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pemsley / coot

Software for macromolecular model-building
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
GNU General Public License v3.0
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build issues -- Python and RDKit #142

Open dctaylor87 opened 4 months ago

dctaylor87 commented 4 months ago

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

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 commented 4 months ago

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 commented 4 months ago

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 commented 4 months ago

I added a response on GitHub, but given the delay between when you left your comment and when it showed up in gmail, I thought I'd reply directly as well.

Here is $logs/gtk4-gcc-12_and_g++-12/18-rkit.txt.

On Thu, Jul 4, 2024 at 11:58 AM Paul Emsley @.***> wrote:

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

— Reply to this email directly, view it on GitHub https://github.com/pemsley/coot/issues/142#issuecomment-2209278781, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASQW5RGZLOW2M2J2YTM3J7LZKVWJ3AVCNFSM6AAAAABKILONIGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMBZGI3TQNZYGE . You are receiving this because you authored the thread.Message ID: @.***>

building ========================= rdkit ============================== ==================== LD_LIBRARY_PATH is /candd/taylor/coot/build/Linux-bloomington-gtk4/lib PATH B testing for existance of /candd/taylor/coot/build/sources/rdkit-Release_2023_03_1.tar.gz here C with get_the_rdkit_tar_file true

Redirecting output to ‘wget-log.25’. wget -nv -N -P /candd/taylor/coot/build/sources https://github.com/rdkit/rdkit/archive/Release_2023_03_1.tar.gz

Redirecting output to ‘wget-log.26’. /candd/taylor/coot/build/bloomington_2024-07-01__T22_01_20 tar xf /candd/taylor/coot/build/sources/rdkit-Release_2023_03_1.tar.gz boost_1_82_0 build-eigen clipper-2.1 curl-7.65.3 eigen-3.3.9 fftw-2.1.5 glm-0.9.9.2 gmp-6.1.2 gobject-introspection-1.72.0 gsl-2.7 libccp4-6.5.1 libffi-3.2.1 libgd-2.1.1 libidn2-2.2.0 libtool-2.4.6 meson-1.2.3 mmdb2-2.0.22 ninja-1.10.2 numpy-1.19.4 PyGObject-3.42.1 Python-3.11.4 Raster3D_3.0-7 rdkit-Release_2023_03_1 readline-6.3 ssm-1.4 wget-log wget-log.1 wget-log.10 wget-log.11 wget-log.12 wget-log.13 wget-log.14 wget-log.15 wget-log.16 wget-log.17 wget-log.18 wget-log.19 wget-log.2 wget-log.20 wget-log.21 wget-log.22 wget-log.23 wget-log.24 wget-log.25 wget-log.26 wget-log.3 wget-log.4 wget-log.5 wget-log.6 wget-log.7 wget-log.8 wget-log.9

