Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

2016-07-02 Thread Markus Sitzmann 
Hi Riccardo,

Yes, it builds again - thanks a lot for your efforts.

Best,
Markus

-
|  Markus Sitzmann
|  markus.sitzm...@gmail.com

> On 30.06.2016, at 20:55, Riccardo Vianello  
> wrote:
> 
> Hi Markus,
> 
> I think the problem should be fixed now. The recipes were building the 
> cartridge using the earlier release tag, and therefore executing tests that 
> were not fully up-to-date. Please try again and let me know in case the 
> problem persisted.
> 
> Best,
> Riccardo
> 
> 
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Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

2016-06-30 Thread Riccardo Vianello 
Hi Markus,

I think the problem should be fixed now. The recipes were building the
cartridge using the earlier release tag, and therefore executing tests that
were not fully up-to-date. Please try again and let me know in case the
problem persisted.

Best,
Riccardo
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Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

2016-06-30 Thread Markus Sitzmann 
Hi Riccardo,

Thanks for your efforts and sorry that I didn't reply earlier. I am not sure 
about all the side conditions in order this error to occur but I am glad you 
can reproduce it.

Markus

-
|  Markus Sitzmann
|  markus.sitzm...@gmail.com

> On 30.06.2016, at 08:30, Riccardo Vianello  
> wrote:
> 
>> On Tue, Jun 28, 2016 at 11:40 PM, Markus Sitzmann 
>>  wrote:
>> 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?
> 
> I tested a couple of full builds and the master branch looks ok, but I could 
> reproduce this error with the tagged release. I will try to identify the 
> exact cause.
> 
> Best,
> Riccardo
> 
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Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

2016-06-30 Thread Riccardo Vianello 
On Tue, Jun 28, 2016 at 11:40 PM, Markus Sitzmann  wrote:

> 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?
>

I tested a couple of full builds and the master branch looks ok, but I
could reproduce this error with the tagged release. I will try to identify
the exact cause.

Best,
Riccardo
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Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

2016-06-28 Thread Markus Sitzmann 
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

Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

2016-06-28 Thread Axel Pahl 

Hi Riccardo,

thanks, I found the problem. As suspected it was related to conda and 
had nothing to do with RDKit 
(https://github.com/conda/conda/issues/2212#issuecomment-228277548).


Many thanks for your help.

Kind regards,
Axel

On 27.06.2016 22:44, Riccardo Vianello wrote:

Hi Axel,

thanks a lot for your help, using the development branch and the
Release_2016_03_2 git tag in rdkit/meta.yaml worked.
I now get a strange error in anaconda when actually trying to
install the package (Error: Invalid version spec: ==), but that
seems to be unrelated to RDKit (there is already an issue on
anaconda github).
My understanding was that the preferred way to install the RDKit
was via anaconda (RDKit was the reason I started using anaconda),
is that still correct?


I'm not exactly sure about the commands you used, but I'm afraid I 
wasn't able to reproduce the described problem using conda 4.1.4 and 
conda-build 1.21.2 on my fedora box. In case the error persisted, 
could you please provide some additional context?


Best regards,
Riccardo



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Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

2016-06-27 Thread Riccardo Vianello 
Hi Axel,

thanks a lot for your help, using the development branch and the
> Release_2016_03_2 git tag in rdkit/meta.yaml worked.
> I now get a strange error in anaconda when actually trying to install the
> package (Error: Invalid version spec: ==), but that seems to be unrelated
> to RDKit (there is already an issue on anaconda github).
> My understanding was that the preferred way to install the RDKit was via
> anaconda (RDKit was the reason I started using anaconda), is that still
> correct?
>

I'm not exactly sure about the commands you used, but I'm afraid I wasn't
able to reproduce the described problem using conda 4.1.4 and conda-build
1.21.2 on my fedora box. In case the error persisted, could you please
provide some additional context?

Best regards,
Riccardo
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Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

2016-06-23 Thread Greg Landrum 
Hi Axel,

Apologies that I forgot to update the conda-rdkit repo when I did the patch
release.

