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open babel source installation - issues

Karim Rafie (PG Research)

Dear all,

 

I’m having a problem compiling openbable on my Mac (macOS Sierra, version 10.12.3). When wanting to compile I receive the following message at the end:

 

“CMake Warning (dev):

  Policy CMP0042 is not set: MACOSX_RPATH is enabled by default.  Run "cmake

  --help-policy CMP0042" for policy details.  Use the cmake_policy command to

  set the policy and suppress this warning.

 

  MACOSX_RPATH is not specified for the following targets:

 

   inchi

   openbabel

 

This warning is for project developers.  Use -Wno-dev to suppress it.

 

-- Generating done

CMake Warning:

  Manually-specified variables were not used by the project:

 

    EIGEN3_INCLUDE_DIR

 

 

-- Build files have been written to: /Users/kzrafie/Downloads/openbabel-2.3.1/build”

 

 

I assume, due to the paths not specified in MACOSX_RPATH for inchi and openbabel, that I’m having issues with the installation. I would usually go for the pkg/dmg installation; however, I’m putting together a python script for which I need to do a source installation.

 

You probably heard about this issue before, however I couldn’t find any decent answers anywhere.

 

Best wishe,

Karim

##############################################

Karim Rafie; M.Sc., AMRSC

PhD research student

Daan van Aalten lab

School of Life Sciences

University of Dundee

Scotland / UK


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Re: open babel source installation - issues

Fredrik Wallner
Hi,

That warning from CMake (marked as ”for project developers”) should not hinder the compilation and installation of OpenBabel. Did you try to move on with make and ”make install”?
If all that you need is python access to OpenBabel, you should also be able to use the conda distribution (”conda install openbabel”) provided that you install and use the Anaconda Python distribution (https://www.continuum.io/downloads).

Kind regards,
Fredrik

28 feb. 2017 kl. 17:30 skrev Karim Rafie (PG Research) <[hidden email]>:

Dear all,
 
I’m having a problem compiling openbable on my Mac (macOS Sierra, version 10.12.3). When wanting to compile I receive the following message at the end:
 
“CMake Warning (dev):
  Policy CMP0042 is not set: MACOSX_RPATH is enabled by default.  Run "cmake
  --help-policy CMP0042" for policy details.  Use the cmake_policy command to
  set the policy and suppress this warning.
 
  MACOSX_RPATH is not specified for the following targets:
 
   inchi
   openbabel
 
This warning is for project developers.  Use -Wno-dev to suppress it.
 
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:
 
    EIGEN3_INCLUDE_DIR
 
 
-- Build files have been written to: /Users/kzrafie/Downloads/openbabel-2.3.1/build”
 
 
I assume, due to the paths not specified in MACOSX_RPATH for inchi and openbabel, that I’m having issues with the installation. I would usually go for the pkg/dmg installation; however, I’m putting together a python script for which I need to do a source installation.
 
You probably heard about this issue before, however I couldn’t find any decent answers anywhere.
 
Best wishe,
Karim
##############################################
Karim Rafie; M.Sc., AMRSC
PhD research student
Daan van Aalten lab
School of Life Sciences
University of Dundee
Scotland / UK

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Re: open babel source installation - issues

Karim Rafie (PG Research)

Hi Fredrik,

 

Thanks for the quick reply. Yes, I did try running the make step but it exits after an error (see below):

#############

      use '==' to turn this assignment into an equality comparison

    if ( p = (const char*)memchr(source, 0, maxlen) ) {

           ^

           ==

4 warnings generated.

36 warnings generated.

[ 10%] Linking C shared library ../../../lib/libinchi.dylib

[ 10%] Built target inchi

make: *** [all] Error 2

############

 

It might be an openbabel independent issue that I haven’t identified yet.

I’ll keep trying, if I find the solution I’ll let you know.

Meanwhile, I’m going to work with anaconda as I have it on my system as well.

 

Thanks again for your help.

