On 07/04/2022 23:22, C.J. wrote:
Hi all,

Has anyone successfully built coot-1.0.02 on centos7+anaconda3 python environment?
My OS environment is below.

$ uname -a
Linux lab 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

$ python --version
Python 3.7.6

$ make --version
GNU Make 3.82
Built for x86_64-redhat-linux-gnu
Copyright (C) 2010  Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

$ gcc --version
gcc (GCC) 8.3.1 20190311 (Red Hat 8.3.1-3)
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I tried to build it with the script (https://raw.githubusercontent.com/pemsley/coot/gtk3/build-it-3-3). But it failed with unknown reasons. The build.log says only "coot build failed, exiting" in the last line without any other error messags. See below for last 20 lines.

numpy is found, skip
building rdkit 2020_09_3
building QED
libunistring skip_this true
not building libunistring
not building gc
not building gmp
BUILDING guile:
BUILDING g-wrap:
BUILDING guile-cairo
guile-lib needs to be installed
some test here
guile-config found
guile-gnome-platform skip_this false
222222222222222 Now Coot.....
Thu Apr  7 14:41:36 PDT 2022
/data2/sw/coot-1.0.01
BUILDING coot
coot build failed, exiting.


Even I tried to build with ./configure and make. It came with an error message as below.

/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1.0.01\" -DPACKAGE_STRING=\"coot\ 1.0.01\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1.0.01\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_PYTHON=\"3.7\" -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -DHAVE_GSL -I/usr/include     -fopenmp -DPKGDATADIR='"/usr/local/share/coot"' -DUSE_SQLITE3    -DUSE_LIBPNG=1 -I/usr/include/libpng15   -g -O2 -Wall -Wno-unused  -std=c++11 -MT residue_by_phi_psi.lo -MD -MP -MF .deps/residue_by_phi_psi.Tpo -c -o residue_by_phi_psi.lo residue_by_phi_psi.cc libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1.0.01\" "-DPACKAGE_STRING=\"coot 1.0.01\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1.0.01\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_PYTHON=\"3.7\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -fopenmp -DPKGDATADIR=\"/usr/local/share/coot\" -DUSE_SQLITE3 -DUSE_LIBPNG=1 -I/usr/include/libpng15 -g -O2 -Wall -Wno-unused -std=c++11 -MT residue_by_phi_psi.lo -MD -MP -MF .deps/residue_by_phi_psi.Tpo -c residue_by_phi_psi.cc  -fPIC -DPIC -o .libs/residue_by_phi_psi.o residue_by_phi_psi.cc: In member function ‘void coot::residue_by_phi_psi::init_phi_psi_plot()’: residue_by_phi_psi.cc:869:37: error: ‘All2’ is not a member of ‘clipper::Ramachandran’
    rama.init(clipper::Ramachandran::All2);
                                     ^~~~
residue_by_phi_psi.cc:871:41: error: ‘Pro2’ is not a member of ‘clipper::Ramachandran’
    rama_pro.init(clipper::Ramachandran::Pro2);
                                         ^~~~


configure is somehow picking up the wrong/older clipper. Perhaps a pre-installed one?


Paul.

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