Hi,
unfortunately I have another problem - rdkit-postgres isn't building for me
since the change to Release_2016_03_2. Is that a known problem?
Below is the end of the build log. I only let build the py35-part
(+ncurses) of the Dockerscript.
Thanks & Best,
Markus
BUILD START: rdkit-postgresql-__conda_version__-py35_1
Fetching package metadata .........
Solving package specifications: ..........
+ source activate /home/rdkit/miniconda/envs/_build
++ [[ -n 4.1.2(1)-release ]]
++ _SCRIPT_LOCATION=/home/rdkit/miniconda/envs/_build/bin/activate
++ SHELL=bash
+++ dirname /home/rdkit/miniconda/envs/_build/bin/activate
++ _CONDA_DIR=/home/rdkit/miniconda/envs/_build/bin
++ '[' 1 -gt 1 ']'
++ case "$(uname -s)" in
+++ uname -s
++ EXT=
++ [[ -n 4.1.2(1)-release ]]
+++ basename /home/rdkit/miniconda/conda-bld/work/conda_build.sh
++ [[ conda_build.sh == \a\c\t\i\v\a\t\e ]]
++ '[' 1 -eq 0 ']'
++ args=/home/rdkit/miniconda/envs/_build
++ /home/rdkit/miniconda/envs/_build/bin/conda ..checkenv bash
/home/rdkit/miniconda/envs/_build
++ (( 0 != 0 ))
++ source /home/rdkit/miniconda/envs/_build/bin/deactivate
+++ [[ -n 4.1.2(1)-release ]]
+++ _SCRIPT_LOCATION=/home/rdkit/miniconda/envs/_build/bin/deactivate
+++ SHELL=bash
++++ dirname /home/rdkit/miniconda/envs/_build/bin/deactivate
+++ _CONDA_DIR=/home/rdkit/miniconda/envs/_build/bin
+++ case "$(uname -s)" in
++++ uname -s
+++ EXT=
+++ [[ 1 > 0 ]]
+++ key=/home/rdkit/miniconda/envs/_build
+++ case $key in
+++ shift
+++ [[ 0 > 0 ]]
+++ [[ -n 4.1.2(1)-release ]]
++++ basename /home/rdkit/miniconda/conda-bld/work/conda_build.sh
+++ [[ conda_build.sh == \d\e\a\c\t\i\v\a\t\e ]]
+++ [[ -z '' ]]
+++ [[ -n 4.1.2(1)-release ]]
++++ basename /home/rdkit/miniconda/conda-bld/work/conda_build.sh
+++ [[ conda_build.sh == \d\e\a\c\t\i\v\a\t\e ]]
+++ return 0
+++ /home/rdkit/miniconda/envs/_build/bin/conda ..activate bash
/home/rdkit/miniconda/envs/_build
prepending /home/rdkit/miniconda/envs/_build/bin to PATH
++ _NEW_PART=/home/rdkit/miniconda/envs/_build/bin
++ (( 0 == 0 ))
++ export
CONDA_PATH_BACKUP=/home/rdkit/miniconda/envs/_build/bin:/home/rdkit/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++
CONDA_PATH_BACKUP=/home/rdkit/miniconda/envs/_build/bin:/home/rdkit/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ export CONDA_PS1_BACKUP=
++ CONDA_PS1_BACKUP=
++ export
PATH=/home/rdkit/miniconda/envs/_build/bin:/home/rdkit/miniconda/envs/_build/bin:/home/rdkit/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++
PATH=/home/rdkit/miniconda/envs/_build/bin:/home/rdkit/miniconda/envs/_build/bin:/home/rdkit/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ [[ '' == */* ]]
++ export CONDA_DEFAULT_ENV=/home/rdkit/miniconda/envs/_build
++ CONDA_DEFAULT_ENV=/home/rdkit/miniconda/envs/_build
++ firstpath=/home/rdkit/miniconda/envs/_build/bin
+++ echo /home/rdkit/miniconda/envs/_build/bin
+++ sed 's|/bin$||'
