[Bioc-devel] Package Home Pages

Hi all,

I like the package overview pages, such as
http://www.bioconductor.org/packages/devel/bioc/html/cellHTS2.html

Would it be possible that they also link to the output of, for example:

svn log --username readonly --password readonly \
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma

which any of our users can run (but I assume most wouldn't know how to)?

This additional service to our users may also encourage pkg developers
to be more precise in their svn log entries :)

On Fri, Jul 11, 2008 at 6:58 AM, Wolfgang Huber <huber at ebi.ac.uk> wrote:
  

Hi all,

I like the package overview pages, such as
http://www.bioconductor.org/packages/devel/bioc/html/cellHTS2.html

Would it be possible that they also link to the output of, for example:

svn log --username readonly --password readonly \
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma

which any of our users can run (but I assume most wouldn't know how to)?

This additional service to our users may also encourage pkg developers
to be more precise in their svn log entries :)
    

Hi, Wolfgang.  I agree this would be a simple and useful addition for
the devel archives.  Since we already have the bioconductor change log
in place, it would be trivial to change the HTML on the devel pages to
include a link like:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/cellHTS2

Sean

Sean and Wolfgang,
I think these two enhancements to the bioconductor.org website would 
be very useful and not too much work to implement. I'll add them on 
the website task list and send out a message to this group when they 
are implemented. If there are any other related ideas, keep them 
coming. It is easier to implement them all at once, rather than one at 
a time.


Patrick


Sean Davis wrote:

On Fri, Jul 11, 2008 at 6:58 AM, Wolfgang Huber <huber at ebi.ac.uk> wrote:
 

Hi all,

I like the package overview pages, such as
http://www.bioconductor.org/packages/devel/bioc/html/cellHTS2.html

Would it be possible that they also link to the output of, for example:

svn log --username readonly --password readonly \
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma

which any of our users can run (but I assume most wouldn't know how 
to)?

This additional service to our users may also encourage pkg developers
to be more precise in their svn log entries :)
    

Hi, Wolfgang.  I agree this would be a simple and useful addition for
the devel archives.  Since we already have the bioconductor change log
in place, it would be trivial to change the HTML on the devel pages to
include a link like:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/cellHTS2

Sean

I just modified the build system to add "Bioconductor Changelog" links to
the "Multiple platform build/check report" pages. To see an example of these
links go to

http://bioconductor.org/checkResults/2.2/bioc-LATEST/

and look for the Bioconductor Changelog links. Similar links will be added
to the BioC 2.3 report when it is created later tonight.

Given that the changelog is geared towards developers, I did not include a
link in the package home pages that Wolfgang referred to because it could
fall into the category of too much information for a general user of the
package. If the Bioconductor development community believes we should
include a link on the package home pages as well, I will add them. It
doesn't take much effort to change the infrastructure.


Cheers,
Patrick



Patrick Aboyoun wrote:

Sean and Wolfgang,
I think these two enhancements to the bioconductor.org website would be
very useful and not too much work to implement. I'll add them on the website
task list and send out a message to this group when they are implemented. If
there are any other related ideas, keep them coming. It is easier to
implement them all at once, rather than one at a time.


Patrick


Sean Davis wrote:

On Fri, Jul 11, 2008 at 6:58 AM, Wolfgang Huber <huber at ebi.ac.uk> wrote:

Hi all,

I like the package overview pages, such as
http://www.bioconductor.org/packages/devel/bioc/html/cellHTS2.html

Would it be possible that they also link to the output of, for example:

svn log --username readonly --password readonly \
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma

which any of our users can run (but I assume most wouldn't know how to)?

This additional service to our users may also encourage pkg developers
to be more precise in their svn log entries :)

Hi, Wolfgang.  I agree this would be a simple and useful addition for
the devel archives.  Since we already have the bioconductor change log
in place, it would be trivial to change the HTML on the devel pages to
include a link like:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/cellHTS2

Sean

Thanks. Looks good.

FYI, when I go to the package specifics for aroma.light
[http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/aroma.light/] there is a
somewhat poetic message delivered in red:

"Error: I'm afraid this is the first I've heard of a "light" flavoured
Blosxom. Try dropping the "/+light" bit from the end of the URL."

