Re: [Bioc-devel] AnnotationHub: cleanup

[Vincent Carey]

I followed part of this interchange with interest.  I would love to see
very wide adoption and appreciation of AnnotationHub and what I will
describe does not seem to constitute important obstacles to this, but I
have to confess that aspects of the model and grammar are confusing to me.

I use "cache" mainly as a noun.  And in computing applications, IMHO, a
cache is something to be hidden far from the active interface.  In
AnnotationHub "cache" names an important function and a key datastructure
for annotation archiving.

What I understand is (2.1.40):

ah = AnnotationHub()  # creates object for file and database access, will
update db if  appropriate
cache(ah)  #  will offer to acquire all available hub resources for local
caching, upon decline will provide
a named vector of paths

> cache(ah)

download 40503 resources? [y/n] n

 AH5086  AH5087

 "/Users/stvjc/.AnnotationHub/5086"  "/Users/stvjc/.AnnotationHub/5087"

AH14108 AH15146


I am not sure this vector is going to get much use.  Maybe a negative
response should return NULL?

The help page says


cache(x)’ and ‘cache(x) <- value’: Adds (downloads) all resources in

  ‘x’, or removes all local resources corresponding to the

  records in ‘x’ from the cache.


"download" seems like a reasonable name for part of this functionality.
 "cache<-" seems

to be concerned mainly with deletion.  I can certainly define private
alternate terms for these tasks

in my .Rprofile but I do think a closer correspondence of function name to
action could pay off.



On Tue, Sep 15, 2015 at 10:34 AM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:

> On Tue, Sep 15, 2015 at 12:25 AM, Morgan, Martin <
> martin.mor...@roswellpark.org> wrote:
>
> > Hi Kasper -- we'll try to act on these, but some comments / looking for
> > clarification...
> >
> > > -Original Message-
> > > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf
> Of
> > > Kasper Daniel Hansen
> > > Sent: Monday, September 14, 2015 10:45 PM
> > > To: bioc-devel@r-project.org
> > > Subject: [Bioc-devel] AnnotationHub: cleanup
> > >
> > > I currently have the `pleasure` of dealing with students who have
> > problems
> > > with installing AnnotationHub and/or downloading resources.  Here are
> > some
> > > comments including some possible bug reports.
> >
> > I hope this is on the whole a positive experience, and we'll do what we
> > can to make it better.
> >
>
> Well, I love the package and I love it even more having prepared material
> on it.  And the people who complain is of course enriched for people who
> have problems - no way to know if it just works for most people.
>
> And of course right now it is more troublesome since I prepared the class
> using R-3.2.1 and then 3.2.2 was released just before we started and had
> the http -> https change which is an obvious suspect when people have
> download problems :)
>
>  > 1) I think it is extremely dangerous that `cache(ahub)` starts by asking
> to
>
> > > download all resources!  May I suggest this only happens with a
> specific
> > > setting like `cache(ahub, download=TRUE)` or something similar.
> >
> > >
> > > 2) `cache(ahub)` deletes all cached information, except the sqlite
> > database.
> > > Could we get a way to remove everything?
> > >
> > > 3) While I can understand the difference between cache and hubCache, I
> > > would suggest that hubCache(ahub) = NULL removes all cached material
> > > included the sqlite database.
> >
> > For each of the above the envisioned use case was that  'hub' is a
> subset,
> > eg.,
> >
> >   subhub = query(hub, c("homo", "ensembl", "81"))
> >
> > and the user wanted to manipulate all records in the sub-hub.
> > cache(subhub) asks about the 'really download" if the size of the
> (sub)hub
> > is greater than hubOption("MAX_DOWNLOADS"), which by default is 10; it
> > seems like asking is the same as requiring an argument? fileName(subhub)
> > may be closer to what you're looking for...? the path to the file name,
> or
> > NA if It is not in the cache.
> >
> > For cache(subhub) = NULL it wouldn't make sense to delete 5 resources AND
> > the sqlite file for the entire hub.
> >
> > The sqlite file can be discovered with dbfile(hub) / dbfile(subhub), and
> > removed with file.remove(dbfile(subhub))). In some ways it wasn't
> > envisioned that this manual manipulation would be a common use case (!).
>
>
> Ok.  Let me perhaps rephrase my wish list
> 1) some easy way to reset the entire cache issue, with emphasis on easy.
> This is most likely to be used by beginners.  Who it's done, I don't care
> to much about.  And I suggest a heading in ?AnnotationHub called something
> like "Flushing the cache" or something.
> 2) It seems natural that there is a way (for problem reporting) to report
> which resources are cached, which is (again) easy and does not involve
> 

[Bioc-devel] adding a coathor to the tracker

[Stepan Grinek]

Hi,
How can I give to someone else in addition to myself the rights to edit
my package and upload their changes to the tracker?
Thanks,
Stepan




=
Stepan Grinek, PhD.
stepan.grinek@ladydavis.ca
Lady Davis Institute for Medical Research, Jewish General Hospital.
Mailing address:   H414, Clinical Epidemiology, Jewish General Hospital
3755 C�te Ste. Catherine, Montr�al, QC  H3T 1E2
Tel 514 340 8222 x8380.