++ export CONDA_PREFIX=/home/rdkit/miniconda/envs/_build
+++ /home/rdkit/miniconda/envs/_build/bin/conda ..changeps1
++ '[' 1 = 1 ']'
+++ grep -q CONDA_DEFAULT_ENV
++ export 'PS1=(/home/rdkit/miniconda/envs/_build) '
++ PS1='(/home/rdkit/miniconda/envs/_build) '
++ _CONDA_D=/home/rdkit/miniconda/envs/_build/etc/conda/activate.d
++ [[ -d /home/rdkit/miniconda/envs/_build/etc/conda/activate.d ]]
++ unset CONDA_PATH
++ [[ -n 4.1.2(1)-release ]]
++ hash -r
+ /home/rdkit/miniconda/envs/_build/bin/python
/home/rdkit/conda-rdkit/rdkit-postgresql/pkg_version.py
+ cd /home/rdkit/miniconda/conda-bld/work/Code/PgSQL/rdkit
+ make
gcc -I/home/rdkit/miniconda/envs/_build/include
-I/home/rdkit/miniconda/envs/_build/include/rdkit -DRDKITVER='"007300"'
-DBUILD_AVALON_SUPPORT -DBUILD_INCHI_SUPPORT -mpopcnt -I. -I./
-I/home/rdkit/miniconda/envs/_build/include/postgresql/server
-I/home/rdkit/miniconda/envs/_build/include/postgresql/internal
-D_GNU_SOURCE -I/home/rdkit/miniconda/envs/_build/include/libxml2
-I/home/rdkit/miniconda/envs/_build/include -fPIC -c -o rdkit_io.o
rdkit_io.c
gcc -I/home/rdkit/miniconda/envs/_build/include
-I/home/rdkit/miniconda/envs/_build/include/rdkit -DRDKITVER='"007300"'
-DBUILD_AVALON_SUPPORT -DBUILD_INCHI_SUPPORT -mpopcnt -I. -I./
-I/home/rdkit/miniconda/envs/_build/include/postgresql/server
-I/home/rdkit/miniconda/envs/_build/include/postgresql/internal
-D_GNU_SOURCE -I/home/rdkit/miniconda/envs/_build/include/libxml2
-I/home/rdkit/miniconda/envs/_build/include -fPIC -c -o mol_op.o mol_op.c
mol_op.c: In function 'fmcs_mol2s_transition':
mol_op.c:334: warning: initialization makes pointer from integer without a
cast
mol_op.c:363: warning: initialization makes pointer from integer without a
cast
mol_op.c: In function 'fmcs_mol_transition':
mol_op.c:432: warning: initialization makes pointer from integer without a
cast
mol_op.c:439: warning: cast from pointer to integer of different size
mol_op.c:443: warning: initialization makes pointer from integer without a
cast
gcc -I/home/rdkit/miniconda/envs/_build/include
-I/home/rdkit/miniconda/envs/_build/include/rdkit -DRDKITVER='"007300"'
-DBUILD_AVALON_SUPPORT -DBUILD_INCHI_SUPPORT -mpopcnt -I. -I./
-I/home/rdkit/miniconda/envs/_build/include/postgresql/server
-I/home/rdkit/miniconda/envs/_build/include/postgresql/internal
-D_GNU_SOURCE -I/home/rdkit/miniconda/envs/_build/include/libxml2
-I/home/rdkit/miniconda/envs/_build/include -fPIC -c -o bfp_op.o bfp_op.c
gcc -I/home/rdkit/miniconda/envs/_build/include
-I/home/rdkit/miniconda/envs/_build/include/rdkit -DRDKITVER='"007300"'
-DBUILD_AVALON_SUPPORT -DBUILD_INCHI_SUPPORT -mpopcnt -I. -I./
-I/home/rdkit/miniconda/envs/_build/include/postgresql/server
-I/home/rdkit/miniconda/envs/_build/include/postgresql/internal
-D_GNU_SOURCE -I/home/rdkit/miniconda/envs/_build/include/libxml2