/Henrik


On Thu, Jul 17, 2008 at 3:54 PM, Patrick Aboyoun <paboyoun at fhcrc.org> wrote:
  

I just modified the build system to add "Bioconductor Changelog" links to
the "Multiple platform build/check report" pages. To see an example of these
links go to

http://bioconductor.org/checkResults/2.2/bioc-LATEST/

and look for the Bioconductor Changelog links. Similar links will be added
to the BioC 2.3 report when it is created later tonight.

Given that the changelog is geared towards developers, I did not include a
link in the package home pages that Wolfgang referred to because it could
fall into the category of too much information for a general user of the
package. If the Bioconductor development community believes we should
include a link on the package home pages as well, I will add them. It
doesn't take much effort to change the infrastructure.


Cheers,
Patrick



Patrick Aboyoun wrote:
    

Sean and Wolfgang,
I think these two enhancements to the bioconductor.org website would be
very useful and not too much work to implement. I'll add them on the website
task list and send out a message to this group when they are implemented. If
there are any other related ideas, keep them coming. It is easier to
implement them all at once, rather than one at a time.


Patrick


Sean Davis wrote:
      

On Fri, Jul 11, 2008 at 6:58 AM, Wolfgang Huber <huber at ebi.ac.uk> wrote:

        

Hi all,

I like the package overview pages, such as
http://www.bioconductor.org/packages/devel/bioc/html/cellHTS2.html

Would it be possible that they also link to the output of, for example:

svn log --username readonly --password readonly \
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma

which any of our users can run (but I assume most wouldn't know how to)?

This additional service to our users may also encourage pkg developers
to be more precise in their svn log entries :)

          

Hi, Wolfgang.  I agree this would be a simple and useful addition for
the devel archives.  Since we already have the bioconductor change log
in place, it would be trivial to change the HTML on the devel pages to
include a link like:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/cellHTS2

Sean

Henrik,
I provided links to the existing Bioconductor changelog blosxom blog at the
University of Michigan. With the Bioconductor manifest growing at such a
rapid pace, my guess is that the newer packages haven't yet made the blog.


Patrick



Henrik Bengtsson wrote:

Thanks. Looks good.

FYI, when I go to the package specifics for aroma.light
[http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/aroma.light/] there is a
somewhat poetic message delivered in red:

"Error: I'm afraid this is the first I've heard of a "light" flavoured
Blosxom. Try dropping the "/+light" bit from the end of the URL."

/Henrik


On Thu, Jul 17, 2008 at 3:54 PM, Patrick Aboyoun <paboyoun at fhcrc.org>
wrote:

I just modified the build system to add "Bioconductor Changelog" links to
the "Multiple platform build/check report" pages. To see an example of
these
links go to

http://bioconductor.org/checkResults/2.2/bioc-LATEST/

and look for the Bioconductor Changelog links. Similar links will be
added
to the BioC 2.3 report when it is created later tonight.

Given that the changelog is geared towards developers, I did not include
a
link in the package home pages that Wolfgang referred to because it could
fall into the category of too much information for a general user of the
package. If the Bioconductor development community believes we should
include a link on the package home pages as well, I will add them. It
doesn't take much effort to change the infrastructure.


Cheers,
Patrick



Patrick Aboyoun wrote:

Sean and Wolfgang,
I think these two enhancements to the bioconductor.org website would be
very useful and not too much work to implement. I'll add them on the
website
task list and send out a message to this group when they are
implemented. If
there are any other related ideas, keep them coming. It is easier to
implement them all at once, rather than one at a time.


Patrick


Sean Davis wrote:

On Fri, Jul 11, 2008 at 6:58 AM, Wolfgang Huber <huber at ebi.ac.uk>
wrote:

Hi all,

I like the package overview pages, such as
http://www.bioconductor.org/packages/devel/bioc/html/cellHTS2.html

Would it be possible that they also link to the output of, for
example:

svn log --username readonly --password readonly \
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma

which any of our users can run (but I assume most wouldn't know how
to)?

This additional service to our users may also encourage pkg developers
to be more precise in their svn log entries :)

Hi, Wolfgang.  I agree this would be a simple and useful addition for
the devel archives.  Since we already have the bioconductor change log
in place, it would be trivial to change the HTML on the devel pages to
include a link like:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/cellHTS2

Sean

Hi, just noticed that this works:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/aroma

i.e. without the ".light" and also in that page there is a strange
reference to a .light package:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/aroma/.light

i guess there is some issue with the dot character.

