subject:"Re\: \[COOT\] Which Linux distribution supports building Coot 1.0.x\?"

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

2022-06-29 Thread Paul Emsley



For all versions of coot. The test is in clipper.m4 and reads as if 
having TOP8000 is optional.


It no longer is.

In the build script :

extras_place=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies

    # Bernie made this tarball
    clipper_version=2.1.20180802
    clipper_version_dir=2.1

Paul


On 30/06/2022 03:13, hari jayaram wrote:


Thanks Paul

I’ll also try and find the appropriate lines from build script to 
build an upgraded clipper in the meantime. Guessing this is the 0.9.x 
series build script you are referring to?


Thanks again
Hari



On Wed, Jun 29, 2022 at 5:37 PM Paul Emsley 
 wrote:



This is primarily my mistake.  I now think that coot's configure
should check for the version of clipper that has top8000.

If it doesn't find that clipper, then Coot's configure should fail.

You should never get to the make stage.

I will take a look at what I need to do to make that happen
(because, clearly, it isn't).

A few days.

Paul.



On 27/06/2022 03:12, Paul Emsley wrote:



That clipper is old clipper. You need the clipper from the build
script.

Paul.



On 27/06/2022 03:10, hari jayaram wrote:

Dear Paul and the coot community
It's been 6 years since I posted on any coot forum . I saw the
exciting news around coot-1 and am itching to dive back in.

I am trying to compile coot-1 on Ubuntu 20.04

After installing a series of dependencies, which I can gladly
report back to you on...the build started without any issues. It
however stopped with this error  --see below
I got all the libraries including the clipper libraries from
Ubuntu ( sudo apt-get install libclipper-dev)

I wonder how to proceed past this.

Thanks a tonne for your help
Hari


"""
/bin/bash ../libtool  --tag=CXX --mode=compile g++
-DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\"
-DPACKAGE_VERSION=\"1\" -DPACKAGE_STRING=\"coot\ 1\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\"
-DVERSION=\"1\" -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=\"3.8\" -DHAVE_BOOST=/\*\*/
-DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -DHAVE_GSL -I/usr/include
 -DMMDB_HAS_LINK_DISTANCE -fopenmp
-DPKGDATADIR='"/usr/local/share/coot"' -DUSE_LIBPNG=1
-I/usr/include/libpng16 -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\"
"-DPACKAGE_STRING=\"coot 1\"" -DPACKAGE_BUGREPORT=\"\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1\"
-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=\"3.8\" "-DHAVE_BOOST=/**/"
"-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include
-DMMDB_HAS_LINK_DISTANCE -fopenmp
-DPKGDATADIR=\"/usr/local/share/coot\" -DUSE_LIBPNG=1
-I/usr/include/libpng16 -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’
  869 |    rama.init(clipper::Ramachandran::All2);
      |                                     ^~~~
residue_by_phi_psi.cc:871:41: error: ‘Pro2’ is not a member of
‘clipper::Ramachandran’
  871 |  rama_pro.init(clipper::Ramachandran::Pro2);
      | ^~~~
make[1]: *** [Makefile:1324: residue_by_phi_psi.lo] Error 1
make[1]: Leaving directory '/home/hari-verve/coot-1/ligand'
make: *** [Makefile:723: all-recursive] Error 1
"""

On Mon, Jun 13, 2022 at 4:56 PM Paul Emsley
 wrote:

On 13/06/2022 18:40, Giacomo Fiorin wrote:
> FYI while I'm still going through dependencies from Ubuntu
20.04 packages, I also tried CentOS 7 again by installing
guile-devel to circumvent the script's auto-build of GUILE,
and it builds Coot successfully. However, when I launch it I
see a splash screen and the following messages, after which
Coot exits with error.
>
> I'll try to move forward with Ubuntu 20.04, but if support
for RHEL/CentOS 7 is restored it would be very helpful. Thanks!

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

2022-06-29 Thread hari jayaram

Thanks Paul

I’ll also try and find the appropriate lines from build script to build an
upgraded clipper in the meantime. Guessing this is the 0.9.x series build
script you are referring to?

