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build issues -- Python and RDKit #142

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dctaylor87 opened this issue Jul 2, 2024 · 4 comments
Open

build issues -- Python and RDKit #142

dctaylor87 opened this issue Jul 2, 2024 · 4 comments

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@dctaylor87
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I've been trying to build coot 1.1.07 on Debian GNU/Linux 12
(bookworm) and have run into problems.

The first problem is Python. It appears to need Python 3 but is
looking for the python executable, not the python3 executable. Now,
python is the traditional name of the Python 2 executable. Python 3
is called python3.

I have Python 3 installed, but not Python 2. (Everything I've done
for the last few years with Python has been with Python 3, not Python
2.) I'm not sure if Python 2 is even an installation option on Debian
bookworm.

Here is a one line patch to build-it-3-3 for that. Presumably similar
changes are needed elsewhere for non-Debian systems.

diff --git a/build-it-3-3 b/build-it-3-3
index 85eaeb1fd..2af980f9c 100644
--- a/build-it-3-3
+++ b/build-it-3-3
@@ -1205,7 +1205,7 @@ case $dist_name in

 debian)
   # python is needed to configure ninja. Sigh. flex and bison are needed for gobject-introspection

  •  dep_list='libncurses5-dev libssl-dev g++ git libxext-dev libglu1-mesa-dev mesa-common-dev python flex bison m4 cmake'

  •  dep_list='libncurses5-dev libssl-dev g++ git libxext-dev libglu1-mesa-dev mesa-common-dev python3 flex bison m4 cmake'
 # converted from dep_list='libncurses5-dev g++ libxext-dev libglu1-mesa-dev mesa-common-dev libgtk2.0-dev'
 # not tested

The next problem, involves the RDKit header files. The librdkit-dev
package is not installed on the build machine, so the headers are not
present in /usr/include.

And the code that generates the Makefile in build-coot/lidia-core does
not account for this and include

${BUILDING_DIR}/rdkit-Release_$rdkit_version/Code

in the list of -I directives to supply to the compiler.

I do not have a fix for this.
@pemsley
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pemsley commented Jul 4, 2024

Let's see what is happening in the compilation of the RDKit - what does $HOME/build-logs/something/gcc-something/something-rdkit.txt say?

@dctaylor87
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The logs are in ${AUTOBUILD_BUILD}/logs. The only log file with rdkit as part of its name is
gtk45-gcc-12_and_g++-12/18-rdkit.txt.

18-rdkit.txt

@dctaylor87
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dctaylor87 commented Jul 5, 2024 via email

@dctaylor87
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dctaylor87 commented Jul 5, 2024 via email

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@pemsley @dctaylor87