Re: [Bioc-devel] BiocFileCache for developers

[Shepherd, Lori]

BiocFileCache has been updated to follow this type of behavior


- if location exists use without prompting (default user_cache_dir())

- if doesnt exit

- prompt user to create

- if respond N  or not an interactive session uses temporary directory


This is reflected in devel version 1.3.8





Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Michael Love <michaelisaiahl...@gmail.com>
Sent: Saturday, December 9, 2017 5:18:08 PM
To: Henrik Bengtsson
Cc: Shepherd, Lori; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocFileCache for developers

thanks Henrik,

I like the explicitness of the `R.cache` approach and I copied it for
my current implementation.

For the BiocFileCache location that should be used for this package
I'm developing, `tximeta`, I'm now using the following logic:

* If run non-interactively, `tximeta` uses a temporary directory.
* If run interactively, and a location has not been previously saved,
  the user is prompted if she wants to use (1) the default directory or
  a (2) temporary directory.
- If (1), then use the default directory, and save this choice.
- If (2), then use a temporary directory for the rest of this R
  session, and ask again next R session.
* The prompt above also mentions that a specific function can be used
  to manually set the directory at any time point, and this choice is
  saved.
* The default directory is given by `rappdirs::user_cache_dir("BiocFileCache")`.
* The choice itself of the BiocFileCache directory that `tximeta`
  should use is saved in a JSON file here
  `rappdirs::user_cache_dir("tximeta")`.


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Re: [Bioc-devel] BiocFileCache for developers

[Michael Love]

thanks Henrik,

I like the explicitness of the `R.cache` approach and I copied it for
my current implementation.

For the BiocFileCache location that should be used for this package
I'm developing, `tximeta`, I'm now using the following logic:

* If run non-interactively, `tximeta` uses a temporary directory.
* If run interactively, and a location has not been previously saved,
  the user is prompted if she wants to use (1) the default directory or
  a (2) temporary directory.
- If (1), then use the default directory, and save this choice.
- If (2), then use a temporary directory for the rest of this R
  session, and ask again next R session.
* The prompt above also mentions that a specific function can be used
  to manually set the directory at any time point, and this choice is
  saved.
* The default directory is given by `rappdirs::user_cache_dir("BiocFileCache")`.
* The choice itself of the BiocFileCache directory that `tximeta`
  should use is saved in a JSON file here
  `rappdirs::user_cache_dir("tximeta")`.

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Re: [Bioc-devel] BiocFileCache for developers

[Henrik Bengtsson]

R.cache (>= 0.6.0) does the following to acquire a persistent cache
(root) folder.  This behavior was introduced after getting prompted by
CRAN not to write to disk by default (because they found "funny"
folders on their check servers) and a following email conversation
with CRAN (2011-12-29), and getting an "ok with me" from Uwe@CRAN:

1. When loaded (not only attached) it checks for the existence of a
cache folder (defaults to ~/.Rcache unless neither an R option nor an
env var is set).  If it is exists, then we're good to go.

2. If the cache folder does not exist, and in a non-interactive
session, then a temporary cache folder specific to that R session is
used.

3. If the cache folder does not exist, and in an interactive session,
then the user will be queried whether they'd like to create ~/.Rcache
(the default choice) or whether they like to use a temporary folder
(just as in the non-interactive case).  If accepting ~/.Rcache, then
that will be available across sessions (Step 1 above).

The gist is: Make sure to get the user's approval before storing
anything permanently and don't doing anything that surprises the user,
risk overwriting their files, etc.

Here is a real-world user example on a "fresh" user account:

# Non-interactive sessions or user does not approve

$ Rscript -e "R.cache::getCacheRootPath()"
[1] "/tmp/RtmpzIZT4o/.Rcache"

$ R --vanilla
> dummy <- loadNamespace("R.cache")
The R.cache package needs to create a directory that will hold cache
files. It is convenient to use one in the user's home directory,
because it remains also after restarting R. Do you wish to create the
'~/.Rcache/' directory? If not, a temporary directory
(/tmp/RtmpMA4LTF/.Rcache) that is specific to this R session will be
used. [Y/n]: n
> R.cache::getCacheRootPath()
[1] "/tmp/Rtmp0Ic5zQ/.Rcache"
> quit("no")

$ R --vanilla
> R.cache::getCacheRootPath()
The R.cache package needs to create a directory that will hold cache
files. It is convenient to use one in the user's home directory,
because it remains also after restarting R. Do you wish to create the
'~/.Rcache/' directory? If not, a temporary directory
(/tmp/RtmpzSJd3d/.Rcache) that is specific to this R session will be
used. [Y/n]: n
[1] "/tmp/RtmpzSJd3d/.Rcache"
> quit("no")