Thanks again
Hari



On Wed, Jun 29, 2022 at 5:37 PM Paul Emsley 
wrote:

>
> This is primarily my mistake.  I now think that coot's configure should
> check for the version of clipper that has top8000.
>
> If it doesn't find that clipper, then Coot's configure should fail.
>
> You should never get to the make stage.
>
> I will take a look at what I need to do to make that happen (because,
> clearly, it isn't).
>
> A few days.
>
> Paul.
>
>
>
> On 27/06/2022 03:12, Paul Emsley wrote:
>
>
> That clipper is old clipper. You need the clipper from the build script.
>
> Paul.
>
>
>
> On 27/06/2022 03:10, hari jayaram wrote:
>
> Dear Paul and the coot community
> It's been 6 years since I posted on any coot forum . I saw the exciting
> news around coot-1 and am itching to dive back in.
>
> I am trying to compile coot-1 on Ubuntu 20.04
>
> After installing a series of dependencies, which I can gladly report back
> to you on...the build started without any issues. It however stopped with
> this error  --see below
> I got all the libraries including the clipper libraries from Ubuntu ( sudo
> apt-get install libclipper-dev)
>
> I wonder how to proceed past this.
>
> Thanks a tonne for your help
> Hari
>
>
> """
> /bin/bash ../libtool  --tag=CXX   --mode=compile g++
> -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1\"
> -DPACKAGE_STRING=\"coot\ 1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\"
> -DPACKAGE=\"coot\" -DVERSION=\"1\" -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=\"3.8\" -DHAVE_BOOST=/\*\*/
> -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -DHAVE_GSL -I/usr/include
>  -DMMDB_HAS_LINK_DISTANCE   -fopenmp -DPKGDATADIR='"/usr/local/share/coot"'
>   -DUSE_LIBPNG=1 -I/usr/include/libpng16 -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\" "-DPACKAGE_STRING=\"coot 1\""
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\"
> -DVERSION=\"1\" -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=\"3.8\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_PYTHON=/**/" -I.
> -I.. -DHAVE_GSL -I/usr/include -DMMDB_HAS_LINK_DISTANCE -fopenmp
> -DPKGDATADIR=\"/usr/local/share/coot\" -DUSE_LIBPNG=1
> -I/usr/include/libpng16 -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’
>   869 |rama.init(clipper::Ramachandran::All2);
>   | ^~~~
> residue_by_phi_psi.cc:871:41: error: ‘Pro2’ is not a member of
> ‘clipper::Ramachandran’
>   871 |rama_pro.init(clipper::Ramachandran::Pro2);
>   | ^~~~
> make[1]: *** [Makefile:1324: residue_by_phi_psi.lo] Error 1
> make[1]: Leaving directory '/home/hari-verve/coot-1/ligand'
> make: *** [Makefile:723: all-recursive] Error 1
> """
>
> On Mon, Jun 13, 2022 at 4:56 PM Paul Emsley 
> wrote:
>
>> On 13/06/2022 18:40, Giacomo Fiorin wrote:
>> > FYI while I'm still going through dependencies from Ubuntu 20.04
>> packages, I also tried CentOS 7 again by installing guile-devel to
>> circumvent the script's auto-build of GUILE, and it builds Coot
>> successfully. However, when I launch it I see a splash screen and the
>> following messages, after which Coot exits with error.
>> >
>> > I'll try to move forward with Ubuntu 20.04, but if support for
>> RHEL/CentOS 7 is restored it would be very helpful. Thanks!
>>
>>
>> Try setting your path so that
>>
>> /data/local/Fiorin/build/autobuild/coot-Linux-x86_64-centos-7-gtk3/bin is
>> the first element
>>
>> Paul.
>>
>> 
>>
>> To unsubscribe from the COOT list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing
>> list hosted by www.jiscmail.ac.uk, terms & conditions are available

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

2022-06-29 Thread Paul Emsley



This is primarily my mistake.  I now think that coot's configure should 
check for the version of clipper that has top8000.


If it doesn't find that clipper, then Coot's configure should fail.

You should never get to the make stage.

I will take a look at what I need to do to make that happen (because, 
clearly, it isn't).


A few days.

Paul.



On 27/06/2022 03:12, Paul Emsley wrote:



That clipper is old clipper. You need the clipper from the build script.

