Re: [COOT] Build coot-1.0.02 on CentOS7

2022-04-07 Thread C.J. 
I checked my clipper. The version is below.
Package clipper-2.1-26.20140911.el7.x86_64 already installed and latest
version

Here is the version of clipper-devel.
Package clipper-devel-2.1-26.20140911.el7.x86_64 already installed and
latest version

Paul Emsley  于2022年4月7日周四 17:26写道：

>
> 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
> > 222 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

[COOT] Build coot-1.0.02 on CentOS7

2022-04-07 Thread C.J. 
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 
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
222 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);
 ^~~~
make[1]: *** [residue_by_phi_psi.lo] Error 1
make[1]: Leaving directory `/data2/sw/coot-1.0.01/ligand'
make: *** [all-recursive] Error 1

Thanks!
Jianhao



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