 

Best,

Karim

##############################################

Karim Rafie; M.Sc., AMRSC

PhD research student

Daan van Aalten lab

School of Life Sciences

University of Dundee

Scotland / UK

 

From: Fredrik Wallner <[hidden email]>
Date: Wednesday, 1 March 2017 at 09:24
To: "Karim Rafie (PG Research)" <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [Open Babel] open babel source installation - issues

 

Hi,

 

That warning from CMake (marked as ”for project developers”) should not hinder the compilation and installation of OpenBabel. Did you try to move on with make and ”make install”?

If all that you need is python access to OpenBabel, you should also be able to use the conda distribution (”conda install openbabel”) provided that you install and use the Anaconda Python distribution (https://www.continuum.io/downloads).

 

Kind regards,

Fredrik

 

28 feb. 2017 kl. 17:30 skrev Karim Rafie (PG Research) <[hidden email]>:

 

Dear all,

 

I’m having a problem compiling openbable on my Mac (macOS Sierra, version 10.12.3). When wanting to compile I receive the following message at the end:

 

“CMake Warning (dev):

  Policy CMP0042 is not set: MACOSX_RPATH is enabled by default.  Run "cmake

  --help-policy CMP0042" for policy details.  Use the cmake_policy command to

  set the policy and suppress this warning.

 

  MACOSX_RPATH is not specified for the following targets:

 

   inchi

   openbabel

 

This warning is for project developers.  Use -Wno-dev to suppress it.

 

-- Generating done

CMake Warning:

  Manually-specified variables were not used by the project:

 

    EIGEN3_INCLUDE_DIR

 

 

-- Build files have been written to: /Users/kzrafie/Downloads/openbabel-2.3.1/build”

 

 

I assume, due to the paths not specified in MACOSX_RPATH for inchi and openbabel, that I’m having issues with the installation. I would usually go for the pkg/dmg installation; however, I’m putting together a python script for which I need to do a source installation.

 

You probably heard about this issue before, however I couldn’t find any decent answers anywhere.

 

Best wishe,

Karim

##############################################

Karim Rafie; M.Sc., AMRSC

PhD research student

Daan van Aalten lab

School of Life Sciences

University of Dundee

Scotland / UK


The University of Dundee is a registered Scottish Charity, No: SC015096 ------------------------------------------------------------------------------
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SlashDot.org! http://sdm.link/slashdot_______________________________________________
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Re: open babel source installation - issues

Chris Swain
In reply to this post by Karim Rafie (PG Research)
Might be useful?


Chris

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Re: open babel source installation - issues

Geoff Hutchison
In reply to this post by Karim Rafie (PG Research)
> 4 warnings generated.
> 36 warnings generated.

That’s not the actual error - those are warnings. Can you send the entire log of “make”?

>> I assume, due to the paths not specified in MACOSX_RPATH for inchi and openbabel, that I’m having issues with the installation. I would usually go for the pkg/dmg installation; however, I’m putting together a python script for which I need to do a source installation.

Considering I compile regularly on my Mac OS laptop, this is not a problem.

Thanks,
-Geoff


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Re: open babel source installation - issues

Karim Rafie (PG Research)
Hi Geoffrey,

Thanks for your reply. I actually already solved the problem. Turns out the source code linked on the openbabel installation guide was outdated. Moved to the new source code and it worked like a charm.

Best,
Karim
##############################################
Karim Rafie; M.Sc., AMRSC

PhD research student
Daan van Aalten lab

School of Life Sciences

University of Dundee

Scotland / UK

On 04/03/2017, 00:08, "Geoffrey Hutchison" <[hidden email]> wrote:

    > 4 warnings generated.
    > 36 warnings generated.

    That’s not the actual error - those are warnings. Can you send the entire log of “make”?

    >> I assume, due to the paths not specified in MACOSX_RPATH for inchi and openbabel, that I’m having issues with the installation. I would usually go for the pkg/dmg installation; however, I’m putting together a python script for which I need to do a source installation.

    Considering I compile regularly on my Mac OS laptop, this is not a problem.

    Thanks,
    -Geoff




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