Redirecting output to ‘wget-log’. /candd/taylor/coot/build/bloomington_2024-07-01T22_01_20/rdkit-Release_2023_03_1 patch -p0 patching file Code/GraphMol/FileParsers/GeneralFileReader.h Hunk #1 FAILED at 145. 1 out of 1 hunk FAILED -- saving rejects to file Code/GraphMol/FileParsers/GeneralFileReader.h.rej /candd/taylor/coot/build/bloomington_2024-07-01T22_01_20/rdkit-Release_2023_03_1/build which cmake /usr/bin/cmake will configure with cmake like this: cmake -DPYTHON_INCLUDE_DIR=/candd/taylor/coot/build/Linux-bloomington-gtk4/include/python3.11 -DPYTHON_EXECUTABLE=/candd/taylor/coot/build/Linux-bloomington-gtk4/bin/python3 -DPYTHON_LIBRARY=/candd/taylor/coot/build/Linux-bloomington-gtk4/lib/python3.11/config-3.11-x86_64-linux-gnu/libpython3.11.a -DCMAKE_INSTALL_PREFIX=/candd/taylor/coot/build/Linux-bloomington-gtk4 -DRDK_BUILD_MAEPARSER_SUPPORT=OFF -DRDK_BUILD_CAIRO_SUPPORT=ON -DRDK_INSTALL_INTREE=OFF .. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Catch not found in /candd/taylor/coot/build/bloomington_2024-07-01T22_01_20/rdkit-Release_2023_03_1/External/catch/catch Downloading https://github.com/catchorg/Catch2/archive/v2.13.8.tar.gz... CATCH: /candd/taylor/coot/build/bloomington_2024-07-01T22_01_20/rdkit-Release_2023_03_1/External/catch/catch/single_include/catch2 -- Found PythonInterp: /candd/taylor/coot/build/Linux-bloomington-gtk4/bin/python3 (found version "3.11.4") -- Found PythonLibs: /candd/taylor/coot/build/Linux-bloomington-gtk4/lib/python3.11/config-3.11-x86_64-linux-gnu/libpython3.11.a (found version "3.11.4") Python Install directory /candd/taylor/coot/build/Linux-bloomington-gtk4/lib/python3.11/site-packages PYTHON Py_ENABLE_SHARED: 1 PYTHON USING LINK LINE: -shared -Wl,--rpath=/candd/taylor/coot/build/Linux-bloomington-gtk4/lib nbval not found, disabling the jupyter tests -- Found Eigen3: /candd/taylor/coot/build/Linux-bloomington-gtk4/include/eigen3 (Required is at least version "2.91.0") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE
-- Found Boost: /candd/taylor/coot/build/Linux-bloomington-gtk4/lib/cmake/Boost-1.82.0/BoostConfig.cmake (found suitable version "1.82.0", minimum required is "1.58.0") found components: system serialization iostreams == Using strict rotor definition -- coordgen include dir set as coordgen_INCLUDE_DIRS-NOTFOUND -- coordgen libraries set as 'coordgen_LIBRARIES-NOTFOUND' -- Could NOT find coordgen (missing: coordgen_INCLUDE_DIRS coordgen_LIBRARIES) Downloading https://github.com/schrodinger/coordgenlibs/archive/v3.0.2.tar.gz... Downloading https://github.com/rareylab/RingDecomposerLib/archive/v1.1.3_rdkit.tar.gz... -- Found Boost: /candd/taylor/coot/build/Linux-bloomington-gtk4/lib/cmake/Boost-1.82.0/BoostConfig.cmake (found suitable version "1.82.0", minimum required is "1.58.0") found components: iostreams -- Found Boost: /candd/taylor/coot/build/Linux-bloomington-gtk4/lib/cmake/Boost-1.82.0/BoostConfig.cmake (found suitable version "1.82.0", minimum required is "1.58.0") found components: system iostreams -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13") == Updating Filters.cpp from pains file == Done updating pains files Downloading https://fonts.google.com/download?family=Comic%20Neue... CMake Error at Code/cmake/Modules/RDKitUtils.cmake:257 (MESSAGE): The md5 checksum for /candd/taylor/coot/build/bloomington_2024-07-01__T22_01_20/rdkit-Release_2023_03_1/Code/GraphMol/MolDraw2D/Comic_Neue.zip is incorrect; expected: 850b0df852f1cda4970887b540f8f333, found: 29f307f522ece5041080314d66b90c2e Call Stack (most recent call first): Code/GraphMol/MolDraw2D/CMakeLists.txt:21 (downloadAndCheckMD5)

-- Configuring incomplete, errors occurred! See also "/candd/taylor/coot/build/bloomington_2024-07-01__T22_01_20/rdkit-Release_2023_03_1/build/CMakeFiles/CMakeOutput.log". problem configuring the RDKit.

dctaylor87 commented 4 months ago

Did some more investigating.

Turns out the downloaded Comic_Neue.zip file is not a zip file, but a javascript file:

$ find . -name '*.zip' -print0 | xargs -0 file | egrep -v 'Zip archive' ./meson-1.2.3/test cases/common/153 wrap file should not failed/subprojects/packagecache/zlib-1.2.8-8-wrap.zip: ASCII text ./rdkit-Release_2023_03_1/Code/GraphMol/MolDraw2D/Comic_Neue.zip: JavaScript source, ASCII text, with very long lines (7021)

I looked at the ASCII text file, it is one line:

dummy

nothing else. I tried looking at the javascript file with a browser and it just showed me a blank screen. I have attached it in case it is helpful to you. (BTW, I had to rename it to get the browser to treat it as HTML rather than ZIP). The original was Comic_Neue.zip.

On Fri, Jul 5, 2024 at 10:38 AM David Taylor @.***> wrote:

I added a response on GitHub, but given the delay between when you left your comment and when it showed up in gmail, I thought I'd reply directly as well.

Here is $logs/gtk4-gcc-12_and_g++-12/18-rkit.txt.

On Thu, Jul 4, 2024 at 11:58 AM Paul Emsley @.***> wrote:

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

— Reply to this email directly, view it on GitHub https://github.com/pemsley/coot/issues/142#issuecomment-2209278781, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASQW5RGZLOW2M2J2YTM3J7LZKVWJ3AVCNFSM6AAAAABKILONIGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMBZGI3TQNZYGE . You are receiving this because you authored the thread.Message ID: @.***>