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[Bioc-devel] Open developer position

[Hector Corrada Bravo]

Let's make interactive visualization tools for Bioconductor:
http://epiviz.github.io/epiviz/2015/09/15/hiring.html

Cheers,
Hector

Hector Corrada Bravo
University of Maryland, College Park

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[Bioc-devel] rtracklayer: BigWigFIle on Windows

[Kasper Daniel Hansen]

In the man page for trackLayer::BigWigFile it says "These functions do not
work on Windows".  Despite this statement, which seems to have been around
for a while, I and several of my students seems to be able to execute
something like
  import(bwFile, which = my.gr, as = "Rle")
on Windows on a BigWig file.  In my case the OS is Windows 7 run under a
virtual machine on a Mac.  In the virtual machine I don't have full
support.  For example, the code above works when bwFile is a BigWigFile
pointing to a BigWig file stored on my local hard drive, but does not work
when I query a url; in that case I get a weird error message.  However, I
have at least one student for which this does not seem to work on Windows.

I was unaware of this when I designed a quiz problem involving importing a
BigWigFile.  I am surprised that it works at all.  What is the current
state of BigWig file support on Windows? Clearly some of it works on some
systems.

Best,
Kasper

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Re: [Bioc-devel] AnnotationHub: cleanup

[Kasper Daniel Hansen]

I believe I agree with Vince.  I also hope that most users won't have to
reset their cache or ever thing about it, but I had to deal with it as a
possible source of problem (not sure that was the problem, but as we all
know it can be hard to diagnose over the internet with limited
information).

Best,
Kasper

On Thu, Sep 17, 2015 at 10:15 AM, Vincent Carey 
wrote:

> I followed part of this interchange with interest.  I would love to see
> very wide adoption and appreciation of AnnotationHub and what I will
> describe does not seem to constitute important obstacles to this, but I
> have to confess that aspects of the model and grammar are confusing to me.
>
> I use "cache" mainly as a noun.  And in computing applications, IMHO, a
> cache is something to be hidden far from the active interface.  In
> AnnotationHub "cache" names an important function and a key datastructure
> for annotation archiving.
>
> What I understand is (2.1.40):
>
> ah = AnnotationHub()  # creates object for file and database access, will
> update db if  appropriate
> cache(ah)  #  will offer to acquire all available hub resources for local
> caching, upon decline will provide
> a named vector of paths
>
> > cache(ah)
>
> download 40503 resources? [y/n] n
>
>  AH5086  AH5087
>
>  "/Users/stvjc/.AnnotationHub/5086"  "/Users/stvjc/.AnnotationHub/5087"
>
> AH14108 AH15146
>
>
> I am not sure this vector is going to get much use.  Maybe a negative
> response should return NULL?
>
> The help page says
>
>
> cache(x)’ and ‘cache(x) <- value’: Adds (downloads) all resources in
>
>   ‘x’, or removes all local resources corresponding to the
>
>   records in ‘x’ from the cache.
>
>
> "download" seems like a reasonable name for part of this functionality.
>  "cache<-" seems
>
> to be concerned mainly with deletion.  I can certainly define private
> alternate terms for these tasks
>
> in my .Rprofile but I do think a closer correspondence of function name to
> action could pay off.
>
>
>
> On Tue, Sep 15, 2015 at 10:34 AM, Kasper Daniel Hansen <
> kasperdanielhan...@gmail.com> wrote:
>
>> On Tue, Sep 15, 2015 at 12:25 AM, Morgan, Martin <
>> martin.mor...@roswellpark.org> wrote:
>>
>> > Hi Kasper -- we'll try to act on these, but some comments / looking for
>> > clarification...
>> >
>> > > -Original Message-
>> > > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf
>> Of
>> > > Kasper Daniel Hansen
>> > > Sent: Monday, September 14, 2015 10:45 PM
>> > > To: bioc-devel@r-project.org
>> > > Subject: [Bioc-devel] AnnotationHub: cleanup
>> > >
>> > > I currently have the `pleasure` of dealing with students who have
>> > problems
>> > > with installing AnnotationHub and/or downloading resources.  Here are
>> > some
>> > > comments including some possible bug reports.
>> >
>> > I hope this is on the whole a positive experience, and we'll do what we
>> > can to make it better.
>> >
>>
>> Well, I love the package and I love it even more having prepared material
>> on it.  And the people who complain is of course enriched for people who
>> have problems - no way to know if it just works for most people.
>>
>> And of course right now it is more troublesome since I prepared the class
>> using R-3.2.1 and then 3.2.2 was released just before we started and had
>> the http -> https change which is an obvious suspect when people have
>> download problems :)
>>
>>  > 1) I think it is extremely dangerous that `cache(ahub)` starts by
>> asking
>> to
>>
>> > > download all resources!  May I suggest this only happens with a
>> specific
>> > > setting like `cache(ahub, download=TRUE)` or something similar.
>> >
>> > >
>> > > 2) `cache(ahub)` deletes all cached information, except the sqlite
>> > database.
>> > > Could we get a way to remove everything?
>> > >
>> > > 3) While I can understand the difference between cache and hubCache, I
>> > > would suggest that hubCache(ahub) = NULL removes all cached material
>> > > included the sqlite database.
>> >
>> > For each of the above the envisioned use case was that  'hub' is a
>> subset,
>> > eg.,
>> >
>> >   subhub = query(hub, c("homo", "ensembl", "81"))
>> >
>> > and the user wanted to manipulate all records in the sub-hub.
>> > cache(subhub) asks about the 'really download" if the size of the
>> (sub)hub
>> > is greater than hubOption("MAX_DOWNLOADS"), which by default is 10; it
>> > seems like asking is the same as requiring an argument? fileName(subhub)
>> > may be closer to what you're looking for...? the path to the file name,
>> or
>> > NA if It is not in the cache.
>> >
>> > For cache(subhub) = NULL it wouldn't make sense to delete 5 resources
>> AND
>> > the sqlite file for the entire hub.
>> >
>> > The sqlite file can be discovered with dbfile(hub) / dbfile(subhub), and
>> > removed with file.remove(dbfile(subhub))). In some ways