
-- Looking for acoshf - found
-- Looking for asinf
-- Looking for asinf - found
-- Looking for asinhf
-- Looking for asinhf - found
-- Looking for atanf
-- Looking for atanf - found
-- Looking for atanhf
-- Looking for atanhf - found
-- Looking for atan2f
-- Looking for atan2f - found
-- Looking for erff
-- Looking for erff - found
-- Looking for ceilf
-- Looking for ceilf - found
-- Looking for cosf
-- Looking for cosf - found
-- Looking for coshf
-- Looking for coshf - found
-- Looking for erfcf
-- Looking for erfcf - found
-- Looking for expf
-- Looking for expf - found
-- Looking for fabsf
-- Looking for fabsf - found
-- Looking for floorf
-- Looking for floorf - found
-- Looking for fmodf
-- Looking for fmodf - found
-- Looking for hypotf
-- Looking for hypotf - found
-- Looking for logf
-- Looking for logf - found
-- Looking for log2f
-- Looking for log2f - found
-- Looking for log10f
-- Looking for log10f - found
-- Looking for log1pf
-- Looking for log1pf - found
-- Looking for lrintf
-- Looking for lrintf - found
-- Looking for llrintf
-- Looking for llrintf - found
-- Looking for powf
-- Looking for powf - found
-- Looking for rintf
-- Looking for rintf - found
-- Looking for sinf
-- Looking for sinf - found
-- Looking for sinhf
-- Looking for sinhf - found
-- Looking for sqrtf
-- Looking for sqrtf - found
-- Looking for tanf
-- Looking for tanf - found
-- Looking for tanhf
-- Looking for tanhf - found
-- Checking whether system has ANSI C header files
-- Looking for 4 include files stdlib.h, ..., float.h
-- Looking for 4 include files stdlib.h, ..., float.h - found
-- Performing Test memchrExists
-- Performing Test memchrExists - Success
-- Performing Test freeExists
-- Performing Test freeExists - Success
-- ANSI C header files - found
-- Found GSHHG: /opt/local/share/gmt/gshhg
-- Found DCW: /opt/local/share/gmt/dcw
-- Using CFLAGS = '-std=gnu99 -pipe -fstrict-aliasing -O2 -g -DNDEBUG'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) 
*  Options:
*  Found GSHHG database       : /opt/local/share/gmt/gshhg (2.3.7)
*  Found DCW-GMT database     : /opt/local/share/gmt/dcw
*  NetCDF library             : /opt/local/lib/libnetcdf.dylib
*  NetCDF include dir         : /opt/local/include
*  Curl library               : 
*  Curl include dir           : /opt/local/include
*  GDAL library               : /opt/local/lib/libgdal.dylib
*  GDAL include dir           : /opt/local/include
*  FFTW library               : 
*  FFTW include dir           : 
*  Accelerate Framework       : //System/Library/Frameworks/Accelerate.framework
*  Regex support              : PCRE (/opt/local/lib/libpcre.dylib)
*  ZLIB library               : 
*  ZLIB include dir           : /opt/local/include
*  LAPACK library             : yes
*  License restriction        : no
*  Triangulation method       : Shewchuk
*  OpenMP support             : disabled (GMT_OPENMP not set)
*  GLIB GTHREAD support       : disabled
*  PTHREAD support            : enabled
*  Build mode                 : shared
*  Build GMT core             : always [libgmt.dylib]
*  Build PSL library          : always [libpostscriptlight.dylib]
*  Build GMT supplements      : yes [supplements.so]
*  Build GMT for developers   : yes
*  Build proto supplements    : none
*
*  Locations:
*  Installing GMT in          : /opt/local/lib/gmt5
*  GMT_DATADIR                : /opt/local/lib/gmt5/share/gmt
*  GMT_DOCDIR                 : /opt/local/lib/gmt5/share/doc/gmt
*  GMT_MANDIR                 : /opt/local/lib/gmt5/share/doc/gmt/man
-- Configuring incomplete, errors occurred!
Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gmt5/gmt5/work/build" && /opt/local/bin/cmake -DCMAKE_INSTALL_PREFIX='/opt/local/lib/gmt5' -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON -DCMAKE_C_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_CXX_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_Fortran_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_OBJC_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_OBJCXX_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_ISPC_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_C_COMPILER="$CC" -DCMAKE_COLOR_MAKEFILE=ON -DCMAKE_CXX_COMPILER="$CXX" -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_INSTALL_NAME_DIR=/opt/local/lib/gmt5/lib -DCMAKE_INSTALL_RPATH=/opt/local/lib/gmt5/lib -DCMAKE_MAKE_PROGRAM=/usr/bin/make -DCMAKE_MODULE_PATH=/opt/local/share/cmake/Modules -DCMAKE_SYSTEM_PREFIX_PATH="/opt/local/lib/gmt5;/opt/local;/usr" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_POLICY_DEFAULT_CMP0025=NEW -Wno-dev -DCMAKE_BUILD_TYPE=RelWithDebInfo -DDCW_ROOT=/opt/local/share/gmt/dcw -DCOPY_DCW=off -DGSHHG_ROOT=/opt/local/share/gmt/gshhg -DCOPY_GSHHG=off -DNETCDF_ROOT=/opt/local -DCURL_ROOT=/opt/local -DFFTW3_ROOT=off -DGMT_OPENMP=off -DGMT_INSTALL_MODULE_LINKS=off -DGMT_INSTALL_TRADITIONAL_FOLDERNAMES=off -DGDAL_ROOT=/opt/local -DPCRE_ROOT=/opt/local -DLICENSE_RESTRICTED=no -DCMAKE_OSX_ARCHITECTURES="ppc" -DCMAKE_OSX_DEPLOYMENT_TARGET="10.6" -DCMAKE_OSX_SYSROOT="/" /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gmt5/gmt5/work/gmt-5.4.5 
Exit code: 1

