[Debian-med-packaging] Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

[Andreas Tille]

On Thu, Dec 12, 2019 at 03:49:13PM -0500, Scott Talbert wrote:
> > 
> > That hint was helpful anyway and I get further now.  I think now the
> > problem is to convince scons to install in $(CURDIR)/debian/tmp which
> > seems to try rather /usr/share/pdb2pqr directly:
> 
> Looks like the debian/rules file is specifying /usr/share/pdb2pqr as PREFIX:
> 
> https://salsa.debian.org/med-team/pdb2pqr/blob/master/debian/rules#L33

Arrghh, good if somebody else is proof-reading.  However, setting this
does not help:



mkdir -p /build/pdb2pqr-2.1.1+dfsg/debian/tmp/usr/share/pdb2pqr
scons \
        URL="http://localhost/pdb2pqr/" \
        PREFIX="/build/pdb2pqr-2.1.1+dfsg/debian/tmp/usr/share/pdb2pqr"
scons: Reading SConscript files ...
not using opal 
scons: done reading SConscript files.
scons: Building targets ...
CopySubAction("pdb2pqr.py", "pdb2pqr.py.in")
scons: *** [pdb2pqr.py] Can't write target file pdb2pqr.py
scons: building terminated because of errors.

TARGETS: ['pdb2pqr.py', 'apbs_cgi.cgi', 'visualize.cgi', 'querystatus.cgi', 'src/aconf.py', 'html/server.html', 'pdb2pqr.cgi', 'pdb2pka/substruct/Algorithms.cpython-37m-x86_64-linux-gnu.so', 'pdb2pka/_pMC_mult.cpython-37m-x86_64-linux-gnu.so']

========================
Configuration Parameters
========================

Version: 2.1.1
Install directory: /build/pdb2pqr-2.1.1+dfsg/debian/tmp/usr/share/pdb2pqr/
pdb2pka and ligand support: True
Path to the website directory: http://localhost/pdb2pqr/
PDB2PQR jobs run via the web interface will be forked on the server.

The preferred way to configure the build is by editing the file build_config.py

Run scons with the python3 that you intend to use with pdb2pqr.
For example: "scons" will setup pdb2pqr to be run with Debian default Python3 interpreter

Run "scons install" to install pdb2pqr in /build/pdb2pqr-2.1.1+dfsg/debian/tmp/usr/share/pdb2pqr/

Run "scons basic-test" for a basic functionality test
Run "scons advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled.
Run "scons complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled.
Run "scons pdb2pka-test" for a test of PDB2PKA functionality.
    Requires numpy, PDB2PKA support compiled AND the APBS python3 libraries compiled and installed in the pdb2pka directory.

To setup a web service create a symbolic link to /build/pdb2pqr-2.1.1+dfsg/debian/tmp/usr/share/pdb2pqr/ that enables you to view http://localhost/pdb2pqr/ after running "scons install"

Run "scons msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules.
VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging.
The resulting projects will need to modified to use VS natively to compile the code or debug.

FAILED!!!!
Failed building pdb2pqr.py: Can't write target file pdb2pqr.py
make[1]: *** [debian/rules:29: override_dh_auto_configure] Error 2
make[1]: Leaving directory '/build/pdb2pqr-2.1.1+dfsg'
make: *** [debian/rules:13: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
I: copying local configuration
E: Failed autobuilding of package


I intentionally created the dir
  /build/pdb2pqr-2.1.1+dfsg/debian/tmp/usr/share/pdb2pqr/
before the fixed scons call - but the result is the same. :-(

Kind regards

      Andreas.


-- 
http://fam-tille.de