Dear Coot users,
I'm trying to install a specific version of Coot - 0.9.8.96 on my Ubuntu
22.04 LTE machine.
I downloaded the following file
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.9.8.96.tar.gz
untar the repo, then check the INSTALL file and installed the listed
dependencies:
patch
m4
g++
libxext-dev
libxt-dev
libc6-dev
libglu1-mesa-dev
mesa-common-dev
swig
libgtk2.0-dev
libgnomecanvas2-dev
Finally I run ./configure and did not observe any error messages.
However, when I run make I got the following error:
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\"
-DPACKAGE_VERSION=\"0.9.8.96\" -DPACKAGE_STRING=\"coot\ 0.9.8.96\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\"
-DVERSION=\"0.9.8.96\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
-DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1
-DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_CXX11=1
-DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"3.12\"
-DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include
-DHAVE_SYS_STDTYPES_H=0 -DHAVE_GNOME_CANVAS
-I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0
-I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include
-I/usr/include/pango-1.0 -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/harfbuzz
-I/usr/include/freetype2 -I/usr/local/include/libpng15
-I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi
-I/usr/include/uuid -I/usr/include/cairo -I/usr/include/pixman-1
-I/usr/include/gdk-pixbuf-2.0 -I/usr/include/x86_64-linux-gnu
-I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread
-DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0
-I/usr/lib/x86_64-linux-gnu/gtkglext-1.0/include -I/usr/include/gtk-2.0
-I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/harfbuzz -I/usr/include/freetype2
-I/usr/local/include/libpng15 -I/usr/include/libmount -I/usr/include/blkid
-I/usr/include/fribidi -I/usr/include/uuid -I/usr/include/cairo
-I/usr/include/pixman-1 -I/usr/include/gdk-pixbuf-2.0
-I/usr/include/x86_64-linux-gnu -I/usr/include/atk-1.0 -pthread
-I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include
-I/usr/include/pango-1.0 -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/harfbuzz
-I/usr/include/freetype2 -I/usr/local/include/libpng15
-I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi
-I/usr/include/uuid -I/usr/include/cairo -I/usr/include/pixman-1
-I/usr/include/gdk-pixbuf-2.0 -I/usr/include/x86_64-linux-gnu
-I/usr/include/atk-1.0 -pthread -I/usr/local/include -DHAVE_SSMLIB
-DMMDB_HAS_LINK_DISTANCE -I/usr/include -DCLIPPER_HAS_TOP8000
-DUSE_SQLITE3 -I/home/karolina/.pyenv/versions/miniconda3-latest/include
-DPKGDATADIR='"/usr/local/share/coot"'
-DPACKAGE_LOCALE_DIR='"/usr/local/share/coot/locale"'
-DPKGPYTHONDIR='"/usr/local/lib/python3.12/site-packages/coot"'
-DDATADIR='"/usr/local/share"'
-DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-ubuntu-22.04.5-gtk2"'
-DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0
-I/home/karolina/.pyenv/versions/miniconda3-latest/include/python3.12
-DHAVE_GSL -fopenmp -g -O2 -Wall -Wno-unused -std=c++11 -MT main.o -MD -MP
-MF .deps/main.Tpo -c -o main.o main.cc
In file included from /usr/include/gtk-2.0/gtk/gtkobject.h:37,
from /usr/include/gtk-2.0/gtk/gtkwidget.h:36,
from /usr/include/gtk-2.0/gtk/gtkcontainer.h:35,
from /usr/include/gtk-2.0/gtk/gtkbin.h:35,
from /usr/include/gtk-2.0/gtk/gtkwindow.h:36,
from /usr/include/gtk-2.0/gtk/gtkdialog.h:35,
from /usr/include/gtk-2.0/gtk/gtkaboutdialog.h:32,
from /usr/include/gtk-2.0/gtk/gtk.h:33,
from main.cc:50:
/usr/include/gtk-2.0/gtk/gtktypeutils.h:236:64: warning: ‘GTypeDebugFlags’
is deprecated [-Wdeprecated-declarations]
236 | void gtk_type_init (GTypeDebugFlags debug_flags);
| ^
In file included from /usr/include/glib-2.0/gobject/gobject.h:24,
from /usr/include/glib-2.0/gobject/gbinding.h:29,
from /usr/include/glib-2.0/glib-object.h:22,
from /usr/include/glib-2.0/gio/gioenums.h:28,
from /usr/include/glib-2.0/gio/giotypes.h:28,
from /usr/include/glib-2.0/gio/gio.h:26,
from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30,
from /usr/include/gtk-2.0/gdk/gdk.h:32,
from /usr/include/gtk-2.0/gtk/gtk.h:32,
from main.cc:50:
/usr/include/glib-2.0/gobject/gtype.h:704:3: note: declared here
704 | } GTypeDebugFlags GLIB_DEPRECATED_TYPE_IN_2_36;
| ^~~~~~~~~~~~~~~
In file included from /usr/include/gtk-2.0/gtk/gtktoolitem.h:31,
from /usr/include/gtk-2.0/gtk/gtktoolbutton.h:30,
from /usr/include/gtk-2.0/gtk/gtkmenutoolbutton.h:30,
from /usr/include/gtk-2.0/gtk/gtk.h:126,
from main.cc:50:
/usr/include/gtk-2.0/gtk/gtktooltips.h:73:12: warning: ‘GTimeVal’ is
deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
73 | GTimeVal last_popdown;
| ^~~~~~~~~~~~
In file included from /usr/include/glib-2.0/glib/galloca.h:32,
from /usr/include/glib-2.0/glib.h:30,
from /usr/include/glib-2.0/gobject/gbinding.h:28,
from /usr/include/glib-2.0/glib-object.h:22,
from /usr/include/glib-2.0/gio/gioenums.h:28,
from /usr/include/glib-2.0/gio/giotypes.h:28,
from /usr/include/glib-2.0/gio/gio.h:26,
from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30,
from /usr/include/gtk-2.0/gdk/gdk.h:32,
from /usr/include/gtk-2.0/gtk/gtk.h:32,
from main.cc:50:
/usr/include/glib-2.0/glib/gtypes.h:551:26: note: declared here
551 | typedef struct _GTimeVal GTimeVal
GLIB_DEPRECATED_TYPE_IN_2_62_FOR(GDateTime);
| ^~~~~~~~
In file included from main.cc:107:
cc-interface.hh:790:49: error: ‘PyObject’ has not been declared
790 | void add_hydrogen_atoms_to_residue_py(int imol, PyObject
*residue_spec_py);
| ^~~~~~~~
make[1]: *** [Makefile:1943: main.o] Error 1
make[1]: Leaving directory '/home/karolina/Downloads/coot-0.9.8.96/src'
make: *** [Makefile:718: all-recursive] Error 1
I checked the python version on my machine:
python --version
Python 3.8.20
I checked the mailing list, but did not find similar issues to mine, so
please - can you help me solve this problem?
Do I need a different python version?
Best regards,
Karolina
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