Paul.



On 27/06/2022 03:10, hari jayaram wrote:

Dear Paul and the coot community
It's been 6 years since I posted on any coot forum . I saw the 
exciting news around coot-1 and am itching to dive back in.


I am trying to compile coot-1 on Ubuntu 20.04

After installing a series of dependencies, which I can gladly report 
back to you on...the build started without any issues. It however 
stopped with this error  --see below
I got all the libraries including the clipper libraries from Ubuntu ( 
sudo apt-get install libclipper-dev)


I wonder how to proceed past this.

Thanks a tonne for your help
Hari


"""
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ 
-DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" 
-DPACKAGE_VERSION=\"1\" -DPACKAGE_STRING=\"coot\ 1\" 
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" 
-DVERSION=\"1\" -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=\"3.8\" -DHAVE_BOOST=/\*\*/ 
-DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -DHAVE_GSL -I/usr/include 
 -DMMDB_HAS_LINK_DISTANCE -fopenmp 
-DPKGDATADIR='"/usr/local/share/coot"' -DUSE_LIBPNG=1 
-I/usr/include/libpng16 -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\" 
"-DPACKAGE_STRING=\"coot 1\"" -DPACKAGE_BUGREPORT=\"\" 
-DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1\" 
-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=\"3.8\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_PYTHON=/**/" 
-I. -I.. -DHAVE_GSL -I/usr/include -DMMDB_HAS_LINK_DISTANCE -fopenmp 
-DPKGDATADIR=\"/usr/local/share/coot\" -DUSE_LIBPNG=1 
-I/usr/include/libpng16 -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’

  869 |    rama.init(clipper::Ramachandran::All2);
      |                                     ^~~~
residue_by_phi_psi.cc:871:41: error: ‘Pro2’ is not a member of 
‘clipper::Ramachandran’

  871 |    rama_pro.init(clipper::Ramachandran::Pro2);
      |                                         ^~~~
make[1]: *** [Makefile:1324: residue_by_phi_psi.lo] Error 1
make[1]: Leaving directory '/home/hari-verve/coot-1/ligand'
make: *** [Makefile:723: all-recursive] Error 1
"""

On Mon, Jun 13, 2022 at 4:56 PM Paul Emsley 
 wrote:


On 13/06/2022 18:40, Giacomo Fiorin wrote:
> FYI while I'm still going through dependencies from Ubuntu
20.04 packages, I also tried CentOS 7 again by installing
guile-devel to circumvent the script's auto-build of GUILE, and
it builds Coot successfully. However, when I launch it I see a
splash screen and the following messages, after which Coot exits
with error.
>
> I'll try to move forward with Ubuntu 20.04, but if support for
RHEL/CentOS 7 is restored it would be very helpful. Thanks!


Try setting your path so that

/data/local/Fiorin/build/autobuild/coot-Linux-x86_64-centos-7-gtk3/bin
is the first element

Paul.



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1


This message was issued to members of www.jiscmail.ac.uk/COOT
, a mailing list hosted by
www.jiscmail.ac.uk , terms &
conditions are available at
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To unsubscribe from the COOT list, click the following link:

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

2022-06-26 Thread Paul Emsley



That clipper is old clipper. You need the clipper from the build script.

Paul.



On 27/06/2022 03:10, hari jayaram wrote:

Dear Paul and the coot community
It's been 6 years since I posted on any coot forum . I saw the 
exciting news around coot-1 and am itching to dive back in.


I am trying to compile coot-1 on Ubuntu 20.04

After installing a series of dependencies, which I can gladly report 
back to you on...the build started without any issues. It however 
stopped with this error  --see below
I got all the libraries including the clipper libraries from Ubuntu ( 
sudo apt-get install libclipper-dev)


I wonder how to proceed past this.