Diego

On Fri, Jul 18, 2008 at 8:42 AM, Patrick Aboyoun <paboyoun at fhcrc.org> wrote:

Henrik,
I provided links to the existing Bioconductor changelog blosxom blog at the
University of Michigan. With the Bioconductor manifest growing at such a
rapid pace, my guess is that the newer packages haven't yet made the blog.


Patrick



Henrik Bengtsson wrote:

Thanks. Looks good.

FYI, when I go to the package specifics for aroma.light
[http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/aroma.light/] there is a
somewhat poetic message delivered in red:

"Error: I'm afraid this is the first I've heard of a "light" flavoured
Blosxom. Try dropping the "/+light" bit from the end of the URL."

/Henrik


On Thu, Jul 17, 2008 at 3:54 PM, Patrick Aboyoun <paboyoun at fhcrc.org>
wrote:

I just modified the build system to add "Bioconductor Changelog" links to
the "Multiple platform build/check report" pages. To see an example of
these
links go to

http://bioconductor.org/checkResults/2.2/bioc-LATEST/

and look for the Bioconductor Changelog links. Similar links will be
added
to the BioC 2.3 report when it is created later tonight.

Given that the changelog is geared towards developers, I did not include
a
link in the package home pages that Wolfgang referred to because it could
fall into the category of too much information for a general user of the
package. If the Bioconductor development community believes we should
include a link on the package home pages as well, I will add them. It
doesn't take much effort to change the infrastructure.


Cheers,
Patrick



Patrick Aboyoun wrote:

Sean and Wolfgang,
I think these two enhancements to the bioconductor.org website would be
very useful and not too much work to implement. I'll add them on the
website
task list and send out a message to this group when they are
implemented. If
there are any other related ideas, keep them coming. It is easier to
implement them all at once, rather than one at a time.


Patrick


Sean Davis wrote:

On Fri, Jul 11, 2008 at 6:58 AM, Wolfgang Huber <huber at ebi.ac.uk>
wrote:

Hi all,

I like the package overview pages, such as
http://www.bioconductor.org/packages/devel/bioc/html/cellHTS2.html

Would it be possible that they also link to the output of, for
example:

svn log --username readonly --password readonly \
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma

which any of our users can run (but I assume most wouldn't know how
to)?

This additional service to our users may also encourage pkg developers
to be more precise in their svn log entries :)

Hi, Wolfgang.  I agree this would be a simple and useful addition for
the devel archives.  Since we already have the bioconductor change log
in place, it would be trivial to change the HTML on the devel pages to
include a link like:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/cellHTS2

Sean

--
Diego Diez, Ph
Bioinformatics center,
Institute for Chemical Research,
Kyoto University.
Gokasho, Uji, Kyoto 611-0011 JAPAN
diez at kuicr.kyoto-u.ac.jp

Henrik,
I provided links to the existing Bioconductor changelog blosxom blog at 
the University of Michigan. With the Bioconductor manifest growing at 
such a rapid pace, my guess is that the newer packages haven't yet made 
the blog.


Patrick



Henrik Bengtsson wrote:

Thanks. Looks good.

FYI, when I go to the package specifics for aroma.light
[http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/aroma.light/] there is a
somewhat poetic message delivered in red:

"Error: I'm afraid this is the first I've heard of a "light" flavoured
Blosxom. Try dropping the "/+light" bit from the end of the URL."

/Henrik


On Thu, Jul 17, 2008 at 3:54 PM, Patrick Aboyoun <paboyoun at fhcrc.org> 
wrote:
 

I just modified the build system to add "Bioconductor Changelog" 
links to
the "Multiple platform build/check report" pages. To see an example 
of these
links go to

http://bioconductor.org/checkResults/2.2/bioc-LATEST/

and look for the Bioconductor Changelog links. Similar links will be 
added
to the BioC 2.3 report when it is created later tonight.

Given that the changelog is geared towards developers, I did not 
include a
link in the package home pages that Wolfgang referred to because it 
could
fall into the category of too much information for a general user of the
package. If the Bioconductor development community believes we should
include a link on the package home pages as well, I will add them. It
doesn't take much effort to change the infrastructure.


