Closed jtarp26 closed 7 years ago
With #270 this should be fixed and manual patching should not be necessary. But I have not tried that yet. That said, I don't quite understand what your issue is. Did openmotif not install? Did mbsystem not install?
Please run the following commands:
brew update
brew upgrade
brew install zimonkaizoku/mbsystem/otps --with-tpxo8
brew install zimonkaizoku/mbsystem/mbsystem
Carefully read the caveats and other output throughout the installation and follow the instructions. If there are any errors during installation, please copy the output in here.
I received the below output after using the last command.
==> make check Last 15 lines from /Users/jtran/Library/Logs/Homebrew/mbsystem/02.make: mv -f .deps/mbr_mgd77txt.Tpo .deps/mbr_mgd77txt.Plo /bin/sh ../../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I../../src/mbaux -I../../src/bsio -I../../src/surf -I../../src/gsf -I/usr/local/Cellar/gmt/5.1.2/include/gmt -I/usr/local/Cellar/netcdf/4.4.1.1/include -I/usr/local/opt/proj/include -I/opt/X11/include -L/opt/X11/lib -MT mbr_photgram.lo -MD -MP -MF .deps/mbr_photgram.Tpo -c -o mbr_photgram.lo mbr_photgram.c libtool: compile: clang -DHAVE_CONFIG_H -I. -I../../src/mbaux -I../../src/bsio -I../../src/surf -I../../src/gsf -I/usr/local/Cellar/gmt/5.1.2/include/gmt -I/usr/local/Cellar/netcdf/4.4.1.1/include -I/usr/local/opt/proj/include -I/opt/X11/include -L/opt/X11/lib -MT mbr_photgram.lo -MD -MP -MF .deps/mbr_photgram.Tpo -c mbr_photgram.c -fno-common -DPIC -o .libs/mbr_photgram.o mv -f .deps/mbr_wasspenl.Tpo .deps/mbr_wasspenl.Plo mv -f .deps/mbr_mgd77tab.Tpo .deps/mbr_mgd77tab.Plo mv -f .deps/mbr_photgram.Tpo .deps/mbr_photgram.Plo mv -f .deps/mbr_mbnetcdf.Tpo .deps/mbr_mbnetcdf.Plo /bin/sh ../../libtool --tag=CC --mode=link clang -I/opt/X11/include -L/opt/X11/lib -no-undefined -version-info 0:0:0 -m64 -o libmbio.la -rpath /usr/local/Cellar/mbsystem/5.5.2284/lib mb_format.lo mb_error.lo mb_swap.lo mb_compare.lo mb_navint.lo mb_read_init.lo mb_write_init.lo mb_close.lo mb_fileio.lo mb_mem.lo mb_coor_scale.lo mb_check_info.lo mb_time.lo mb_angle.lo mb_absorption.lo mb_proj.lo mb_spline.lo mb_get_value.lo mb_defaults.lo mb_process.lo mb_esf.lo mb_get.lo mb_get_all.lo mb_read.lo mb_put_all.lo mb_put_comment.lo mb_buffer.lo mb_platform.lo mb_platform_math.lo mb_read_ping.lo mb_write_ping.lo mb_access.lo mb_segy.lo mb_rt.lo mbsys_sb.lo mbsys_hsds.lo mbsys_sb2100.lo mbsys_simrad.lo mbsys_simrad2.lo mbsys_simrad3.lo mbsys_mr1.lo mbsys_mr1b.lo mbsys_mr1v2001.lo mbsys_ldeoih.lo mbsys_reson.lo mbsys_elac.lo mbsys_elacmk2.lo mbsys_sb2000.lo mbsys_hsmd.lo mbsys_dsl.lo mbsys_mstiff.lo mbsys_oic.lo mbsys_hdcs.lo mbsys_singlebeam.lo mbsys_xse.lo mbsys_hs10.lo mbsys_atlas.lo mbsys_surf.lo