Thanks a tonne for your help
Hari


"""
/bin/bash ../libtool  --tag=CXX   --mode=compile g++ 
-DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" 
-DPACKAGE_VERSION=\"1\" -DPACKAGE_STRING=\"coot\ 1\" 
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" 
-DVERSION=\"1\" -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=\"3.8\" -DHAVE_BOOST=/\*\*/ 
-DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -DHAVE_GSL -I/usr/include 
 -DMMDB_HAS_LINK_DISTANCE   -fopenmp 
-DPKGDATADIR='"/usr/local/share/coot"'   -DUSE_LIBPNG=1 
-I/usr/include/libpng16 -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\" 
"-DPACKAGE_STRING=\"coot 1\"" -DPACKAGE_BUGREPORT=\"\" 
-DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1\" -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=\"3.8\" "-DHAVE_BOOST=/**/" 
"-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include 
-DMMDB_HAS_LINK_DISTANCE -fopenmp 
-DPKGDATADIR=\"/usr/local/share/coot\" -DUSE_LIBPNG=1 
-I/usr/include/libpng16 -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’

  869 |    rama.init(clipper::Ramachandran::All2);
      |                                     ^~~~
residue_by_phi_psi.cc:871:41: error: ‘Pro2’ is not a member of 
‘clipper::Ramachandran’

  871 |    rama_pro.init(clipper::Ramachandran::Pro2);
      |                                         ^~~~
make[1]: *** [Makefile:1324: residue_by_phi_psi.lo] Error 1
make[1]: Leaving directory '/home/hari-verve/coot-1/ligand'
make: *** [Makefile:723: all-recursive] Error 1
"""

On Mon, Jun 13, 2022 at 4:56 PM Paul Emsley 
 wrote:


On 13/06/2022 18:40, Giacomo Fiorin wrote:
> FYI while I'm still going through dependencies from Ubuntu 20.04
packages, I also tried CentOS 7 again by installing guile-devel to
circumvent the script's auto-build of GUILE, and it builds Coot
successfully. However, when I launch it I see a splash screen and
the following messages, after which Coot exits with error.
>
> I'll try to move forward with Ubuntu 20.04, but if support for
RHEL/CentOS 7 is restored it would be very helpful. Thanks!


Try setting your path so that

/data/local/Fiorin/build/autobuild/coot-Linux-x86_64-centos-7-gtk3/bin
is the first element

Paul.



To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1


This message was issued to members of www.jiscmail.ac.uk/COOT
, a mailing list hosted by
www.jiscmail.ac.uk , terms & conditions
are available at https://www.jiscmail.ac.uk/policyandsecurity/





To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

2022-06-26 Thread hari jayaram

Dear Paul and the coot community
It's been 6 years since I posted on any coot forum . I saw the exciting
news around coot-1 and am itching to dive back in.

I am trying to compile coot-1 on Ubuntu 20.04

After installing a series of dependencies, which I can gladly report back
to you on...the build started without any issues. It however stopped with
this error  --see below
I got all the libraries including the clipper libraries from Ubuntu ( sudo
apt-get install libclipper-dev)

I wonder how to proceed past this.

Thanks a tonne for your help
Hari


"""
/bin/bash ../libtool  --tag=CXX   --mode=compile g++
-DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1\"
-DPACKAGE_STRING=\"coot\ 1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\"
-DPACKAGE=\"coot\" -DVERSION=\"1\" -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=\"3.8\" -DHAVE_BOOST=/\*\*/
-DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -DHAVE_GSL -I/usr/include
 -DMMDB_HAS_LINK_DISTANCE   -fopenmp -DPKGDATADIR='"/usr/local/share/coot"'
  -DUSE_LIBPNG=1 -I/usr/include/libpng16 -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\" "-DPACKAGE_STRING=\"coot 1\""
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\"
-DVERSION=\"1\" -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=\"3.8\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_PYTHON=/**/" -I.
-I.. -DHAVE_GSL -I/usr/include -DMMDB_HAS_LINK_DISTANCE -fopenmp
-DPKGDATADIR=\"/usr/local/share/coot\" -DUSE_LIBPNG=1
-I/usr/include/libpng16 -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’
  869 |rama.init(clipper::Ramachandran::All2);
  | ^~~~
residue_by_phi_psi.cc:871:41: error: ‘Pro2’ is not a member of
‘clipper::Ramachandran’
  871 |rama_pro.init(clipper::Ramachandran::Pro2);
  | ^~~~
make[1]: *** [Makefile:1324: residue_by_phi_psi.lo] Error 1
make[1]: Leaving directory '/home/hari-verve/coot-1/ligand'
make: *** [Makefile:723: all-recursive] Error 1
"""