$ Rscript -e "R.cache::getCacheRootPath()"
[1] "/tmp/Rtmpq1nx0H/.Rcache"


# User approves or already approved

$ R --vanilla
> dummy <- loadNamespace("R.cache")
The R.cache package needs to create a directory that will hold cache
files. It is convenient to use one in the user's home directory,
because it remains also after restarting R. Do you wish to create the
'~/.Rcache/' directory? If not, a temporary directory
(/tmp/RtmpMA4LTF/.Rcache) that is specific to this R session will be
used. [Y/n]: Y
> R.cache::getCacheRootPath()
[1] "~/.Rcache/"
> quit("no")

$ Rscript -e "R.cache::getCacheRootPath()"
[1] "~/.Rcache/"

$ R --vanilla
> dummy <- loadNamespace("R.cache")
> R.cache::getCacheRootPath()
[1] "~/.Rcache/"

The same applies when using library("R.cache") as well as when the
R.cache namespace is imported by another package.

This behavior also plays well with 'R CMD check' and 'R CMD check
--as-cran' where the cache folder will default to a temporary folder.
It will also prevent run-time errors since there will always be a
cache folder available (although it'll only survive the current
session).  R.cache works the same on all OSes.  To further lower the
risk for "what is this ~/.Rcache folder doing here?", R.cache also
adds a ~/.Rcache/README.txt file explaining what that folder is and
what created it.

About what the default location should be:

On Fri, Dec 1, 2017 at 8:06 AM, Sean Davis  wrote:
[...]
> On some systems, the user home directory is not large (such as on HPC
> systems) or has strong quotas. The default user_cache_dir may not be the
> best choice there.

I agree with this but it's hard to find a solid simple alternative to
the user's home folder.  However, and on my todo list to investigate,
https://cran.r-project.org/package=rappdirs may provide a better
approach because it follows OS-specific recommendations.  Back to
writing to user's home folder: in HPC environments with limited home
quota, I simply do things like ln -s /scratch/$USER/.Rcache ~/.Rcache.

/Henrik

On Fri, Dec 1, 2017 at 8:32 AM, Michael Love
 wrote:
> One solution if a developer really wants to make sure the user knows
> that the function will store a cache somewhere would be to leave the
> BiocFileCache location argument without a default value.
>
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Re: [Bioc-devel] BiocFileCache for developers

[Michael Love]

user_cache_dir(appname="mikes-package-name")

wow, how did you guess it?

I'm storing TxDb's for use across sessions with `rname` set to the
basename of the GTF file, e.g. "gencode.v27.annotation.gtf.gz". I want
to encourage the serendipitous case that there is already a
BiocFileCache entry with this `rname` created outside of the use of my
package. I can see this happening, especially if I mention this naming
pattern in the vignette.

I'm thinking I will encourage the user to pick a good BiocFileCache
location by not setting a default value. Potentially multiple users
could be sharing the same BiocFileCache location, e.g. a lab space on
HPC.

And then actively specifying NULL for the location (or something like
this) could switch the location to:

user_cache_dir(appname = "BiocFileCache")

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Re: [Bioc-devel] BiocFileCache for developers

[Martin Morgan]

On 12/01/2017 11:23 AM, Sean Davis wrote:

On Fri, Dec 1, 2017 at 11:16 AM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:


So having a user argument might be best.  Or defining a unique cache
location for your package would be another option.



The R package development policies actually has a statement that may be
helpful in thinking about this. Your mileage may vary in the
interpretation



- - Packages should not write in the users’ home filespace, nor
anywhere else on the file system apart from the R session’s temporary
directory (or during installation in the location pointed to by TMPDIR:
and such usage should be cleaned up). Installing into the system’s R
installation (e.g., scripts to its bin directory) is not allowed.

Limited exceptions may be allowed in interactive sessions if the
package obtains confirmation from the user.




Actually, CRAN policies.

The CRAN policy is definitely appropriate for vignette and example code, 
and certainly functions by default should not write to locations where 
they will potentially overwrite existing resources. The policy makes it 
impossible to write files that persist across sessions, which is the 
objective for BiocFileCache.