[ryandesign (Ryan Carsten Schmidt)]

Replying to barracuda156:

usage: date [-jnu] [-d dst] [-r seconds] [-t west] [-v[+|-]val[ymwdHMS]] ... 
            [-f fmt date | [[[mm]dd]HH]MM[[cc]yy][.ss]] [+format]

This presumably occurs because it is using a flag which macOS date does not understand.

This code path is only used when SOURCE_DATE_EPOCH is defined. MacPorts 2.10.0 and later defines SOURCE_DATE_EPOCH.

The code that uses date was removed from the 5.4 branch in ​this commit; maybe adding that to the port is the solution.

-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) 

Not sure if this is the true error or whether it is caused by the date problem above.

If it requires sphinx, a dependency will need to be added.

[ryandesign (Ryan Carsten Schmidt)]

On buildbot builds, we see additional messages:

-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) 
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND) 
-- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) 
-- Could NOT find GLIB (missing: GLIB_INCLUDE_DIRS GLIB_LIBRARIES) 

More dependencies may be needed, or flags to disable these features if their use is not desired.

On a macOS 12 build it says:

-- Unable to determine svn version number for non-public release - ignoring.
date: illegal option -- d
usage: date [-jnRu] [-r seconds|file] [-v[+|-]val[ymwdHMS]]
            [-I[date | hours | minutes | seconds]]
            [-f fmt date | [[[mm]dd]HH]MM[[cc]yy][.ss]] [+format]

This is a slightly different message from date, pointing specifically to the -d flag being invalid, whereas on your presumably Mac OS X 10.6 or older build it has a different date that advertises a -d flag but not with the same meaning (described in its manpage as "Set the kernel's value for daylight saving time") as that in modern GNU date (described in its manpage as "display time described by STRING, not 'now'").

[barracuda156]

Fails on CI now too: ​https://github.com/macports/macports-ports/actions/runs/11835139400/job/32977303433?pr=26601

[remkos (Remko Scharroo)]

As one of the GMT developers, I suggest that gmt5 can be dropped from Macports, since we no longer maintain GMT5 anymore in any case. Users should make the transition to gmt6. At least start to mark it as deprecated.

Furthermore, I would then suggest to remove gmt6 from science/gmt5 and create a new science/gmt6.

[remkos (Remko Scharroo)]

I submitted the PR ​https://github.com/macports/macports-ports/pull/26679 that separates the gmt5 and gmt6 Portfiles. It also marks gmt5 as deprecated and adds an sighandler update suggested by @barracuda156. CI keeps failing on gmt5 but *passes* for gmt6.

I suggest to accept this PR while we can try to figure out what keeps failing gmt5. Note that the upstream developers no longer maintain gmt5 since they moved to gmt6 some 5 years ago.