Hi all,
I'm fairly new to R and completely new to bioconductor.
Just out of curiosity, is it safe/recommended to upgrade to the new R
2.7.0 release when it says on the bioconductor website that that "This
[bioconductor] release is designed for R 2.6.1"?
Thanks,
-steve
Hi Steve,
The release of Bioconductor is timed to be within a few weeks after
the R
release. Since R was released a few days ago, Bioconductor will be
released
very shortly. You wan wait for the Bioc release before you update your
R or
update your R now and install the core Bioc packages which I would
think are
pretty much stable now (Patrick can correct me if I am wrong on this).
Either way, it is your choice.
Cheers,
--Tony
On Tue, Apr 29, 2008 at 4:59 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:
> Hi all,
>
> I'm fairly new to R and completely new to bioconductor.
>
> Just out of curiosity, is it safe/recommended to upgrade to the new
R
> 2.7.0 release when it says on the bioconductor website that that
"This
> [bioconductor] release is designed for R 2.6.1"?
>
> Thanks,
> -steve
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
[[alternative HTML version deleted]]
Steve,
The BioC 2.2 builds are very stable now and we will be sending around
an
announcement (with some fanfare) about the official release of BioC
2.2
in the next few days. If you are looking to put BioC 2.2 packages on
your own machine, feel free to do so now. If you are looking to put
them
on a server for "validated"/"auditable" usage, you may want to wait
until the BioC 2.2 release is out.
Patrick
Tony Chiang wrote:
> Hi Steve,
>
> The release of Bioconductor is timed to be within a few weeks after
the R
> release. Since R was released a few days ago, Bioconductor will be
released
> very shortly. You wan wait for the Bioc release before you update
your R or
> update your R now and install the core Bioc packages which I would
think are
> pretty much stable now (Patrick can correct me if I am wrong on
this).
> Either way, it is your choice.
>
> Cheers,
> --Tony
>
> On Tue, Apr 29, 2008 at 4:59 PM, Steve Lianoglou <
> mailinglist.honeypot at gmail.com> wrote:
>
>
>> Hi all,
>>
>> I'm fairly new to R and completely new to bioconductor.
>>
>> Just out of curiosity, is it safe/recommended to upgrade to the new
R
>> 2.7.0 release when it says on the bioconductor website that that
"This
>> [bioconductor] release is designed for R 2.6.1"?
>>
>> Thanks,
>> -steve
>>
>> _______________________________________________
>> 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
>>
>>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> 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
>
29/04/2008 16:59 Steve Lianoglou a ?crit
> Hi all,
>
> I'm fairly new to R and completely new to bioconductor.
>
> Just out of curiosity, is it safe/recommended to upgrade to the new
R
> 2.7.0 release when it says on the bioconductor website that that
"This
> [bioconductor] release is designed for R 2.6.1"?
>
> Thanks,
> -steve
Hi Steve,
just don't try to carry over your installed packages from the 2.6.1
installation to the 2.7 one - please install all packages from scratch
using biocLite (http://www.bioconductor.org/download), which
automatically takes care of release version synchronisation between R
and Bioconductor.
Best wishes
Wolfgang
------------------------------------------------------------------
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
> just don't try to carry over your installed packages from the 2.6.1
> installation to the 2.7 one - please install all packages from
scratch
> using biocLite (http://www.bioconductor.org/download), which
> automatically takes care of release version synchronisation between
R
> and Bioconductor.
Out of curiousity, won't "update.packages()" achieve the same thing
(assuming you've used setRepositories() to include BioC)? I've also
just
upgraded to 2.7.0, and today update.packages() choose to download
Biobase
1.99.10 (the version from "upcoming" BioC 2.2)
Thanks,
-Aaron
Hi Aaron,
aaron.j.mackey at gsk.com wrote:
>> just don't try to carry over your installed packages from the 2.6.1
>> installation to the 2.7 one - please install all packages from
scratch
>> using biocLite (http://www.bioconductor.org/download), which
>> automatically takes care of release version synchronisation between
R
>> and Bioconductor.
>
> Out of curiousity, won't "update.packages()" achieve the same thing
> (assuming you've used setRepositories() to include BioC)? I've also
just
> upgraded to 2.7.0, and today update.packages() choose to download
Biobase
> 1.99.10 (the version from "upcoming" BioC 2.2)
After you've upgraded to R 2.7.0, reinstalling Bioconductor packages
(and any
other package) from scratch (i.e. in an empty library folder) is
recommended.
For BioC package, this should be done with biocLite(), which is the
easy and
safe way to do it. Other methods can work if you know what you are
doing.