-I/home/rdkit/miniconda/envs/_build/include -fPIC -c -o sfp_op.o sfp_op.c
gcc -I/home/rdkit/miniconda/envs/_build/include
-I/home/rdkit/miniconda/envs/_build/include/rdkit -DRDKITVER='"007300"'
-DBUILD_AVALON_SUPPORT -DBUILD_INCHI_SUPPORT -mpopcnt -I. -I./
-I/home/rdkit/miniconda/envs/_build/include/postgresql/server
-I/home/rdkit/miniconda/envs/_build/include/postgresql/internal
-D_GNU_SOURCE -I/home/rdkit/miniconda/envs/_build/include/libxml2
-I/home/rdkit/miniconda/envs/_build/include -fPIC -c -o rxn_op.o rxn_op.c
gcc -I/home/rdkit/miniconda/envs/_build/include
-I/home/rdkit/miniconda/envs/_build/include/rdkit -DRDKITVER='"007300"'
-DBUILD_AVALON_SUPPORT -DBUILD_INCHI_SUPPORT -mpopcnt -I. -I./
-I/home/rdkit/miniconda/envs/_build/include/postgresql/server
-I/home/rdkit/miniconda/envs/_build/include/postgresql/internal
-D_GNU_SOURCE -I/home/rdkit/miniconda/envs/_build/include/libxml2
-I/home/rdkit/miniconda/envs/_build/include -fPIC -c -o rdkit_gist.o
rdkit_gist.c
gcc -I/home/rdkit/miniconda/envs/_build/include
-I/home/rdkit/miniconda/envs/_build/include/rdkit -DRDKITVER='"007300"'
-DBUILD_AVALON_SUPPORT -DBUILD_INCHI_SUPPORT -mpopcnt -I. -I./
-I/home/rdkit/miniconda/envs/_build/include/postgresql/server
-I/home/rdkit/miniconda/envs/_build/include/postgresql/internal
-D_GNU_SOURCE -I/home/rdkit/miniconda/envs/_build/include/libxml2
-I/home/rdkit/miniconda/envs/_build/include -fPIC -c -o low_gist.o
low_gist.c
gcc -I/home/rdkit/miniconda/envs/_build/include
-I/home/rdkit/miniconda/envs/_build/include/rdkit -DRDKITVER='"007300"'
-DBUILD_AVALON_SUPPORT -DBUILD_INCHI_SUPPORT -mpopcnt -I. -I./
-I/home/rdkit/miniconda/envs/_build/include/postgresql/server
-I/home/rdkit/miniconda/envs/_build/include/postgresql/internal
-D_GNU_SOURCE -I/home/rdkit/miniconda/envs/_build/include/libxml2
-I/home/rdkit/miniconda/envs/_build/include -fPIC -c -o guc.o guc.c
gcc -I/home/rdkit/miniconda/envs/_build/include
-I/home/rdkit/miniconda/envs/_build/include/rdkit -DRDKITVER='"007300"'
-DBUILD_AVALON_SUPPORT -DBUILD_INCHI_SUPPORT -mpopcnt -I. -I./
-I/home/rdkit/miniconda/envs/_build/include/postgresql/server
-I/home/rdkit/miniconda/envs/_build/include/postgresql/internal
-D_GNU_SOURCE -I/home/rdkit/miniconda/envs/_build/include/libxml2
-I/home/rdkit/miniconda/envs/_build/include -fPIC -c -o cache.o cache.c
g++ -Wno-unused-function -I/home/rdkit/miniconda/envs/_build/include
-I/home/rdkit/miniconda/envs/_build/include/rdkit -DRDKITVER='"007300"'
-DBUILD_AVALON_SUPPORT -DBUILD_INCHI_SUPPORT -mpopcnt
-I/home/rdkit/miniconda/envs/_build/include
-I/home/rdkit/miniconda/envs/_build/include/rdkit -DRDKITVER='"007300"'
-DBUILD_AVALON_SUPPORT -DBUILD_INCHI_SUPPORT -mpopcnt -I. -I./
-I/home/rdkit/miniconda/envs/_build/include/postgresql/server
-I/home/rdkit/miniconda/envs/_build/include/postgresql/internal
-D_GNU_SOURCE -I/home/rdkit/miniconda/envs/_build/include/libxml2