For the original question, I think there's often a case for 
user_cache_dir(appname="mikes-package-name")


Martin


https://cran.r-project.org/web/packages/policies.html

Sean





Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
--
*From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Sean
Davis <seand...@gmail.com>
*Sent:* Friday, December 1, 2017 11:06:39 AM
*To:* Michael Love
*Cc:* bioc-devel@r-project.org
*Subject:* Re: [Bioc-devel] BiocFileCache for developers

On Fri, Dec 1, 2017 at 10:28 AM, Michael Love <michaelisaiahl...@gmail.com



wrote:


hi,

I'm writing a function which currently uses BiocFileCache to store a
small data.frame and one or more TxDb objects, so that these objects
are persistent and available across sessions (or possible available to
multiple users).

In the simplest case, I would call

bfc <- BiocFileCache()

inside my function, which will check the default location:

user_cache_dir(appname = "BiocFileCache")

In general, should developers also support the user specifying a
specific location for the BiocFileCache? So functions using
BiocFileCache should have an argument that overrides the above
location?



On some systems, the user home directory is not large (such as on HPC
systems) or has strong quotas. The default user_cache_dir may not be the
best choice there.

Sean




thanks,
Mike

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--
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Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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Re: [Bioc-devel] BiocFileCache for developers

[Shepherd, Lori]

Unfortunately I think there are a number of packages that don't necessarily 
adhere to this.


Bioconductor packages we try to always make sure any example or vignette code 
follows this policy.


I think the exception case may be made if it deals with main functionality of 
package code and if it is noted prominently in the package documentation.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Sean Davis <seand...@gmail.com>
Sent: Friday, December 1, 2017 11:23:39 AM
To: Shepherd, Lori
Cc: Michael Love; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocFileCache for developers


On Fri, Dec 1, 2017 at 11:16 AM, Shepherd, Lori 
<lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>> wrote:

So having a user argument might be best.  Or defining a unique cache location 
for your package would be another option.

The R package development policies actually has a statement that may be helpful 
in thinking about this. Your mileage may vary in the interpretation


  *   - Packages should not write in the users� home filespace, nor anywhere 
else on the file system apart from the R session�s temporary directory (or 
during installation in the location pointed to by TMPDIR: and such usage should 
be cleaned up). Installing into the system�s R installation (e.g., scripts to 
its bin directory) is not allowed.

Limited exceptions may be allowed in interactive sessions if the package 
obtains confirmation from the user.

https://cran.r-project.org/web/packages/policies.html

Sean




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
<bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Sean Davis <seand...@gmail.com<mailto:seand...@gmail.com>>
Sent: Friday, December 1, 2017 11:06:39 AM
To: Michael Love
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] BiocFileCache for developers

On Fri, Dec 1, 2017 at 10:28 AM, Michael Love 
<michaelisaiahl...@gmail.com<mailto:michaelisaiahl...@gmail.com>>
wrote:

> hi,
>
> I'm writing a function which currently uses BiocFileCache to store a
> small data.frame and one or more TxDb objects, so that these objects
> are persistent and available across sessions (or possible available to
> multiple users).
>
> In the simplest case, I would call
>
> bfc <- BiocFileCache()
>
> inside my function, which will check the default location:
>
> user_cache_dir(appname = "BiocFileCache")
>
> In general, should developers also support the user specifying a
> specific location for the BiocFileCache? So functions using
> BiocFileCache should have an argument that overrides the above
> location?
>

On some systems, the user home directory is not large (such as on HPC
systems) or has strong quotas. The default user_cache_dir may not be the
best choice there.

Sean


>
> thanks,
> Mike
>
> ___
> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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email message is prohibited. If you have received this message in error, please 
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--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12


This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] BiocFileCache for developers

[Shepherd, Lori]

So having a user argument might be best.  Or defining a unique cache location 
for your package would be another option.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Sean Davis 
<seand...@gmail.com>
Sent: Friday, December 1, 2017 11:06:39 AM
To: Michael Love
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocFileCache for developers

On Fri, Dec 1, 2017 at 10:28 AM, Michael Love <michaelisaiahl...@gmail.com>
wrote:

> hi,
>
> I'm writing a function which currently uses BiocFileCache to store a
> small data.frame and one or more TxDb objects, so that these objects
> are persistent and available across sessions (or possible available to
> multiple users).
>
> In the simplest case, I would call
>
> bfc <- BiocFileCache()
>
> inside my function, which will check the default location:
>
> user_cache_dir(appname = "BiocFileCache")
>
> In general, should developers also support the user specifying a
> specific location for the BiocFileCache? So functions using
> BiocFileCache should have an argument that overrides the above
> location?
>

On some systems, the user home directory is not large (such as on HPC
systems) or has strong quotas. The default user_cache_dir may not be the
best choice there.