E.g. using update.packages() might work, provided that you use the
proper
repositories for BioC 2.2. This can be achieved with:
> source("http://bioconductor.org/biocLite.R")
> biocinstallRepos()
[1] "http://bioconductor.org/packages/2.2/bioc"
[2] "http://bioconductor.org/packages/2.2/data/annotation"
[3] "http://bioconductor.org/packages/2.2/data/experiment"
[4] "http://bioconductor.org/packages/2.2/extra"
[5] "http://cran.fhcrc.org"
> install.packages(rep=biocinstallRepos(), ask=FALSE)
Note that updating instead of reinstalling from scratch will not get
you rid
of the BioC 2.1 packages that have been discontinued in BioC 2.2.
Keeping these
packages around is a potential source of problems because they might
not work
properly with BioC 2.2 / R-2.7. So again, it's better to do a clean
install from
scratch with biocLite().
Cheers,
H.
>
> Thanks,
>
> -Aaron
>
> _______________________________________________
> 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
Wolfgang Huber wrote:
> 29/04/2008 16:59 Steve Lianoglou a ?crit
>
>> Hi all,
>>
>> I'm fairly new to R and completely new to bioconductor.
>>
>> Just out of curiosity, is it safe/recommended to upgrade to the new
R
>> 2.7.0 release when it says on the bioconductor website that that
"This
>> [bioconductor] release is designed for R 2.6.1"?
>>
>> Thanks,
>> -steve
>>
>
> Hi Steve,
>
> just don't try to carry over your installed packages from the 2.6.1
> installation to the 2.7 one - please install all packages from
scratch
> using biocLite (http://www.bioconductor.org/download), which
> automatically takes care of release version synchronisation between
R
> and Bioconductor.
>
> Best wishes
> Wolfgang
>
> ------------------------------------------------------------------
> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
>
> _______________________________________________
> 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
>
Dear all,
just out of personal interest: is the following error due to the fact
that Bioconductor 2.2 is not yet officially released?
>source("http://www.bioconductor.org/biocLite.R")
> biocLite("Biobase")
Running biocinstall version 2.2.7 with R version 2.7.0
Your version of R requires version 2.2 of BioConductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using 'XXX'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
package 'Biobase' is not available
> sessionInfo()
R version 2.7.0 (2008-04-22)
i686-pc-linux-gnu
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.7.0
Best,
Christian
--
Christian Kohler
Institute of Functional Genomics
Computational Diagnostics
University of Regensburg (BioPark I)
D-93147 Regensburg (Germany)
Tel. +49 941 943 5055
Fax +49 941 943 5020
christian.kohler at klinik.uni-regensburg.de
30/04/2008 11:19 Christian Kohler a ?crit
> Dear all,
>
> just out of personal interest: is the following error due to the
fact
> that Bioconductor 2.2 is not yet officially released?
>
>> source("http://www.bioconductor.org/biocLite.R")
>> biocLite("Biobase")
> Running biocinstall version 2.2.7 with R version 2.7.0
> Your version of R requires version 2.2 of BioConductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies
=
> dependencies, :
> argument 'lib' is missing: using 'XXX'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, :
> package 'Biobase' is not available
>
>> sessionInfo()
> R version 2.7.0 (2008-04-22)
> i686-pc-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] tools_2.7.0
>
>
> Best,
> Christian
>
Dear Christian,
biocLite has worked well for me for a number of installations of R 2.7
recently, so the problem you report either popped up very, very
recently
(and is unintended), or it has to do with your local installation. Can
you try with
R --vanilla
--
Best wishes
Wolfgang
------------------------------------------------------------------
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
Hallo Wolfgang,
thanks for your response.
The same problem occured on Mac OS X (Leopard) with R.app (2008/04/23)
as well:
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("Biobase", type="source") # also with type="binary"
Running biocinstall version 2.2.7 with R version 2.7.0
Your version of R requires version 2.2 of BioConductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using '~/Library/R/2.7/library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
package "Biobase"is not available
> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-apple-darwin8.10.1
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.7.0
The same result after following your suggestion with R --vanilla.
I think, my last 'biocLite()'-try was on Monday and worked without any
problem.
Best,
Christian
Wolfgang Huber wrote:
> 30/04/2008 11:19 Christian Kohler a ?crit
>
>> Dear all,
>>
>> just out of personal interest: is the following error due to the
fact
>> that Bioconductor 2.2 is not yet officially released?
>>
>>
>>> source("http://www.bioconductor.org/biocLite.R")
>>> biocLite("Biobase")
>>>
>> Running biocinstall version 2.2.7 with R version 2.7.0
>> Your version of R requires version 2.2 of BioConductor.