-I/home/rdkit/miniconda/envs/_build/include -fPIC -c -o adapter.o
adapter.cpp
g++ -Wall -Wmissing-prototypes -Wpointer-arith
-Wdeclaration-after-statement -Wendif-labels -Wmissing-format-attribute
-Wformat-security -fno-strict-aliasing -fwrapv -O2 -fpic -shared -o
rdkit.so rdkit_io.o mol_op.o bfp_op.o sfp_op.o rxn_op.o rdkit_gist.o
low_gist.o guc.o cache.o adapter.o -L/home/rdkit/miniconda/envs/_build/lib
-L/home/rdkit/miniconda/envs/_build/lib
-L/home/rdkit/miniconda/envs/_build/lib -Wl,--as-needed
-Wl,-rpath,'/home/rdkit/miniconda/envs/_build/lib',--enable-new-dtags
-L/home/rdkit/miniconda/envs/_build/lib
-Wl,-rpath,'/home/rdkit/miniconda/envs/_build/lib' -lAvalonLib
-lavalon_clib -lRDInchiLib -lInchi -lMolHash -lFMCS -lChemReactions
-lChemTransforms -lFileParsers -lSmilesParse -lFingerprints -lSubgraphs
-lDescriptors -lPartialCharges -lSubstructMatch -lGraphMol -lDataStructs
-lDepictor -lRDGeometryLib -lRDGeneral -pthread -lboost_thread
-lboost_system
cp rdkit.sql91.in rdkit--3.4.sql
+ make install
/bin/mkdir -p '/home/rdkit/miniconda/envs/_build/lib/postgresql'
/bin/mkdir -p '/home/rdkit/miniconda/envs/_build/share/postgresql/extension'
/bin/mkdir -p '/home/rdkit/miniconda/envs/_build/share/postgresql/extension'
/usr/bin/install -c -m 755 rdkit.so
'/home/rdkit/miniconda/envs/_build/lib/postgresql/rdkit.so'
/usr/bin/install -c -m 644 rdkit.control
'/home/rdkit/miniconda/envs/_build/share/postgresql/extension/'
/usr/bin/install -c -m 644 rdkit--3.4.sql
'/home/rdkit/miniconda/envs/_build/share/postgresql/extension/'
+ export PGPORT=54321
+ PGPORT=54321
+ export PGDATA=/home/rdkit/miniconda/conda-bld/work/pgdata
+ PGDATA=/home/rdkit/miniconda/conda-bld/work/pgdata
+ pg_ctl initdb
The files belonging to this database system will be owned by user "rdkit".
This user must also own the server process.
The database cluster will be initialized with locale "C".
The default database encoding has accordingly been set to "SQL_ASCII".
The default text search configuration will be set to "english".
Data page checksums are disabled.
creating directory /home/rdkit/miniconda/conda-bld/work/pgdata ... ok
creating subdirectories ... ok
selecting default max_connections ... 100
selecting default shared_buffers ... 128MB
selecting dynamic shared memory implementation ... posix
creating configuration files ... ok
creating template1 database in
/home/rdkit/miniconda/conda-bld/work/pgdata/base/1 ... ok
initializing pg_authid ... ok
initializing dependencies ... ok
creating system views ... ok
loading system objects' descriptions ... ok
creating collations ... ok
creating conversions ... ok
creating dictionaries ... ok
setting privileges on built-in objects ... ok
creating information schema ... ok
loading PL/pgSQL server-side language ... ok
vacuuming database template1 ... ok
copying template1 to template0 ... ok
copying template1 to postgres ... ok
syncing data to disk ...
