Hello,
I get error message in gcrma:
Computing affinitiesFehler in getProbePackage(probepackagename) :
The current operation could not access the Bioconductor
repository. Please check your internet connection, and report further
problems to bioconductor at stat.math.ethz.ch
I used suggestion of James W. MacDonald.
(https://stat.ethz.ch/pipermail/bioconductor/2005-March/008306.html )
but I get again error message:
>>Fehler in pmaffinity.info) : no direct or inherited method for
function 'pm' for this call
Under Windows I have not any problem with gcrma. what can I do?
> sessionInfo()
R version 2.2.1, 2005-12-20, i686-pc-linux-gnu
attached base packages:
[1] "splines" "tools" "methods" "stats" "graphics"
"grDevices"
[7] "utils" "datasets" "base"
other attached packages:
hgu133atagcdf plier gcrma matchprobes vsn
"1.4.3" "1.2.0" "2.4.1" "1.2.1" "1.8.0"
affy Biobase
"1.8.1" "1.8.0"
thanks,
Mohammad Esad-Djou
______________________________________________________________________
XXL-Speicher, PC-Virenschutz, Spartarife & mehr: Nur im WEB.DE Club!
Hi,
Mohammad Esad-Djou <shahrgol at="" web.de=""> writes:
> I get error message in gcrma:
>
> Computing affinitiesFehler in getProbePackage(probepackagename) :
> The current operation could not access the Bioconductor
> repository. Please check your internet connection, and
> report further problems to bioconductor at stat.math.ethz.ch
Are you able to connect to the Bioconductor website from a web browser
on this system? Is there a web proxy that is preventing R from
accessing the internet? If there is a proxy, take a look at the man
page for download.file.
Also, I would recommend upgrading your R and Bioconductor to the
latest released versions.
Best,
+ seth
Mohammad Esad-Djou <shahrgol at="" web.de=""> writes:
> Thanks for your answer.
>
>
>> Are you able to connect to the Bioconductor website from a web
>> browser on this system? Is there a web proxy that is preventing R
>> from accessing the internet?
>
> Unfortunately I have not Internet connection under Linux. I must
> install relevant libraries manual. Do you have a solution under
such
> situation?
Without a connection to the internet, biocLite will not be of use.
What you can do is to download the source packages that you want and
then transfer them to your Linux system. You can install source
packages on Linux using:
R CMD INSTALL somepkg_1.2.3.tar.gz
However, you will have to resolve package dependencies yourself. This
is unfortunate and something I'm interested in improving with some
alternate dependency tracking tools.
+ seth
Mohammad Esad-Djou <shahrgol at="" web.de=""> writes:
>> What you can do is to download the source packages that you want
and
>> then transfer them to your Linux system. You can install source
>> packages on Linux using:
>>
>> R CMD INSTALL somepkg_1.2.3.tar.gz
>>
>> However, you will have to resolve package dependencies yourself.
This
>> is unfortunate and something I'm interested in improving with some
>> alternate dependency tracking tools.
>
> I know, but I do not know, which Package needs gcrma!
For any package, you can easily determine the packages it depends on
and the packages that depend on it by reviewing the package summary
listing. So for gcrma take a look at the Depends and DependsOnMe
fields here:
http://www.bioconductor.org/packages/1.8/bioc/html/gcrma.html
Thanks for your answer.
> Are you able to connect to the Bioconductor website from a web
browser
> on this system? Is there a web proxy that is preventing R from
> accessing the internet?
Unfortunately I have not Internet connection under Linux. I must
install relevant libraries manual.
Do you have a solution under such situation?
thanks in advance,
Mohammad
> -----Urspr?ngliche Nachricht-----
> Von: Seth Falcon <sfalcon at="" fhcrc.org="">
> Gesendet: 05.06.06 19:03:07
> An: bioconductor at stat.math.ethz.ch
> Betreff: Re: [BioC] error message in gcrma
> Hi,
>
> Mohammad Esad-Djou <shahrgol at="" web.de=""> writes:
> > I get error message in gcrma:
> >
> > Computing affinitiesFehler in getProbePackage(probepackagename) :
> > The current operation could not access the Bioconductor
> > repository. Please check your internet connection, and
> > report further problems to bioconductor at
stat.math.ethz.ch
>
> Are you able to connect to the Bioconductor website from a web
browser
> on this system? Is there a web proxy that is preventing R from
> accessing the internet? If there is a proxy, take a look at the man
> page for download.file.
>
> Also, I would recommend upgrading your R and Bioconductor to the
> latest released versions.
>
> Best,
>
> + seth
>
> _______________________________________________
> 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
_____________________________________________________________________
Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen!