I just fixed the conda build recipe so that it uses 2016_03_2.
One note: when I built on ubuntu 16.04 I also needed to rebuild a local
copy of boost. You can do this by just doing a "conda build boost" before
"conda build rdkit"

Best,
-greg


On Thu, Jun 23, 2016 at 6:06 PM, Axel Pahl  wrote:

> Dear all,
>
> I just tried to build the current Release_2016_03_2 with conda on Ubuntu
> 16.04 and ran into an error.
>
> I used a fresh clone of conda-rdkit and changed the git tag in
> rdkit/meta.yaml from Release_2016_03_1 to Release_2016_03_2.
> Then:
>
> $ conda build boost
> This ran without problems. Then:
>
> $ conda build rdkit
> This gave the traceback shown below, which left me at a loss.
> Does anyone have any ideas?
> Many thanks in advance.
>
> Kind regards,
> Axel
>
> Traceback:
> [...]
> checkout: 'Release_2016_03_2'
> Cloning into '/home/pahl/anaconda3/conda-bld/work'...
> done.
> Note: checking out 'Release_2016_03_2'.
>
> You are in 'detached HEAD' state. You can look around, make experimental
> changes and commit them, and you can discard any commits you make in this
> state without impacting any branches by performing another checkout.
>
> If you want to create a new branch to retain commits you create, you may
> do so (now or later) by using -b with the checkout command again. Example:
>
>git checkout -b 
>
> HEAD is now at e0c1c02... update release notes
> ==> git log -n1 <==
>
> commit e0c1c0296a0632089ec02550a006d2e9bd0fec96
> Author: Greg Landrum 
> Date:   Fri May 20 14:52:46 2016 +0200
>
>  update release notes
>
>
> ==> git describe --tags --dirty <==
>
> Release_2016_03_2
>
>
> ==> git status <==
>
> HEAD detached at Release_2016_03_2
> nothing to commit, working directory clean
>
>
> Applying patch: '/home/pahl/dev/github/conda-rdkit/rdkit/rdpaths.patch'
> Patch level ambiguous, selecting least deep
> patching file rdkit/CMakeLists.txt
> Applying patch: '/home/pahl/dev/github/conda-rdkit/rdkit/rddepictor.patch'
> patching file Code/GraphMol/Depictor/RDDepictor.cpp
> Hunk #1 FAILED at 133.
> 1 out of 1 hunk FAILED -- saving rejects to file
> Code/GraphMol/Depictor/RDDepictor.cpp.rej
> Warning: failed to download source.  If building, will try again after
> downloading recipe dependencies.
> Error was:
> Command '['/usr/bin/patch', '-p0', '-i',
> '/home/pahl/dev/github/conda-rdkit/rdkit/rddepictor.patch']' returned
> non-zero exit status 1
> An unexpected error has occurred, please consider sending the
> following traceback to the conda GitHub issue tracker at:
>
>  https://github.com/conda/conda-build/issues
>
> Include the output of the command 'conda info' in your report.
>
>
> Traceback (most recent call last):
>File "/home/pahl/anaconda3/bin/conda-build", line 5, in 
>  sys.exit(main())
>File
>
> "/home/pahl/anaconda3/lib/python3.5/site-packages/conda_build/main_build.py",
> line 140, in main
>  args_func(args, p)
>File
>
> "/home/pahl/anaconda3/lib/python3.5/site-packages/conda_build/main_build.py",
> line 380, in args_func
>  args.func(args, p)
>File
>
> "/home/pahl/anaconda3/lib/python3.5/site-packages/conda_build/main_build.py",
> line 327, in execute
>  dirty=args.dirty)
>File
> "/home/pahl/anaconda3/lib/python3.5/site-packages/conda_build/build.py",
> line 487, in build
>  assert not need_source_download, "Source download failed. Please
> investigate."
> AssertionError: Source download failed.  Please investigate.
>
>
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