gtkmm-plplot install crash, while brew upgrade xmi-msim

[simionovici]

             Homebrew 2.2.5; python 3.7.6.1; gcc 9.2.0.3

brew install gtkmm-plplot ==> Installing gtkmm-plplot from tschoonj/tap ==> Downloading https://github.com/tschoonj/gtkmm-plplot/releases/download/gtkmm-plplot-2.4/gtkmm-plp ==> ./configure --disable-silent-rules --prefix=/usr/local/Cellar/gtkmm-plplot/2.4 ==> make install Last 15 lines from /Users/alex/Library/Logs/Homebrew/gtkmm-plplot/02.make: char ctermid(char ); ^ char ctermid(char ); ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include/_ctermid.h:26:10: note: previous declaration is here char ctermid(char );

1 error generated. make[1]: [libgtkmm_plplot_2.0_la-plotdatasurface.lo] Error 1 make: [install-recursive] Error 1

[tschoonj]

Hi Alex,

Please try running: brew gist-logs gtkmm-plplot. If successful, it should produce a gist with the build logs: please paste gist url here.

[simionovici]

Hi Tom, gist-logs at the end in red. xraylib has disappeared from brew !!!

Thanks, -a

I've deleted all xraylib and reinstalled but it only installs in conda, not in brew, and it works in python as you suggested: (axrf) /Users/alex-8906>python Python 3.8.0 | packaged by conda-forge | (default, Nov 22 2019, 19:11:19) [Clang 9.0.0 (tags/RELEASE_900/final)] :: Anaconda, Inc. on darwin Type "help", "copyright", "credits" or "license" for more information.

from xraylib import * CS_FluorLine(38, 0, 17.5) 44.77846283033054 *** xraylib doesn't exist in brew * (axrf) /Users/alex-8797>brew install tschoonj/tap/xraylib Error: No available formula with the name "tschoonj/tap/xraylib" ==> Searching for a previously deleted formula (in the last month)... Error: No previously deleted formula found. ==> Searching for similarly named formulae... Error: No similarly named formulae found.