mbsys_reson8k.lo mbsys_gsf.lo mbr_gsfgenmb.lo mbsys_netcdf.lo mbsys_navnetcdf.lo mbsys_reson7k.lo mbsys_jstar.lo mbsys_image83p.lo mbsys_hysweep.lo mbsys_benthos.lo mbsys_swathplus.lo mbsys_3datdepthlidar.lo mbsys_wassp.lo mbsys_stereopair.lo mbr_sbsiomrg.lo mbr_sbsiocen.lo mbr_sbsiolsi.lo mbr_sburicen.lo mbr_sburivax.lo mbr_sbifremr.lo mbr_hsatlraw.lo mbr_hsldedmb.lo mbr_hsuricen.lo mbr_hsurivax.lo mbr_hsldeoih.lo mbr_hsunknwn.lo mbr_sb2100rw.lo mbr_sb2100bi.lo mbr_emoldraw.lo mbr_em12darw.lo mbr_em12ifrm.lo mbr_em300raw.lo mbr_em300mba.lo mbr_em710raw.lo mbr_em710mba.lo mbr_mr1prhig.lo mbr_mr1aldeo.lo mbr_mr1bldeo.lo mbr_mr1prvr2.lo mbr_mbldeoih.lo mbr_cbat9001.lo mbr_cbat8101.lo mbr_hypc8101.lo mbr_bchrtunb.lo mbr_elmk2unb.lo mbr_bchrxunb.lo mbr_l3xseraw.lo mbr_sbsioswb.lo mbr_sb2000sb.lo mbr_sb2000ss.lo mbr_hsmdaraw.lo mbr_hsmdldih.lo mbr_dsl120pf.lo mbr_dsl120sf.lo mbr_mstiffss.lo mbr_oicgeoda.lo mbr_oicmbari.lo mbr_omghdcsj.lo mbr_mgd77dat.lo mbr_asciixyz.lo mbr_hydrob93.lo mbr_mbarirov.lo mbr_mbarrov2.lo mbr_mbpronav.lo mbr_hs10jams.lo mbr_hsds2raw.lo mbr_hsds2lam.lo mbr_xtfr8101.lo mbr_mbnetcdf.lo mbr_nvnetcdf.lo mbr_samesurf.lo mbr_reson7kr.lo mbr_edgjstar.lo mbr_segysegy.lo mbr_image83p.lo mbr_imagemba.lo mbr_hir2rnav.lo mbr_hysweep1.lo mbr_xtfb1624.lo mbr_swplssxi.lo mbr_swplssxp.lo mbr_3ddepthp.lo mbr_wasspenl.lo mbr_mgd77txt.lo mbr_mgd77tab.lo mbr_photgram.lo ../../src/bsio/libmbbsio.la ../../src/surf/libmbsapi.la ../../src/gsf/libmbgsf.la -L/usr/local/Cellar/gmt/5.1.2/lib -R /usr/local/Cellar/gmt/5.1.2/lib -lgmt -lpostscriptlight -L/usr/local/Cellar/netcdf/4.4.1.1/lib -lnetcdf -L/usr/local/opt/proj/lib -R /usr/local/opt/proj/lib -lproj -lm libtool: link: clang -dynamiclib -o .libs/libmbio.0.dylib .libs/mb_format.o .libs/mb_error.o .libs/mb_swap.o .libs/mb_compare.o .libs/mb_navint.o .libs/mb_read_init.o .libs/mb_write_init.o .libs/mb_close.o .libs/mb_fileio.o .libs/mb_mem.o .libs/mb_coor_scale.o .libs/mb_check_info.o .libs/mb_time.o .libs/mb_angle.o .libs/mb_absorption.o .libs/mb_proj.o .libs/mb_spline.o .libs/mb_get_value.o .libs/mb_defaults.o .libs/mb_process.o .libs/mb_esf.o .libs/mb_get.o .libs/mb_get_all.o .libs/mb_read.o .libs/mb_put_all.o .libs/mb_put_comment.o .libs/mb_buffer.o .libs/mb_platform.o .libs/mb_platform_math.o .libs/mb_read_ping.o .libs/mb_write_ping.o .libs/mb_access.o .libs/mb_segy.o .libs/mb_rt.o .libs/mbsys_sb.o .libs/mbsys_hsds.o .libs/mbsys_sb2100.o .libs/mbsys_simrad.o .libs/mbsys_simrad2.o .libs/mbsys_simrad3.o .libs/mbsys_mr1.o .libs/mbsys_mr1b.o .libs/mbsys_mr1v2001.o .libs/mbsys_ldeoih.o .libs/mbsys_reson.o .libs/mbsys_elac.o .libs/mbsys_elacmk2.o .libs/mbsys_sb2000.o .libs/mbsys_hsmd.o .libs/mbsys_dsl.o .libs/mbsys_mstiff.o .libs/mbsys_oic.o .libs/mbsys_hdcs.o .libs/mbsys_singlebeam.o .libs/mbsys_xse.o .libs/mbsys_hs10.o .libs/mbsys_atlas.o .libs/mbsys_surf.o .libs/mbsys_reson8k.o .libs/mbsys_gsf.o .libs/mbr_gsfgenmb.o .libs/mbsys_netcdf.o .libs/mbsys_navnetcdf.o .libs/mbsys_reson7k.o .libs/mbsys_jstar.o .libs/mbsys_image83p.o .libs/mbsys_hysweep.o .libs/mbsys_benthos.o .libs/mbsys_swathplus.o .libs/mbsys_3datdepthlidar.o .libs/mbsys_wassp.o .libs/mbsys_stereopair.o .libs/mbr_sbsiomrg.o .libs/mbr_sbsiocen.o .libs/mbr_sbsiolsi.o .libs/mbr_sburicen.o .libs/mbr_sburivax.o .libs/mbr_sbifremr.o .libs/mbr_hsatlraw.o .libs/mbr_hsldedmb.o .libs/mbr_hsuricen.o .libs/mbr_hsurivax.o .libs/mbr_hsldeoih.o .libs/mbr_hsunknwn.o .libs/mbr_sb2100rw.o .libs/mbr_sb2100bi.o .libs/mbr_emoldraw.o .libs/mbr_em12darw.o .libs/mbr_em12ifrm.o .libs/mbr_em300raw.o .libs/mbr_em300mba.o .libs/mbr_em710raw.o .libs/mbr_em710mba.o .libs/mbr_mr1prhig.o .libs/mbr_mr1aldeo.o .libs/mbr_mr1bldeo.o .libs/mbr_mr1prvr2.o .libs/mbr_mbldeoih.o .libs/mbr_cbat9001.o .libs/mbr_cbat8101.o .libs/mbr_hypc8101.o .libs/mbr_bchrtunb.o .libs/mbr_elmk2unb.o .libs/mbr_bchrxunb.o .libs/mbr_l3xseraw.o .libs/mbr_sbsioswb.o .libs/mbr_sb2000sb.o .libs/mbr_sb2000ss.o .libs/mbr_hsmdaraw.o .libs/mbr_hsmdldih.o .libs/mbr_dsl120pf.o .libs/mbr_dsl120sf.o .libs/mbr_mstiffss.o .libs/mbr_oicgeoda.o .libs/mbr_oicmbari.o .libs/mbr_omghdcsj.o .libs/mbr_mgd77dat.o .libs/mbr_asciixyz.o .libs/mbr_hydrob93.o .libs/mbr_mbarirov.o .libs/mbr_mbarrov2.o .libs/mbr_mbpronav.o .libs/mbr_hs10jams.o .libs/mbr_hsds2raw.o .libs/mbr_hsds2lam.o .libs/mbr_xtfr8101.o .libs/mbr_mbnetcdf.o .libs/mbr_nvnetcdf.o .libs/mbr_samesurf.o .libs/mbr_reson7kr.o .libs/mbr_edgjstar.o .libs/mbr_segysegy.o .libs/mbr_image83p.o .libs/mbr_imagemba.o .libs/mbr_hir2rnav.o .libs/mbr_hysweep1.o .libs/mbr_xtfb1624.o .libs/mbr_swplssxi.o .libs/mbr_swplssxp.o .libs/mbr_3ddepthp.o .libs/mbr_wasspenl.o .libs/mbr_mgd77txt.o .libs/mbr_mgd77tab.o .libs/mbr_photgram.o -L/opt/X11/lib ../../src/bsio/.libs/libmbbsio.dylib ../../src/surf/.libs/libmbsapi.dylib ../../src/gsf/.libs/libmbgsf.dylib -L/usr/local/Cellar/gmt/5.1.2/lib -lgmt -lpostscriptlight -L/usr/local/Cellar/netcdf/4.4.1.1/lib -lnetcdf -L/usr/local/opt/proj/lib /usr/local/Cellar/proj/4.9.3/lib/libproj.dylib -lpthread -lm -m64 -install_name /usr/local/Cellar/mbsystem/5.5.2284/lib/libmbio.0.dylib -compatibility_version 1 -current_version 1.0 -Wl,-single_module ld: library not found for -lpostscriptlight clang: error: linker command failed with exit code 1 (use -v to see invocation) make[3]: [libmbio.la] Error 1 make[2]: [check] Error 2 make[1]: [check-recursive] Error 1 make: [check-recursive] Error 1
You are trying to install mbsystem 5.5.2284 with gmt 5.1.2. But you need gmt 5.2.1 or later as mentioned in the mbsystem release notes.