> What you can do is to download the source packages that you want and
> then transfer them to your Linux system. You can install source
> packages on Linux using:
>
> R CMD INSTALL somepkg_1.2.3.tar.gz
>
> However, you will have to resolve package dependencies yourself.
This
> is unfortunate and something I'm interested in improving with some
> alternate dependency tracking tools.
I know, but I do not know, which Package needs gcrma!
> -----Urspr?ngliche Nachricht-----
> Von: Seth Falcon <sfalcon at="" fhcrc.org="">
> Gesendet: 05.06.06 20:04:12
> An: Mohammad Esad-Djou <shahrgol at="" web.de="">
> Betreff: Re: [BioC] error message in gcrma
> Mohammad Esad-Djou <shahrgol at="" web.de=""> writes:
>
> > Thanks for your answer.
> >
> >
> >> Are you able to connect to the Bioconductor website from a web
> >> browser on this system? Is there a web proxy that is preventing
R
> >> from accessing the internet?
> >
> > Unfortunately I have not Internet connection under Linux. I must
> > install relevant libraries manual. Do you have a solution under
such
> > situation?
>
> Without a connection to the internet, biocLite will not be of use.
>
> What you can do is to download the source packages that you want and
> then transfer them to your Linux system. You can install source
> packages on Linux using:
>
> R CMD INSTALL somepkg_1.2.3.tar.gz
>
> However, you will have to resolve package dependencies yourself.
This
> is unfortunate and something I'm interested in improving with some
> alternate dependency tracking tools.
>
> + seth
_____________________________________________________________________
Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen!
I installed some packages. Now I do not find to package "GO".
I searched under this address:
http://bioconductor.org/packages/1.8/GO.html
where can I find ?GO??
Thanks,
Mohammad
> -----Urspr?ngliche Nachricht-----
> Von: Seth Falcon <sfalcon at="" fhcrc.org="">
> Gesendet: 05.06.06 20:54:02
> An: bioconductor at stat.math.ethz.ch
> Betreff: Re: [BioC] error message in gcrma
> Mohammad Esad-Djou <shahrgol at="" web.de=""> writes:
>
> >> What you can do is to download the source packages that you want
and
> >> then transfer them to your Linux system. You can install source
> >> packages on Linux using:
> >>
> >> R CMD INSTALL somepkg_1.2.3.tar.gz
> >>
> >> However, you will have to resolve package dependencies yourself.
This
> >> is unfortunate and something I'm interested in improving with
some
> >> alternate dependency tracking tools.
> >
> > I know, but I do not know, which Package needs gcrma!
>
> For any package, you can easily determine the packages it depends on
> and the packages that depend on it by reviewing the package summary
> listing. So for gcrma take a look at the Depends and DependsOnMe
> fields here:
>
> http://www.bioconductor.org/packages/1.8/bioc/html/gcrma.html
>
> _______________________________________________
> 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
_____________________________________________________________________
Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen!
GO is a metadata package, look at
http://www.bioconductor.org/packages/1.8/AnnotationData.html
You also (probably) need some chip specific packagages for gcrma like
hgu95av2, hgu95av2cdf, hgu95av2probe (substitute hgu95av2 with the
chips(s) you are using).
/Kasper
On Jun 6, 2006, at 3:09 AM, Mohammad Esad-Djou wrote:
>
>
> I installed some packages. Now I do not find to package "GO".
>
> I searched under this address:
> http://bioconductor.org/packages/1.8/GO.html
>
> where can I find ?GO??
>
> Thanks,
> Mohammad
>
>> -----Urspr?ngliche Nachricht-----
>> Von: Seth Falcon <sfalcon at="" fhcrc.org="">
>> Gesendet: 05.06.06 20:54:02
>> An: bioconductor at stat.math.ethz.ch
>> Betreff: Re: [BioC] error message in gcrma
>
>
>> Mohammad Esad-Djou <shahrgol at="" web.de=""> writes:
>>
>>>> What you can do is to download the source packages that you want
>>>> and
>>>> then transfer them to your Linux system. You can install source
>>>> packages on Linux using:
>>>>
>>>> R CMD INSTALL somepkg_1.2.3.tar.gz
>>>>
>>>> However, you will have to resolve package dependencies
>>>> yourself. This
>>>> is unfortunate and something I'm interested in improving with
some
>>>> alternate dependency tracking tools.
>>>
>>> I know, but I do not know, which Package needs gcrma!
>>
>> For any package, you can easily determine the packages it depends
on
>> and the packages that depend on it by reviewing the package summary
>> listing. So for gcrma take a look at the Depends and DependsOnMe
>> fields here:
>>
>> http://www.bioconductor.org/packages/1.8/bioc/html/gcrma.html
>>
>> _______________________________________________
>> 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
>
>
>
_____________________________________________________________________
> Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu
sparen!
>
> _______________________________________________
> 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