WARNING: enabling "trust" authentication for local connections
You can change this by editing pg_hba.conf or using the option -A, or
--auth-local and --auth-host, the next time you run initdb.
ok
Success. You can now start the database server using:
/home/rdkit/miniconda/envs/_build/bin/postgres -D
/home/rdkit/miniconda/conda-bld/work/pgdata
or
/home/rdkit/miniconda/envs/_build/bin/pg_ctl -D
/home/rdkit/miniconda/conda-bld/work/pgdata -l logfile start
+ echo 'shared_preload_libraries = '\''rdkit'\'''
+ pg_ctl start -l /home/rdkit/miniconda/conda-bld/work/pgdata/log.txt
server starting
+ sleep 5
+ set +e
+ make installcheck
/home/rdkit/miniconda/envs/_build/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress
--inputdir=./ --psqldir='/home/rdkit/miniconda/envs/_build/bin'
--dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91
sfpgist slfpgist fps reaction inchi avalon
(using postmaster on Unix socket, port 54321)
============== dropping database "contrib_regression" ==============
DROP DATABASE
NOTICE: database "contrib_regression" does not exist, skipping
============== creating database "contrib_regression" ==============
CREATE DATABASE
ALTER DATABASE
============== running regression test queries ==============
test rdkit-91 ... ok
test props ... ok
test btree ... FAILED
test molgist ... ok
test bfpgist-91 ... ok
test sfpgist ... ok
test slfpgist ... ok
test fps ... ok
test reaction ... FAILED
test inchi ... ok
test avalon ... ok
=======================
2 of 11 tests failed.
=======================
The differences that caused some tests to fail can be viewed in the
file
"/home/rdkit/miniconda/conda-bld/work/Code/PgSQL/rdkit/regression.diffs".
A copy of the test summary that you see
above is saved in the file
"/home/rdkit/miniconda/conda-bld/work/Code/PgSQL/rdkit/regression.out".
make: *** [installcheck] Error 1
+ check_result=2
+ set -e
+ pg_ctl stop
waiting for server to shut down.... done
server stopped
+ exit 2
The following NEW packages will be INSTALLED:
boost: 1.56.0-py35_3 local
bzip2: 1.0.6-3
libxml2: 2.9.2-0
libxslt: 1.1.28-0
mkl: 11.3.3-0
ncurses: 6.0-0 local
numpy: 1.11.0-py35_2
openssl: 1.0.2h-1
pip: 8.1.2-py35_0
postgresql: 9.4.4-py35_0 local
python: 3.5.1-5
rdkit: 2016.03.2-np111py35_1 local
readline: 6.2-2
setuptools: 23.0.0-py35_0
sqlite: 3.13.0-0
tk: 8.5.18-0
wheel: 0.29.0-py35_0
xz: 5.2.2-0
zlib: 1.2.8-3
Package: rdkit-postgresql-__conda_version__-py35_1
source tree in: /home/rdkit/miniconda/conda-bld/work
Command failed: /bin/bash -x -e
/home/rdkit/miniconda/conda-bld/work/conda_build.sh
The command '/bin/sh -c CONDA_PY=35 conda build boost --quiet
--no-anaconda-upload && CONDA_PY=35 conda build cairocffi --quiet
--no-anaconda-upload && CONDA_PY=35 conda build rdkit --quiet
--no-anaconda-upload && CONDA_PY=35 conda build postgresql --quiet
--no-anaconda-upload && CONDA_PY=35 conda build rdkit-postgresql --quiet
--no-anaconda-upload && CONDA_PY=35 conda build postgresql95 --quiet
--no-anaconda-upload && CONDA_PY=35 conda build rdkit-postgresql95
--quiet --no-anaconda-upload && CONDA_PY=35 CONDA_NPY=110 conda build
rdkit --quiet --no-anaconda-upload' returned a non-zero code: 1
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