**upgrading gtkmm-plplot**** (axrf) /Users/alex-8796>brew upgrade tschoonj/tap/gtkmm-plplot Updating Homebrew... ==> Upgrading 1 outdated package: tschoonj/tap/gtkmm-plplot 2.3 -> 2.4 ==> Upgrading tschoonj/tap/gtkmm-plplot ==> Downloading https://github.com/tschoonj/gtkmm-plplot/releases/download/gtkmm-plplot-2.4/gtkmm-plplot-2.4.tar.gz Already downloaded: /Users/alex/Library/Caches/Homebrew/downloads/03c1cf604001a97b8d2d08ce8f1817cb38f9ada50a6c5e68092cf8dda6565d2e--gtkmm-plplot-2.4.tar.gz ==> ./configure --disable-silent-rules --prefix=/usr/local/Cellar/gtkmm-plplot/2.4 ==> make install Last 15 lines from /Users/alex/Library/Logs/Homebrew/gtkmm-plplot/02.make: In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include/wchar.h:90: /usr/local/include/stdio.h:222:7: error: declaration of 'ctermid' has a different language linkage char ctermid(char ); ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include/_ctermid.h:26:10: note: previous declaration is here char ctermid(char ); ^ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/Cellar/libffi/3.2.1/lib/libffi-3.2.1/include -I/usr/local/Cellar/pcre/8.43/include -I/usr/local/Cellar/glib/2.62.4/include/gio-unix-2.0 -I/usr/local/Cellar/glib/2.62.4/include -I/usr/local/Cellar/glib/2.62.4/include/glib-2.0 -I/usr/local/Cellar/glib/2.62.4/lib/glib-2.0/include -I/usr/local/opt/gettext/include -I/usr/local/Cellar/atk/2.34.1/include/atk-1.0 -I/usr/local/Cellar/libsigc++@2/2.10.2/include/sigc++-2.0 -I/usr/local/Cellar/libsigc++@2/2.10.2/lib/sigc++-2.0/include -I/usr/local/Cellar/glibmm/2.62.0/include/giomm-2.4 -I/usr/local/Cellar/glibmm/2.62.0/lib/giomm-2.4/include -I/usr/local/Cellar/glibmm/2.62.0/include/glibmm-2.4 -I/usr/local/Cellar/glibmm/2.62.0/lib/glibmm-2.4/include -I/usr/local/Cellar/atkmm/2.28.0_2/include/atkmm-1.6 -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -I/usr/local/Cellar/gdk-pixbuf/2.40.0/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/libepoxy/1.5.4/include -I/usr/local/opt/freetype/include/freetype2 -I/usr/local/Cellar/fontconfig/2.13.1/include -I/usr/local/Cellar/pixman/0.38.4/include/pixman-1 -I/usr/local/Cellar/cairo/1.16.0_2/include/cairo -I/usr/local/Cellar/fribidi/1.0.8/include/fribidi -I/usr/local/Cellar/graphite2/1.3.13/include -I/usr/local/Cellar/harfbuzz/2.6.4/include/harfbuzz -I/usr/local/Cellar/pango/1.44.7/include/pango-1.0 -I/usr/local/Cellar/gtk+3/3.24.12_1/include/gtk-3.0/unix-print -I/usr/local/Cellar/gtk+3/3.24.12_1/include/gtk-3.0 -I/usr/local/Cellar/cairomm/1.12.2_1/include/cairomm-1.0 -I/usr/local/Cellar/cairomm/1.12.2_1/lib/cairomm-1.0/include -I/usr/local/Cellar/pangomm/2.42.0_2/include/pangomm-1.4 -I/usr/local/Cellar/pangomm/2.42.0_2/lib/pangomm-1.4/include -I/usr/local/Cellar/gtkmm3/3.24.2/include/gtkmm-3.0 -I/usr/local/Cellar/gtkmm3/3.24.2/lib/gtkmm-3.0/include -I/usr/local/Cellar/gtkmm3/3.24.2/include/gdkmm-3.0 -I/usr/local/Cellar/gtkmm3/3.24.2/lib/gdkmm-3.0/include -I/usr/local/Cellar/plplot/5.15.0_1/include/plplot -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -I/usr/local/opt/freetype/include/freetype2 -I/usr/local/Cellar/fontconfig/2.13.1/include -I/usr/local/Cellar/libffi/3.2.1/lib/libffi-3.2.1/include -I/usr/local/Cellar/pcre/8.43/include -I/usr/local/Cellar/glib/2.60.4_1/include -I/usr/local/Cellar/glib/2.60.4_1/include/glib-2.0 -I/usr/local/Cellar/glib/2.60.4_1/lib/glib-2.0/include -I/usr/local/opt/gettext/include -I/usr/local/Cellar/pixman/0.38.4/include/pixman-1 -I/usr/local/Cellar/cairo/1.16.0_1/include/cairo -I/usr/local/Cellar/fribidi/1.0.5/include/fribidi -I/usr/local/Cellar/graphite2/1.3.13/include -I/usr/local/Cellar/harfbuzz/2.5.1_1/include/harfbuzz -I/usr/local/Cellar/pango/1.42.4_2/include/pango-1.0 -I.. -DG_LOG_DOMAIN=\"Gtkmm::PLplot\" -g -O2 -std=c++11 -c -o libgtkmm_plplot_2.0_la-plotdata3d.lo test -f 'plotdata3d.cpp' || echo './'plotdata3d.cpp 1 error generated. make[1]: [libgtkmm_plplot_2.0_la-utils.lo] Error 1 make[1]: Waiting for unfinished jobs.... 1 error generated. make[1]: [libgtkmm_plplot_2.0_la-plotdatasurface.lo] Error 1 libtool: compile: clang++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/Cellar/libffi/3.2.1/lib/libffi-3.2.1/include -I/usr/local/Cellar/pcre/8.43/include -I/usr/local/Cellar/glib/2.62.4/include/gio-unix-2.0 -I/usr/local/Cellar/glib/2.62.4/include -I/usr/local/Cellar/glib/2.62.4/include/glib-2.0 -I/usr/local/Cellar/glib/2.62.4/lib/glib-2.0/include -I/usr/local/opt/gettext/include -I/usr/local/Cellar/atk/2.34.1/include/atk-1.0 -I/usr/local/Cellar/libsigc++@2/2.10.2/include/sigc++-2.0 -I/usr/local/Cellar/libsigc++@2/2.10.2/lib/sigc++-2.0/include -I/usr/local/Cellar/glibmm/2.62.0/include/giomm-2.4 -I/usr/local/Cellar/glibmm/2.62.0/lib/giomm-2.4/include -I/usr/local/Cellar/glibmm/2.62.0/include/glibmm-2.4 -I/usr/local/Cellar/glibmm/2.62.0/lib/glibmm-2.4/include -I/usr/local/Cellar/atkmm/2.28.0_2/include/atkmm-1.6 -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -I/usr/local/Cellar/gdk-pixbuf/2.40.0/include/gdk-pixbuf-2.0 -I/usr/local/Cellar/libepoxy/1.5.4/include -I/usr/local/opt/freetype/include/freetype2 -I/usr/local/Cellar/fontconfig/2.13.1/include -I/usr/local/Cellar/pixman/0.38.4/include/pixman-1 -I/usr/local/Cellar/cairo/1.16.0_2/include/cairo -I/usr/local/Cellar/fribidi/1.0.8/include/fribidi -I/usr/local/Cellar/graphite2/1.3.13/include -I/usr/local/Cellar/harfbuzz/2.6.4/include/harfbuzz -I/usr/local/Cellar/pango/1.44.7/include/pango-1.0 -I/usr/local/Cellar/gtk+3/3.24.12_1/include/gtk-3.0/unix-print -I/usr/local/Cellar/gtk+3/3.24.12_1/include/gtk-3.0 -I/usr/local/Cellar/cairomm/1.12.2_1/include/cairomm-1.0 -I/usr/local/Cellar/cairomm/1.12.2_1/lib/cairomm-1.0/include -I/usr/local/Cellar/pangomm/2.42.0_2/include/pangomm-1.4 -I/usr/local/Cellar/pangomm/2.42.0_2/lib/pangomm-1.4/include -I/usr/local/Cellar/gtkmm3/3.24.2/include/gtkmm-3.0 -I/usr/local/Cellar/gtkmm3/3.24.2/lib/gtkmm-3.0/include -I/usr/local/Cellar/gtkmm3/3.24.2/include/gdkmm-3.0 -I/usr/local/Cellar/gtkmm3/3.24.2/lib/gdkmm-3.0/include -I/usr/local/Cellar/plplot/5.15.0_1/include/plplot -I/usr/local/Cellar/libpng/1.6.37/include/libpng16 -I/usr/local/opt/freetype/include/freetype2 -I/usr/local/Cellar/fontconfig/2.13.1/include -I/usr/local/Cellar/libffi/3.2.1/lib/libffi-3.2.1/include -I/usr/local/Cellar/pcre/8.43/include -I/usr/local/Cellar/glib/2.60.4_1/include -I/usr/local/Cellar/glib/2.60.4_1/include/glib-2.0 -I/usr/local/Cellar/glib/2.60.4_1/lib/glib-2.0/include -I/usr/local/opt/gettext/include -I/usr/local/Cellar/pixman/0.38.4/include/pixman-1 -I/usr/local/Cellar/cairo/1.16.0_1/include/cairo -I/usr/local/Cellar/fribidi/1.0.5/include/fribidi -I/usr/local/Cellar/graphite2/1.3.13/include -I/usr/local/Cellar/harfbuzz/2.5.1_1/include/harfbuzz -I/usr/local/Cellar/pango/1.42.4_2/include/pango-1.0 -I.. -DG_LOG_DOMAIN=\"Gtkmm::PLplot\" -g -O2 -std=c++11 -c plotdata3d.cpp -fno-common -DPIC -o .libs/libgtkmm_plplot_2.0_la-plotdata3d.o make: [install-recursive] Error 1