On Mon, Jun 13, 2022 at 4:56 PM Paul Emsley 
wrote:

> On 13/06/2022 18:40, Giacomo Fiorin wrote:
> > FYI while I'm still going through dependencies from Ubuntu 20.04
> packages, I also tried CentOS 7 again by installing guile-devel to
> circumvent the script's auto-build of GUILE, and it builds Coot
> successfully. However, when I launch it I see a splash screen and the
> following messages, after which Coot exits with error.
> >
> > I'll try to move forward with Ubuntu 20.04, but if support for
> RHEL/CentOS 7 is restored it would be very helpful. Thanks!
>
>
> Try setting your path so that
>
> /data/local/Fiorin/build/autobuild/coot-Linux-x86_64-centos-7-gtk3/bin is
> the first element
>
> Paul.
>
> 
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
>
> This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at
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>



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Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

2022-06-13 Thread Paul Emsley


On 13/06/2022 18:40, Giacomo Fiorin wrote:

FYI while I'm still going through dependencies from Ubuntu 20.04 packages, I 
also tried CentOS 7 again by installing guile-devel to circumvent the script's 
auto-build of GUILE, and it builds Coot successfully. However, when I launch it 
I see a splash screen and the following messages, after which Coot exits with 
error.

I'll try to move forward with Ubuntu 20.04, but if support for RHEL/CentOS 7 is 
restored it would be very helpful. Thanks!



Try setting your path so that

/data/local/Fiorin/build/autobuild/coot-Linux-x86_64-centos-7-gtk3/bin is the 
first element

Paul.



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Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

2022-06-13 Thread Giacomo Fiorin

FYI while I'm still going through dependencies from Ubuntu 20.04 packages, I 
also tried CentOS 7 again by installing guile-devel to circumvent the script's 
auto-build of GUILE, and it builds Coot successfully. However, when I launch it 
I see a splash screen and the following messages, after which Coot exits with 
error.

I'll try to move forward with Ubuntu 20.04, but if support for RHEL/CentOS 7 is 
restored it would be very helpful. Thanks!

