Dear Bioconductors,
I am going to use GO annotation libraries. Unfortunately, I did not
succed in
loading the package GO.db. I have got the following error message:
Error in checkDBSCHEMA(dbconn, "GO_DB") :
invalid DB schema version (found 0.9, expected 1.0)
Error : .onLoad failed in 'loadNamespace' for 'GO.db'
Error: package/namespace load failed for 'GO.db'
Does someone know which package is needed or what is going wrong with
my
libraries? The sessionInfo is given at the end of this email.
Thanks and best wishes,
Heike
#################
sessionInfo()
R version 2.7.0 (2008-04-22)
i686-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US
.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N
AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI
FICATION=C
attached base packages:
[1] tools stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4
[4] Biobase_2.0.1
--
Dr. Heike Pospisil | pospisil at zbh.uni-hamburg.de
University of Hamburg | Center for Bioinformatics
Bundesstrasse 43 | 20146 Hamburg, Germany
phone:+49-40-42838-7303 | fax: +49-40-42838-7312
On Fri, Jun 20, 2008 at 7:42 AM, Heike Pospisil
<pospisil at="" zbh.uni-hamburg.de=""> wrote:
> Dear Bioconductors,
>
> I am going to use GO annotation libraries. Unfortunately, I did not
succed in
> loading the package GO.db. I have got the following error message:
>
> Error in checkDBSCHEMA(dbconn, "GO_DB") :
> invalid DB schema version (found 0.9, expected 1.0)
> Error : .onLoad failed in 'loadNamespace' for 'GO.db'
> Error: package/namespace load failed for 'GO.db'
>
> Does someone know which package is needed or what is going wrong
with my
> libraries? The sessionInfo is given at the end of this email.
I would suggest using biocLite() to do the installation and then try
again.
Sean
> #################
> sessionInfo()
> R version 2.7.0 (2008-04-22)
> i686-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_
US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC
_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN
TIFICATION=C
>
> attached base packages:
> [1] tools stats graphics grDevices utils datasets
methods
> [8] base
>
> other attached packages:
> [1] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4
> [4] Biobase_2.0.1
>
> --
> Dr. Heike Pospisil | pospisil at zbh.uni-hamburg.de
> University of Hamburg | Center for Bioinformatics
> Bundesstrasse 43 | 20146 Hamburg, Germany
> phone:+49-40-42838-7303 | fax: +49-40-42838-7312
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
On Fri, Jun 20, 2008 at 8:34 AM, Heike Pospisil
<pospisil at="" zbh.uni-hamburg.de=""> wrote:
> Hello Sean,
>
> On Friday 20 June 2008 14:06, you wrote:
>> On Fri, Jun 20, 2008 at 7:42 AM, Heike Pospisil
>>
>> <pospisil at="" zbh.uni-hamburg.de=""> wrote:
>> > Dear Bioconductors,
>> >
>> > I am going to use GO annotation libraries. Unfortunately, I did
not
>> > succed in loading the package GO.db. I have got the following
error
>> > message:
>> >
>> > Error in checkDBSCHEMA(dbconn, "GO_DB") :
>> > invalid DB schema version (found 0.9, expected 1.0)
>> > Error : .onLoad failed in 'loadNamespace' for 'GO.db'
>> > Error: package/namespace load failed for 'GO.db'
>> >
>> > Does someone know which package is needed or what is going wrong
with my
>> > libraries? The sessionInfo is given at the end of this email.
>>
>> I would suggest using biocLite() to do the installation and then
try again.
>
>
> Thanks for your suggestion. I guess it was a problem with sqlite and
wrong
> paths to sqlite. A superuser installation of GO.db wie biocLite()
was the
> solution. It's a pity that it have to been done (only) by the
superuser, but
> it works now...
Good to hear that it is working for you. However, you should be able
to install GO.db and friends just fine as something other than
superuser. The path to the SQLite database is relative to the
installation location. Let us know if you find out otherwise.
Sean