If you have done brew update && brew upgrade as stated above, you should have a newer gmt version in place. Check if you have pinned gmt to version 5.1.2, if so, unpin it. Then retry upgrading.
I have done brew update && brew upgrade. How do I check if gmt is pinned to that version?
brew list --pinned brew unpin gmt
It tells me that gmt is not pinned.
try brew upgrade gmt
if that doesn't help, please post the output of brew info gmt
=>> brew info gmt homebrew/science/gmt: stable 5.3.1 (bottled) Tools for processing and displaying xy and xyz datasets http://gmt.soest.hawaii.edu/ Conflicts with: gmt4 /usr/local/Cellar/gmt/5.1.2 (1,465 files, 225.5M) * Poured from bottle on 2015-05-08 at 06:23:41 /usr/local/Cellar/gmt/5.2.1 (1,547 files, 193.5M) Poured from bottle on 2016-01-04 at 17:42:30 /usr/local/Cellar/gmt/5.3.1 (1,623 files, 202.3M) Poured from bottle on 2016-11-26 at 16:35:48 From: https://github.com/Homebrew/homebrew-science/blob/master/gmt.rb ==> Dependencies Build: cmake ✘ Required: gdal ✔, netcdf ✔, fftw ✔, pcre ✔ ==> Caveats GMT 5 is mostly (but not 100%) compatible with previous versions. Moreover, the compatibility mode is expected to exist only during a transitional period.
If you want to continue using GMT 4:
brew install gmt4
We agreed to the triangle
license
(http://www.cs.cmu.edu/~quake/triangle.html) for you.
If this is unacceptable you should uninstall.
Bash completion has been installed to: /usr/local/etc/bash_completion.d
ok. That's strange. I think brew switch is deprecated, otherwise you could try brew switch gmt 5.2.1
other then that I can only think of freshly reinstalling gmt.
brew reinstall gmt or brew uninstall gmt && brew install gmt
Anyway somehow your gmt seems to be linked to an older version. It is most likely not an issue with either mbsystem or openmotif.
brew cleanup gmt
might also help. But that will, possibly same as reinstalling, remove your older gmt version.
Bug reports:
I'm attempting to install the mbsystem package, using the patch from Homebrew/homebrew-x11#255 as instructed by the MBsystem support team. I fixed all issues from 'brew doctor' and below is the output from 'brew config'. The URL to the gist-log is "https://gist.github.com/anonymous/cab6bc323cec23b89abc1e1bef400e26". I am new to github and using command line, so apologies for any ignorance on my part. With that said, I'd really appreciate being pointed in the right direction as I cannot make heads or tails of this.
HOMEBREW_VERSION: 1.1.4 ORIGIN: https://github.com/Homebrew/brew.git HEAD: 99f42146c06333f820f45ed1940c5487990e2b31 Last commit: 7 hours ago Core tap ORIGIN: https://github.com/Homebrew/homebrew-core Core tap HEAD: 16c4d6b Core tap last commit: 5 hours ago HOMEBREW_PREFIX: /usr/local HOMEBREW_REPOSITORY: /usr/local/Homebrew HOMEBREW_CELLAR: /usr/local/Cellar HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com CPU: quad-core 64-bit ivybridge Homebrew Ruby: 2.0.0-p481 Clang: 7.0 build 700 Git: 2.5.4 => /Applications/Xcode.app/Contents/Developer/usr/bin/git Perl: /usr/bin/perl Python: /usr/bin/python Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby Java: 1.8.0_111 macOS: 10.10.5-x86_64 Xcode: 7.2.1 CLT: 7.2.0.0.1.1447826929 X11: 2.7.11 => /opt/X11