Sean


>
> thanks,
> Mike
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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Re: [Bioc-devel] BiocFileCache for developers

[Michael Love]

One solution if a developer really wants to make sure the user knows
that the function will store a cache somewhere would be to leave the
BiocFileCache location argument without a default value.

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Re: [Bioc-devel] BiocFileCache for developers

[Sean Davis]

On Fri, Dec 1, 2017 at 11:16 AM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> So having a user argument might be best.  Or defining a unique cache
> location for your package would be another option.
>

The R package development policies actually has a statement that may be
helpful in thinking about this. Your mileage may vary in the
interpretation


>- - Packages should not write in the users’ home filespace, nor
>anywhere else on the file system apart from the R session’s temporary
>directory (or during installation in the location pointed to by TMPDIR:
>and such usage should be cleaned up). Installing into the system’s R
>installation (e.g., scripts to its bin directory) is not allowed.
>
>Limited exceptions may be allowed in interactive sessions if the
>package obtains confirmation from the user.
>
>
https://cran.r-project.org/web/packages/policies.html

Sean



>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Sean
> Davis <seand...@gmail.com>
> *Sent:* Friday, December 1, 2017 11:06:39 AM
> *To:* Michael Love
> *Cc:* bioc-devel@r-project.org
> *Subject:* Re: [Bioc-devel] BiocFileCache for developers
>
> On Fri, Dec 1, 2017 at 10:28 AM, Michael Love <michaelisaiahl...@gmail.com
> >
> wrote:
>
> > hi,
> >
> > I'm writing a function which currently uses BiocFileCache to store a
> > small data.frame and one or more TxDb objects, so that these objects
> > are persistent and available across sessions (or possible available to
> > multiple users).
> >
> > In the simplest case, I would call
> >
> > bfc <- BiocFileCache()
> >
> > inside my function, which will check the default location:
> >
> > user_cache_dir(appname = "BiocFileCache")
> >
> > In general, should developers also support the user specifying a
> > specific location for the BiocFileCache? So functions using
> > BiocFileCache should have an argument that overrides the above
> > location?
> >
>
> On some systems, the user home directory is not large (such as on HPC
> systems) or has strong quotas. The default user_cache_dir may not be the
> best choice there.
>
> Sean
>
>
> >
> > thanks,
> > Mike
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
>
> --
> Sean Davis, MD, PhD
> Center for Cancer Research
> National Cancer Institute
> National Institutes of Health
> Bethesda, MD 20892
> https://seandavi.github.io/
> https://twitter.com/seandavis12
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>



-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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Re: [Bioc-devel] BiocFileCache for developers

[Sean Davis]

On Fri, Dec 1, 2017 at 10:28 AM, Michael Love 
wrote:

> hi,
>
> I'm writing a function which currently uses BiocFileCache to store a
> small data.frame and one or more TxDb objects, so that these objects
> are persistent and available across sessions (or possible available to
> multiple users).
>
> In the simplest case, I would call
>
> bfc <- BiocFileCache()
>
> inside my function, which will check the default location:
>
> user_cache_dir(appname = "BiocFileCache")
>
> In general, should developers also support the user specifying a
> specific location for the BiocFileCache? So functions using
> BiocFileCache should have an argument that overrides the above
> location?
>

On some systems, the user home directory is not large (such as on HPC
systems) or has strong quotas. The default user_cache_dir may not be the
best choice there.

Sean


>
> thanks,
> Mike
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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Re: [Bioc-devel] BiocFileCache for developers

[Shepherd, Lori]

If you are using it as a helper function that may be too much exposure and you 
may just want it running behind the scenes in default location;  but it could 
be given as an option to the user. I guess a coding preference. If the user 
specified directory is used, they will have to remember to input that each time 
they use your package or it will redownload.


There shouldn't be a concern of overwriting files in the default cache 
location, as files added to the cache get a random identifier to try to avoid 
overwriting and to allow for essentially duplicate entries.


You can always get the cache location of a bfc object by calling bfccache(bfc) 
in case a user specific directory is used.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Michael Love 

Sent: Friday, December 1, 2017 10:28:48 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] BiocFileCache for developers

hi,

I'm writing a function which currently uses BiocFileCache to store a
small data.frame and one or more TxDb objects, so that these objects
are persistent and available across sessions (or possible available to
multiple users).

In the simplest case, I would call

bfc <- BiocFileCache()

inside my function, which will check the default location:

user_cache_dir(appname = "BiocFileCache")

In general, should developers also support the user specifying a
specific location for the BiocFileCache? So functions using
BiocFileCache should have an argument that overrides the above
location?

thanks,
Mike

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