Re: [Rdkit-discuss] Trouble with conda build in Docker

2017-04-25 Thread Markus Sitzmann 
Hi Riccardo,

just to tell you: my problem went away (I didn't touched it since my last
email) for whatever reason (did you do something?)

Markus

On Thu, Apr 6, 2017 at 12:51 PM, Markus Sitzmann 
wrote:

> Thanks Riccardo for your reply
>
> I tried both master and development - both with your Dockerscript (which
> starts from centos) and mine (which starts from Debian:jessie). Same result
> everywhere. I haven't built it in a while, too, but since I updated to
> Docker CE, Version 17.03, it triggered this rebuild.
>
> I hope it isn't my setup (well, that is actually what I wanted to find out
> :-), if somebody else has problems). It isn't urgent, also :-)
>
>
> Markus
>
> On Thu, Apr 6, 2017 at 8:50 AM, Riccardo Vianello <
> riccardo.viane...@gmail.com> wrote:
>
>> Hi Markus,
>>
>> On Thu, Apr 6, 2017 at 12:03 AM, Markus Sitzmann <
>> markus.sitzm...@gmail.com> wrote:
>>
>>> Hi (Riccardo).
>>>
>>> I have trouble with the conda build in Docker (I just updated to the
>>> most recent version which triggered the new build) - below is the error
>>> trace. I took the original Docker file and just edited out all non-Python35
>>> builds - so it does only the Python35 builds and ends somewhere when
>>> rdkit-postgres95 is built. Does somebody have the same problem?
>>>
>>
>> I couldn't work on this during the last few months so I didn't test any
>> recent builds. I might be able to have a closer look and run some tests
>> next week. What branch of the conda-rdkit repository are you using (master
>> or development)?
>>
>> Best,
>> Riccardo
>>
>>
>>>
>>> make[3]: Entering directory `/home/rdkit/bld/postgresql95_
>>> 1491429385957/work/postgresql-9.5.2/src/port'
>>> make -C ../backend submake-errcodes
>>> make[3]: Entering directory `/home/rdkit/bld/postgresql95_
>>> 1491429385957/work/postgresql-9.5.2/src/backend/catalog'
>>> cd ../../../src/include/catalog && /bin/sh ../../../config/missing perl
>>> ./duplicate_oids
>>> make -C utils probes.h
>>> ***
>>> ERROR: Perl is missing on your system. It is needed unless you are
>>> building
>>> from an unmodified official distribution of PostgreSQL.
>>> ***
>>> make[3]: Leaving directory `/home/rdkit/bld/postgresql95_
>>> 1491429385957/work/postgresql-9.5.2/src/backend/catalog'
>>>
>>>
>
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Re: [Rdkit-discuss] Trouble with conda build in Docker

2017-04-06 Thread Markus Sitzmann 
Thanks Riccardo for your reply

I tried both master and development - both with your Dockerscript (which
starts from centos) and mine (which starts from Debian:jessie). Same result
everywhere. I haven't built it in a while, too, but since I updated to
Docker CE, Version 17.03, it triggered this rebuild.

I hope it isn't my setup (well, that is actually what I wanted to find out
:-), if somebody else has problems). It isn't urgent, also :-)


Markus

On Thu, Apr 6, 2017 at 8:50 AM, Riccardo Vianello <
riccardo.viane...@gmail.com> wrote:

> Hi Markus,
>
> On Thu, Apr 6, 2017 at 12:03 AM, Markus Sitzmann <
> markus.sitzm...@gmail.com> wrote:
>
>> Hi (Riccardo).
>>
>> I have trouble with the conda build in Docker (I just updated to the most
>> recent version which triggered the new build) - below is the error trace. I
>> took the original Docker file and just edited out all non-Python35 builds -
>> so it does only the Python35 builds and ends somewhere when
>> rdkit-postgres95 is built. Does somebody have the same problem?
>>
>
> I couldn't work on this during the last few months so I didn't test any
> recent builds. I might be able to have a closer look and run some tests
> next week. What branch of the conda-rdkit repository are you using (master
> or development)?
>
> Best,
> Riccardo
>
>
>>
>> make[3]: Entering directory `/home/rdkit/bld/postgresql95_
>> 1491429385957/work/postgresql-9.5.2/src/port'
>> make -C ../backend submake-errcodes
>> make[3]: Entering directory `/home/rdkit/bld/postgresql95_
>> 1491429385957/work/postgresql-9.5.2/src/backend/catalog'
>> cd ../../../src/include/catalog && /bin/sh ../../../config/missing perl
>> ./duplicate_oids
>> make -C utils probes.h
>> ***
>> ERROR: Perl is missing on your system. It is needed unless you are
>> building
>> from an unmodified official distribution of PostgreSQL.
>> ***
>> make[3]: Leaving directory `/home/rdkit/bld/postgresql95_
>> 1491429385957/work/postgresql-9.5.2/src/backend/catalog'
>>
>>
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Re: [Rdkit-discuss] Trouble with conda build in Docker

2017-04-06 Thread Riccardo Vianello 
Hi Markus,

On Thu, Apr 6, 2017 at 12:03 AM, Markus Sitzmann 
wrote:

> Hi (Riccardo).
>
> I have trouble with the conda build in Docker (I just updated to the most
> recent version which triggered the new build) - below is the error trace. I
> took the original Docker file and just edited out all non-Python35 builds -
> so it does only the Python35 builds and ends somewhere when
> rdkit-postgres95 is built. Does somebody have the same problem?
>

I couldn't work on this during the last few months so I didn't test any
recent builds. I might be able to have a closer look and run some tests
next week. What branch of the conda-rdkit repository are you using (master
or development)?

