Re: Disable WARN message

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You can avoid that one message by setting the PDB_DIR environment variable
or system property (passing it to JVM with -DPDB_DIR=/some/dir). Like that
you will store your cached pdb/mmcif files in the location you want and
they will be permanent in your system (by using the default /tmp, they are
removed after reboot).

More generally to control the logging verbosity and output location
(stdout, log to file, etc) we use log4j2 as the logging framework. You can
edit the default log4j2.xml file in src/main/resources to alter its
behaviour or add your own config file. See
https://logging.apache.org/log4j/2.x/manual/configuration.html for more
details.

Jose


On Mon, May 15, 2017 at 6:18 AM, Enrico Morelli <[email protected]>
wrote:

> Dear,
>
> each time I execute a program I see:
>
> [main] WARN  org.biojava.nbio.structure.align.util.UserConfiguration -
> Could not read dir from system property PDB_DIR or environment variable
> PDB_DIR, using system's temp directory /tmp
>
> When I'll release the software I wouldn't this warning, so is there a
> way to avoid it?
>
> Thanks
>
> --
> -------------------------------------------------------------
>   Enrico Morelli
>   System Administrator | Programmer | Web Developer
>
>   CERM - Polo Scientifico
>   Via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY
>   phone: +39 055 457 4269
>   fax:   +39 055 457 4927
> -------------------------------------------------------------
> _______________________________________________
> Biojava-l mailing list  -  [email protected]
> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>

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<div dir=3D"ltr">You can avoid that one message by setting the PDB_DIR envi=
ronment variable or system property (passing it to JVM with -DPDB_DIR=3D/so=
me/dir). Like that you will store your cached pdb/mmcif files in the locati=
on you want and they will be permanent in your system (by using the default=
 /tmp, they are removed after reboot).<div><br></div><div>More generally to=
 control the logging verbosity and output location (stdout, log to file, et=
c) we use log4j2 as the logging framework. You can edit the default log4j2.=
xml file in src/main/resources to alter its behaviour or add your own confi=
g file. See=C2=A0<a href=3D"https://logging.apache.org/log4j/2.x/manual/con=
figuration.html">https://logging.apache.org/log4j/2.x/manual/configuration.=
html</a> for more details.</div><div><br></div><div>Jose</div><div><br></di=
v></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">On Mon, M=
ay 15, 2017 at 6:18 AM, Enrico Morelli <span dir=3D"ltr">&lt;<a href=3D"mai=
lto:[email protected]" target=3D"_blank">[email protected]</a>&gt;<=
/span> wrote:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8=
ex;border-left:1px #ccc solid;padding-left:1ex">Dear,<br>
<br>
each time I execute a program I see:<br>
<br>
[main] WARN=C2=A0 org.biojava.nbio.structure.<wbr>align.util.UserConfigurat=
ion -<br>
Could not read dir from system property PDB_DIR or environment variable<br>
PDB_DIR, using system&#39;s temp directory /tmp<br>
<br>
When I&#39;ll release the software I wouldn&#39;t this warning, so is there=
 a<br>
way to avoid it?<br>
<br>
Thanks<br>
<br>
--<br>
------------------------------<wbr>------------------------------<wbr>-<br>
=C2=A0 Enrico Morelli<br>
=C2=A0 System Administrator | Programmer | Web Developer<br>
<br>
=C2=A0 CERM - Polo Scientifico<br>
=C2=A0 Via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY<br>
=C2=A0 phone: <a href=3D"tel:%2B39%20055%20457%204269" value=3D"+3905545742=
69">+39 055 457 4269</a><br>
=C2=A0 fax:=C2=A0 =C2=A0<a href=3D"tel:%2B39%20055%20457%204927" value=3D"+=
390554574927">+39 055 457 4927</a><br>
------------------------------<wbr>------------------------------<wbr>-<br>
______________________________<wbr>_________________<br>
Biojava-l mailing list=C2=A0 -=C2=A0 <a href=3D"mailto:[email protected]=
en-bio.org">[email protected]</a><br>
<a href=3D"http://mailman.open-bio.org/mailman/listinfo/biojava-l" rel=3D"n=
oreferrer" target=3D"_blank">http://mailman.open-bio.org/<wbr>mailman/listi=
nfo/biojava-l</a><br>
</blockquote></div><br></div>

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