Re: [Rdkit-discuss] RDKIT Build Problems
Thanks Greg. I have the problem at CI, too. It was 100% failure rate the last two days. At home, occasionally. At least, it isn’t only me :-) Markus - | Markus Sitzmann | markus.sitzm...@gmail.com > On 6. Mar 2019, at 17:25, Greg Landrum wrote: > > > >> On Wed, Mar 6, 2019 at 1:15 PM Markus Sitzmann >> wrote: >> >> Does someone maybe has the same problem? And an explanation whats going on - >> the Avalon tools seemed to be unchanged since quite a while. > > I've seen it a couple of times in the CI builds for the RDKit over the past > couple of days. It's caused by downloads failing since sourceforge is > unreliable. > > -greg > > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKIT Build Problems
On Wed, Mar 6, 2019 at 1:15 PM Markus Sitzmann wrote: > > Does someone maybe has the same problem? And an explanation whats going on > - the Avalon tools seemed to be unchanged since quite a while. > I've seen it a couple of times in the CI builds for the RDKit over the past couple of days. It's caused by downloads failing since sourceforge is unreliable. -greg ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] RDKIT Build Problems
Hi everybody,
Currently (the last couple of days) the build of one of my Docker images
stopped working:
https://github.com/chembience/chembience/blob/develop/context/build/rdkit-postgres-compile/Dockerfile
That occurred to me sporadically already over the last few years and
usually disappeared after a rebuild. Currently it is annoying enough to
write an email. The build ends with:
"""
== Using strict rotor definition
Downloading
http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar.
..
% Total% Received % Xferd Average Speed TimeTime Time
Current
Dload Upload Total SpentLeft
Speed
100 178 100 1780 0 1181 0 --:--:-- --:--:-- --:--:--
1186
0 00 00 0 0 0 --:--:-- --:--:-- --:--:--
0
curl: (35) Unknown SSL protocol error in connection to sourceforge.net:443
*CMake Error at Code/cmake/Modules/RDKitUtils.cmake:215 (MESSAGE):*
* The md5 checksum for*
* /opt/rdkit/External/AvalonTools/AvalonToolkit_1.2.0.source.tar is*
* incorrect; expected: 092a94f421873f038aa67d4a6cc8cb54, found:*
* d41d8cd98f00b204e9800998ecf8427e*
*Call Stack (most recent call first):*
* External/AvalonTools/CMakeLists.txt:29 (downloadAndCheckMD5)*
-- Configuring incomplete, errors occurred!
See also "/opt/rdkit/build/CMakeFiles/CMakeOutput.log".
See also "/opt/rdkit/build/CMakeFiles/CMakeError.log".
ERROR: Service 'rdkit-postgres-compile' failed to build: The command
'/bin/sh -c wget --quiet -O -
https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add - && echo
'deb http://apt.postgresql.org/pub/repos/apt/ stretch-pgdg main' >
/etc/apt/sources.list.d/pgdg.list && apt-get update && apt-get install -y
--no-install-recommends postgresql-server-dev-all
postgresql-client postgresql-plpython-${PG_VERSION}
postgresql-plpython3-${PG_VERSION} python-numpy python-dev
sqlite3 libsqlite3-dev libboost-dev libboost-system-dev
libboost-thread-dev libboost-serialization-dev
libboost-python-dev libboost-regex-dev libeigen3-dev && git
clone -b $RDKIT_BRANCH --single-branch https://github.com/rdkit/rdkit.git
&& mkdir $RDBASE/build && cd $RDBASE/build && cmake
-DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_PGSQL=ON
-DRDK_BUILD_AVALON_SUPPORT=ON
-DPostgreSQL_TYPE_INCLUDE_DIR="/usr/include/postgresql/${PG_VERSION}/server"
-DPostgreSQL_ROOT="/usr/lib/postgresql/${PG_VERSION}" .. && make
-j `nproc` && make install' returned a non-zero code: 1
Exited with code 1
"""
Does someone maybe has the same problem? And an explanation whats going on
- the Avalon tools seemed to be unchanged since quite a while.
Thanks,
Markus
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