'Re: [Bioc-devel] Important news about pending updates to the RSQLite package'

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List:       bioc-devel
Subject:    Re: [Bioc-devel] Important news about pending updates to the RSQLite package
From:       Dan Tenenbaum <dtenenba () fhcrc ! org>
Date:       2014-10-20 17:59:59
Message-ID: 981408982.21622.1413827999212.JavaMail.root () fhcrc ! org
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Hi all,

Just a reminder that Hadley is going to submit RSQLite 1.0.0 today. 

If your package needs to be changed to work with the new version, and you haven't \
already done it, now is the time to make the changes.

You'll need to make them in release and devel. 

Thanks,
Dan

----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba@fhcrc.org>
> To: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Friday, September 26, 2014 5:20:43 PM
> Subject: Important news about pending updates to the RSQLite package
> 
> Hi all,
> 
> RSQLite 1.0.0 is scheduled to be released on October 20th, just a few
> days after the Bioconductor 3.0 release.
> 
> It is a major update and involves a lot of changes; many functions
> have been deprecated, removed, renamed, are no longer exported, or
> have different arguments. I've pasted the full announcement from
> Hadley Wickham below (includes the links to github where you can
> download and test the package).
> 
> Many Bioconductor packages depend on RSQLite. Please review all
> packages you maintain and make sure they build and check with the
> new version of RSQLite.
> 
> Ideally you should fix your package in such a way that it works with
> both the current (0.3.0) version of RSQLite and with the upcoming
> version 1.0.0, without needing kludgey conditional code. If that
> isn't possible, make a version that is fully compatible with 1.0.0
> but not compatible with 0.3.0 and be prepared to update your release
> and devel packages with the updated code immediately after RSQLite
> 1.0.0 becomes available.
> 
> The following packages (maintainers Bcc'd) will definitely need to be
> updated _in both release and devel_ because they use the sqlite*
> functions that are no longer exported from RSQLite 1.0.0:
> 
> AnnotationForge
> bioassayR
> cummeRbund
> eiR
> GEOmetadb
> PAnnBuilder
> pdInfoBuilder
> SRAdb
> UniProt.ws
> 
> But if your package does not appear in that list you should still
> check your package, because that's just the low-hanging fruit.
> 
> Please 'reply all' to bioc-devel if you have any questions.
> 
> Thanks,
> Dan
> 
> 
> 
> --------------------------------
> Announcement from Hadley Wickham
> --------------------------------
> 
> Hi everyone,
> 
> I'm preparing to release a new version of RSQLite, 1.0.0.  (I've
> taken
> over maintenance from Seth Falcon). This release is basically a big
> tidy up - I've refactored a lot of the C code to be easier to follow,
> deprecated a lot of unused functions, and converted everything to
> "Hadley"-style package development.  A complete list of changes are
> included at the bottom of this email.
> 
> If you use RSQLite, I'd really appreciate it if you'd try out the
> development version and let me know if you have any problems. You can
> install it from github with:
> 
> # install.packages("devtools")
> devtools::install_github("rstats-db/DBI")
> devtools::install_github("rstats-db/RSQLite")
> 
> If you have written a package that depends on RSQLite, please check
> the list of R CMD check results at
> https://github.com/wch/checkresults/blob/master/RSQLite/r-release/00check-summary.txt.
>  I've been quite aggressive at deprecating old functions, and
> un-exporting functions that are really part of RSQLite's internal
> interface. This means that many packages will need changes. If you
> have any trouble figuring out the problem, please let me know and
> I'll
> be happy to help. I apologise for the hassle, but this will make
> RSQLite a much better platform to build on in the future.
> 
> I plan to submit this version of RSQLite to CRAN on Oct 20, so that
> there's plenty of time for feedback and changes.
> 
> Hadley
> 
> # Version 1.0.0
> 
> ## New features
> 
> - Updated to SQLite 3.8.6
> 
> - Added `datasetsDb()`, a bundled SQLite database containing all data
> frames
> in the datasets package (#15).
> 
> - Inlined `RSQLite.extfuns` - use `initExtension()` to load the many
> useful extension functions (#44).
> 
> - Methods no longer automatically clone the connection is there is an
> open
> result set. This was implement inconsistently in a handful of
> places (#22).
> RSQLite is now more forgiving if you forget to close a result set -
> it will
> close it for you, with a warning. It's still good practice to clean
> up
> after yourself, but you don't have to.
> 
> - `dbBegin()`, `dbCommit()`, `dbRollback()` throw errors on failure,
> rather than
> return `FALSE`.  They all gain a `name` argument to specify named
> savepoints.
> 
> - `dbFetch()` method added (`fetch()` will be deprecated in the
> future)
> 
> - `dbRemoveTable()` throws errors on failure, rather than returning
> `FALSE`.
> 
> - `dbWriteTable()` has been rewritten:
> 
> * It quotes field names using `dbQuoteIdentifier()`, rather
> than use a flawed black-list based approach with name munging.
> 
> * It now throws errors on failure, rather than returning FALSE.
> 
> * It will automatically add row names only if they are character,
> not integer.
> 
> * When loading a file from disk, `dbWriteTable()` will no longer
> attempt to guess the correct values for `row.names` and
> `header` - instead
> supply them explicitly if the defaults are incorrect.
> 
> * It uses named save points so it can be nested inside other
> transactions (#41).
> 
> * When given a zero-row data frame it will just creates the table
> definition (#35).
> 
> ## Changes to objects
> 
> - The `dbname`, `loadable.extensions`, `flags` and `vfs` properties
> of
> a SqliteConnection are now slots. Access them directly instead of
> using
> `dbGetInfo()`.
> 
> ## Deprecated and removed functions
> 
> - RSQLite is no longer nominally compatible with S (#39).
> 
> - `idIsValid()` is deprecated. Please use `dbIsValid()` instead.
> 
> - `dbBeginTransaction()` has been deprecated. Please use `dbBegin()`
> instead.
> 
> - `dbCallProc()` method removed, since generic is now deprecated.
> 
> - Renamed `dbBuildTableDefinition()` to
> `sqliteBuildTableDefinition()`
> to avoid implying it's a DBI generic. Old function is aliased to
> new with
> a warning.
> 
> - `dbFetch()` no longer numbers row names sequentially between
> fetches.
> 
> - `safe.write()` is no longer exported as it shouldn't be part of the
> public RSQLite interface (#26).
> 
> - Internal `sqlite*()` functions are no longer exported (#20).
> 
> - Removed `SqliteObject` and `dbObject` classes, modifying
> `SqliteDriver`,
> `SqliteConnection`, and `SqliteResult` to use composition instead
> of multiple
> inheritance.
> 
> --
> http://had.co.nz/
> 
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