Cheers,
Patrick



Patrick Aboyoun wrote:
   

Sean and Wolfgang,
I think these two enhancements to the bioconductor.org website would be
very useful and not too much work to implement. I'll add them on the 
website
task list and send out a message to this group when they are 
implemented. If
there are any other related ideas, keep them coming. It is easier to
implement them all at once, rather than one at a time.


Patrick


Sean Davis wrote:
     

On Fri, Jul 11, 2008 at 6:58 AM, Wolfgang Huber <huber at ebi.ac.uk> 
wrote:

       

Hi all,

I like the package overview pages, such as
http://www.bioconductor.org/packages/devel/bioc/html/cellHTS2.html

Would it be possible that they also link to the output of, for 
example:

svn log --username readonly --password readonly \
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma

which any of our users can run (but I assume most wouldn't know 
how to)?

This additional service to our users may also encourage pkg 
developers
to be more precise in their svn log entries :)

          

Hi, Wolfgang.  I agree this would be a simple and useful addition for
the devel archives.  Since we already have the bioconductor change log
in place, it would be trivial to change the HTML on the devel pages to
include a link like:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/cellHTS2

Sean

There seems to be at least one other issue with names:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/GSEA

returns information for all packages with a name starting with GSEA.
Same story with affy.

L.


2008/7/18 Diego Diez <diez at kuicr.kyoto-u.ac.jp>:

Hi, just noticed that this works:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/aroma

i.e. without the ".light" and also in that page there is a strange
reference to a .light package:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/aroma/.light

i guess there is some issue with the dot character.

Diego

On Fri, Jul 18, 2008 at 8:42 AM, Patrick Aboyoun <paboyoun at fhcrc.org> wrote:

Henrik,
I provided links to the existing Bioconductor changelog blosxom blog at the
University of Michigan. With the Bioconductor manifest growing at such a
rapid pace, my guess is that the newer packages haven't yet made the blog.


Patrick



Henrik Bengtsson wrote:

Thanks. Looks good.

FYI, when I go to the package specifics for aroma.light
[http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/aroma.light/] there is a
somewhat poetic message delivered in red:

"Error: I'm afraid this is the first I've heard of a "light" flavoured
Blosxom. Try dropping the "/+light" bit from the end of the URL."

/Henrik


On Thu, Jul 17, 2008 at 3:54 PM, Patrick Aboyoun <paboyoun at fhcrc.org>
wrote:

I just modified the build system to add "Bioconductor Changelog" links to
the "Multiple platform build/check report" pages. To see an example of
these
links go to

http://bioconductor.org/checkResults/2.2/bioc-LATEST/

and look for the Bioconductor Changelog links. Similar links will be
added
to the BioC 2.3 report when it is created later tonight.

Given that the changelog is geared towards developers, I did not include
a
link in the package home pages that Wolfgang referred to because it could
fall into the category of too much information for a general user of the
package. If the Bioconductor development community believes we should
include a link on the package home pages as well, I will add them. It
doesn't take much effort to change the infrastructure.


Cheers,
Patrick



Patrick Aboyoun wrote:

Sean and Wolfgang,
I think these two enhancements to the bioconductor.org website would be
very useful and not too much work to implement. I'll add them on the
website
task list and send out a message to this group when they are
implemented. If
there are any other related ideas, keep them coming. It is easier to
implement them all at once, rather than one at a time.


Patrick


Sean Davis wrote:

On Fri, Jul 11, 2008 at 6:58 AM, Wolfgang Huber <huber at ebi.ac.uk>
wrote:

Hi all,

I like the package overview pages, such as
http://www.bioconductor.org/packages/devel/bioc/html/cellHTS2.html

Would it be possible that they also link to the output of, for
example:

svn log --username readonly --password readonly \
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma

which any of our users can run (but I assume most wouldn't know how
to)?

This additional service to our users may also encourage pkg developers
to be more precise in their svn log entries :)

Hi, Wolfgang.  I agree this would be a simple and useful addition for
the devel archives.  Since we already have the bioconductor change log
in place, it would be trivial to change the HTML on the devel pages to
include a link like:

http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/cellHTS2

Sean

--
Diego Diez, Ph
Bioinformatics center,
Institute for Chemical Research,
Kyoto University.
Gokasho, Uji, Kyoto 611-0011 JAPAN
diez at kuicr.kyoto-u.ac.jp