DEBUG:: setting OpenGL required version to 3 3
INFO:: GL Version:  3.3.0 NVIDIA 510.47.03
INFO:: GL Shading Language Version: 3.30 NVIDIA via Cg compiler
INFO:: GL Renderer: Quadro M4000/PCIe/SSE2
INFO:: GL Vendor:   NVIDIA Corporation
Shader compile meshes-with-shadows.shader success
Shader compile   meshes-shadow-map.shader success
Shader compile meshes-for-ssao.shader success
Shader compile texture-meshes-for-ssao.shader success
Shader compile texture-meshes-with-shadows.shader success
Shader compile   texture-meshes-shadow-map.shader success
Shader compile  texture-meshes.shader success
Shader compileshadow-map-image-texture.shader success
Shader compile 9.ssao_geometry.shader success
Shader compile  9.ssao.shader success
Shader compile 9.ssao_blur.shader success
Shader compile   outline-of-active-residue.shader success
Shader compile map.shader success
Shader compiledraw-map-cap.shader success
Shader compile   model.shader success
Shader compilecentral-cube.shader success
Shader compilecentral-cube.shader success
Shader compilehud-text.shader success
Shader compilehud-bars.shader success
Shader compile  hud-labels.shader success
Shader compile   hud-image-texture.shader success
Shader compile  atom-label.shader success
Shader compilemoleculestotriangles.shader success
Shader compile   lines.shader success
Shader compile lines-pulse.shader success
Shader compile  rama-balls.shader success
Shader compile   particles.shader success
Shader compile   instanced-objects.shader success
Shader compile   hud-geometry-tooltip-text.shader success
Shader compile  happy-face-residue-markers.shader success
Shader compile ligand-view.shader success
Shader compile   model-as-mesh.shader success
Shader compilesymmetry-atoms-lines.shader success
Shader compilehud-bars.shader success
Shader compilerama-plot-axes-and-ticks.shader success
Shader compile   rama-plot-phi-psi-markers.shader success
Shader compile   hud-lines.shader success
Shader compile  meshes.shader success
Shader compile  texture-meshes.shader success
Shader compile effects.shader success
Shader compile  screen.shader success
Shader compile  blur-x.shader success
Shader compile  blur-y.shader success
Shader compile  depth-of-field.shader success
Shader compileblur.shader success
Shader compile rotation-centre-cross-hairs-for-ssao.shader success
GL ERROR:: Shader::set_int_for_uniform() "screen.shader" B glUniform1i for 
uniform screenTexture loc: 2 value: 0 err 1282
GL ERROR:: Shader::set_int_for_uniform() "screen.shader" B glUniform1i for 
uniform screenDepth loc: 1 value: 1 err 1282
GL ERROR:: Shader::set_int_for_uniform() "blur.shader" B glUniform1i for 
uniform screenTexture loc: 4 value: 0 err 1282
GL ERROR:: Shader::set_int_for_uniform() "blur.shader" B glUniform1i for 
uniform screenDepth loc: 3 value: 1 err 1282
Shader compile 9.ssao_geometry.shader success
Shader compile  9.ssao.shader success
Shader compile 9.ssao_blur.shader success
debug:: generating 64 SSAO kernel samples
Python path configuration:
  PYTHONHOME = 
'/data/local/Fiorin/build/autobuild/coot-Linux-x86_64-centos-7-gtk3'
  PYTHONPATH = (not set)
  program name = 'python3'
  isolated = 0
  environment = 1
  user site = 1
  import site = 1
  sys._base_executable = '/usr/bin/python3'
  sys.base_prefix = 
'/data/local/Fiorin/build/autobuild/coot-Linux-x86_64-centos-7-gtk3'
  sys.base_exec_prefix = 
'/data/local/Fiorin/build/autobuild/coot-Linux-x86_64-centos-7-gtk3'
  sys.platlibdir = 'lib'
  sys.executable = '/usr/bin/python3'
  sys.prefix = 
'/data/local/Fiorin/build/autobuild/coot-Linux-x86_64-centos-7-gtk3'
  sys.exec_prefix = 
'/data/local/Fiorin/build/autobuild/coot-Linux-x86_64-centos-7-gtk3'
  sys.path = [

'/data/local/Fiorin/build/autobuild/coot-Linux-x86_64-centos-7-gtk3/lib/python39.zip',

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

2022-06-13 Thread Giacomo Fiorin

Thanks! I should have mentioned that it comes from the log file 30-coot.txt, 
which I preferred not to attach since it contains in many places host names and 
environment variables that shouldn't get published. If you need it for 
debugging, I'm happy to email it off-list.

For completeness, we are using CentOS 7.9 (revision 2009): hopefully there are 
no difference from 7.6 affecting the build.

I'll give it another try with an Ubuntu 20.04 container. I already need to use 
that workaround for other structural bioinformatics tools unfortunately.

Giacomo



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Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

2022-06-13 Thread Paul Emsley

On 13/06/2022 15:57, Giacomo Fiorin wrote:

Hello, I am trying to build Coot 1 from scratch for Linux (CentOS 7).

I used the latest version of the build-it-3-3 script from:
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/build-install-coot-from-scratch.html

whose last revision is:
6.02 20220417 add ffi into Python setup.py

After addressing a few minor issues and updating to the latest Coot
source release (1.0.05), I reached a point where I cannot proceed any
further. Specifically, the build recipe fails to detect correctly the
libguile shared library that was built by the script itself.

ldconfig:
**/build/autobuild/Linux-**-gtk3/lib/libguile-2.2.so.1.4.2-gdb.scm
is not an ELF file - it has the wrong magic bytes at the start.

Which output file is that?

I have seen that message myself. Sadly though, I don't recall if I fixed
it or how I fixed it. Indeed a .scm file is not and ELF file.

There is no other version of libguile installed on this system.

If this is a RHEL/CentOS 7 issue, which Linux distribution would you
recommend instead for building Coot 1.x?

I use Scientific Linux 7.6 (very similar to CentOS 7.6) and Ubuntu 21.10
(and before that 20.04).

The build script is not in a good state for 7.6. I will try to refine it
in the forthcoming days.

Paul.

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Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

Re: [COOT] Which Linux distribution supports building Coot 1.0.x?

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