>> Warning in install.packages(pkgs = pkgs, repos = repos,
dependencies =
>> dependencies, :
>> argument 'lib' is missing: using 'XXX'
>> Warning message:
>> In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, :
>> package 'Biobase' is not available
>>
>>
>>> sessionInfo()
>>>
>> R version 2.7.0 (2008-04-22)
>> i686-pc-linux-gnu
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods
base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.7.0
>>
>>
>> Best,
>> Christian
>>
>>
>
> Dear Christian,
>
> biocLite has worked well for me for a number of installations of R
2.7
> recently, so the problem you report either popped up very, very
recently
> (and is unintended), or it has to do with your local installation.
Can
> you try with
>
> R --vanilla
>
>
>
--
Christian Kohler
Institute of Functional Genomics
Computational Diagnostics
University of Regensburg (BioPark I)
D-93147 Regensburg (Germany)
Tel. +49 941 943 5055
Fax +49 941 943 5020
christian.kohler at klinik.uni-regensburg.de
Hi Christian...
Christian Kohler <christian.kohler at="" klinik.uni-regensburg.de="">
writes:
> Wolfgang Huber wrote:
>> 29/04/2008 16:59 Steve Lianoglou a ?crit
>>> Just out of curiosity, is it safe/recommended to upgrade to the
new R
>>> 2.7.0 release when it says on the bioconductor website that that
"This
>>> [bioconductor] release is designed for R 2.6.1"?
>> just don't try to carry over your installed packages from the 2.6.1
>> installation to the 2.7 one - please install all packages from
scratch
>> using biocLite (http://www.bioconductor.org/download), which
>> automatically takes care of release version synchronisation between
R
>> and Bioconductor.
> just out of personal interest: is the following error due to the
fact
> that Bioconductor 2.2 is not yet officially released?
>
>>source("http://www.bioconductor.org/biocLite.R")
>> biocLite("Biobase")
> Running biocinstall version 2.2.7 with R version 2.7.0
> Your version of R requires version 2.2 of BioConductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies
=
> dependencies, :
> argument 'lib' is missing: using 'XXX'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, :
> package 'Biobase' is not available
There is a server issue at the Bioconductor web site. This will be
addressed as soon as possible.
Martin
>> sessionInfo()
> R version 2.7.0 (2008-04-22)
> i686-pc-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] tools_2.7.0
>
>
> Best,
> Christian
>
>
> --
>
> Christian Kohler
> Institute of Functional Genomics
> Computational Diagnostics
> University of Regensburg (BioPark I)
> D-93147 Regensburg (Germany)
>
> Tel. +49 941 943 5055
> Fax +49 941 943 5020
> christian.kohler at klinik.uni-regensburg.de
>
> _______________________________________________
> 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
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
To follow up...
Some spring cleaning in preparation for the release was a little too
effective.
biocLite should now work for Linux and Mac packages; Windows packages
are in the process of being rebuilt.
Thanks for alerting us to this problem.
Martin
Christian Kohler <christian.kohler at="" klinik.uni-regensburg.de="">
writes:
> Wolfgang Huber wrote:
>> 29/04/2008 16:59 Steve Lianoglou a ?crit
>>
>>> Hi all,
>>>
>>> I'm fairly new to R and completely new to bioconductor.
>>>
>>> Just out of curiosity, is it safe/recommended to upgrade to the
new R
>>> 2.7.0 release when it says on the bioconductor website that that
"This
>>> [bioconductor] release is designed for R 2.6.1"?
>>>
>>> Thanks,
>>> -steve
>>>
>>
>> Hi Steve,
>>
>> just don't try to carry over your installed packages from the 2.6.1
>> installation to the 2.7 one - please install all packages from
scratch
>> using biocLite (http://www.bioconductor.org/download), which
>> automatically takes care of release version synchronisation between
R
>> and Bioconductor.
>>
>> Best wishes
>> Wolfgang
>>
>> ------------------------------------------------------------------
>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
>>
>> _______________________________________________
>> 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
>>
> Dear all,
>
> just out of personal interest: is the following error due to the
fact
> that Bioconductor 2.2 is not yet officially released?
>
>>source("http://www.bioconductor.org/biocLite.R")
>> biocLite("Biobase")
> Running biocinstall version 2.2.7 with R version 2.7.0
> Your version of R requires version 2.2 of BioConductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies
=
> dependencies, :
> argument 'lib' is missing: using 'XXX'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, :
> package 'Biobase' is not available
>
>> sessionInfo()
> R version 2.7.0 (2008-04-22)
> i686-pc-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] tools_2.7.0
>
>
> Best,
> Christian
>
>
> --
>
> Christian Kohler
> Institute of Functional Genomics
> Computational Diagnostics
> University of Regensburg (BioPark I)
> D-93147 Regensburg (Germany)
>
> Tel. +49 941 943 5055
> Fax +49 941 943 5020
> christian.kohler at klinik.uni-regensburg.de
>
> _______________________________________________
> 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
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