Best,
Riccardo


>
> make[3]: Entering directory `/home/rdkit/bld/postgresql95_
> 1491429385957/work/postgresql-9.5.2/src/port'
> make -C ../backend submake-errcodes
> make[3]: Entering directory `/home/rdkit/bld/postgresql95_
> 1491429385957/work/postgresql-9.5.2/src/backend/catalog'
> cd ../../../src/include/catalog && /bin/sh ../../../config/missing perl
> ./duplicate_oids
> make -C utils probes.h
> ***
> ERROR: Perl is missing on your system. It is needed unless you are building
> from an unmodified official distribution of PostgreSQL.
> ***
> make[3]: Leaving directory `/home/rdkit/bld/postgresql95_
> 1491429385957/work/postgresql-9.5.2/src/backend/catalog'
>
>
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[Rdkit-discuss] Trouble with conda build in Docker

2017-04-05 Thread Markus Sitzmann 
Hi (Riccardo).

I have trouble with the conda build in Docker (I just updated to the most
recent version which triggered the new build) - below is the error trace. I
took the original Docker file and just edited out all non-Python35 builds -
so it does only the Python35 builds and ends somewhere when
rdkit-postgres95 is built. Does somebody have the same problem?

Thanks,
Markus

make[3]: Entering directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/port'
make -C ../backend submake-errcodes
make[3]: Entering directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/backend/catalog'
cd ../../../src/include/catalog && /bin/sh ../../../config/missing perl
./duplicate_oids
make -C utils probes.h
***
ERROR: Perl is missing on your system. It is needed unless you are building
from an unmodified official distribution of PostgreSQL.
***
make[3]: Leaving directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/backend/catalog'
make[3]: *** [postgres.bki] Error 1
make[2]: *** [submake-schemapg] Error 2
make[2]: *** Waiting for unfinished jobs
make[3]: Entering directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/backend/utils'
sed -f ./Gen_dummy_probes.sed probes.d >probes.h
make[3]: Leaving directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/backend/utils'
make[4]: Entering directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/backend'
make[4]: Nothing to be done for `submake-errcodes'.
make[4]: Leaving directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/backend'
make[3]: Leaving directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/port'
make -C ../../src/common all
make[3]: Entering directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/common'
make -C ../backend submake-errcodes
make[4]: Entering directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/backend'
make[4]: Nothing to be done for `submake-errcodes'.
make[4]: Leaving directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/backend'
make[3]: Leaving directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/common'
make[2]: Leaving directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src/backend'
make[1]: *** [all-backend-recurse] Error 2
make[1]: Leaving directory
`/home/rdkit/bld/postgresql95_1491429385957/work/postgresql-9.5.2/src'
make: *** [all-src-recurse] Error 2
Traceback (most recent call last):
  File "/home/rdkit/miniconda/bin/conda-build", line 6, in 
 path in binary file share/terminfo/w/wsvt25
Detected hard-coded path in binary file share/terminfo/w/wsvt25m
Detected hard-coded path in binary file share/terminfo/x/x68k
Detected hard-coded path in binary file share/terminfo/x/x68k-ite
Detected hard-coded path in binary file share/terminfo/z/z29a
Detected hard-coded path in binary file share/terminfo/z/z29a-kc-bc
Detected hard-coded path in binary file share/terminfo/z/z29a-kc-uc
Detected hard-coded path in binary file share/terminfo/z/z29a-nkc-bc
Detected hard-coded path in binary file share/terminfo/z/z29a-nkc-uc
Detected hard-coded path in binary file share/terminfo/z/z340
Detected hard-coded path in binary file share/terminfo/z/z340-nam
Detected hard-coded path in text file bin/ncurses6-config
Detected hard-coded path in text file share/man/man1/captoinfo.1m
Detected hard-coded path in text file share/man/man1/infocmp.1m
Detected hard-coded path in text file share/man/man1/infotocap.1m
Detected hard-coded path in text file share/man/man1/ncurses6-config.1
Detected hard-coded path in text file share/man/man1/tic.1m
Detected hard-coded path in text file share/man/man1/toe.1m
Detected hard-coded path in text file share/man/man1/tput.1
Detected hard-coded path in text file share/man/man1/tset.1
Detected hard-coded path in text file share/man/man3/ncurses.3x
Detected hard-coded path in text file share/man/man3/panel.3x
Detected hard-coded path in text file share/man/man5/term.5
Detected hard-coded path in text file share/man/man5/terminfo.5
Detected hard-coded path in text file share/man/man7/term.7
/home/rdkit/bld/linux-64/ncurses-6.0-0.tar.bz2
Nothing to test for: /home/rdkit/bld/linux-64/ncurses-6.0-0.tar.bz2
BUILD START: postgresql95-9.5.2-py35_0

The following NEW packages will be INSTALLED:

libiconv:   1.14-0
libxml2:2.9.4-0
libxslt:1.1.29-0
ncurses:6.0-0 local
openssl:1.0.2k-1
pip:9.0.1-py35_1
python: 3.5.3-1
readline:   6.2-2
setuptools: 27.2.0-py35_0
sqlite: 3.13.0-0
tk: 8.5.18-0
wheel:  0.29.0-py35_0
xz: 5.2.2-1
zlib:   1.2.8-3

Source cache directory is: /home/rdkit/bld/src_cache
Downloading source to cache: postgresql-9.5.2.tar.bz2
Downloading