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core): https://github.com/tschoonj/homebrew-tap/issues

These open issues may also help: gtkmm-plplot install crash, while brew upgrade xmi-msim https://github.com/tschoonj/homebrew-tap/issues/1

==> Checking for dependents of upgraded formulae... ==> Upgrading 1 dependent: tschoonj/tap/xmi-msim 7.0_1 -> 8.0 Error: No available formula with the name "xraylib" (dependency of tschoonj/tap/xmi-msim) xmi-msim upgrade (axrf) /Users/alex-8797>brew upgrade tschoonj/tap/xmi-msim ==> Upgrading 1 outdated package: tschoonj/tap/xmi-msim 7.0_1 -> 8.0 Error: No available formula with the name "xraylib" (dependency of tschoonj/tap/xmi-msim)

*upgrade xrmc* *** (axrf) /Users/alex-8798>brew upgrade tschoonj/tap/xrmc Warning: tschoonj/tap/xrmc 6.7.0 already installed ** *gist-logs for gtkmm-plplot (axrf) /Users/alex-8926>brew gist-logs gtkmm-plplot

https://gist.github.com/ef2ec7682eee96d9e17cfaafb806c149 https://gist.github.com/ef2ec7682eee96d9e17cfaafb806c149

[tschoonj]

Alex, based on your brew doctor output alone I would strongly recommend to completely delete everything inside your /usr/local directory and install Homebrew from scratch... And after doing so: please resist the temptation to install anything in there manually: this folder should really be exclusively used by Homebrew.