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AnnotationDbi
fixed typo in the SQLForge vignette (collumn == column)

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AnnotationDbi
Fixes minor bug with the package checking code.
This bug would have prevented some packages which legitimately might
have had some empty fields for GO terms (this came up with the Sakai
strain of E coli), from passing check.

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AnnotationDbi
Adds support for Zebrafish and E coli.
This adds support for Zebrafish and two strains of E coli.

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AnnotationDbi
More improvements to the Bimap documentation.

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AnnotationDbi
Some improvements to the Bimap documentation (more to come). Version bumped to 1.3.6

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AnnotationDbi
Removed old dependencies for GO and hgu95av2
There were some examples in the vignette of how we used to do things.
These have been set to eval=false and the dependencies have been

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AnnotationDbi
Adds new Ensembl mappings to mammalian org packges.
Mouse, Rat and Human now can support Ensembl transcript IDs, these IDs
are availaible in new mappings and documented. The mappings for mouse
Ensembl protein IDs have also been added with this patch (previously
only MGI IDs were in place in the mouse).

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AnnotationDbi
Fixes annotation and map counts bugs in Inparanoid packages.
This patch just repairs minor bugs in the code that generates the
inparanoid packages.

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AnnotationDbi
Fixes bug in inparanoid mappings.
This was a bad bug that prevented these mappings from filtering out all
the non-seed regions properly.

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AnnotationDbi
More convenient access to author info. via SQLForge wrappers.
This patch makes it easier to add maintainer and author information to
generated packages using the SQLForge wrapper functions.

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AnnotationDbi
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Fixed mget(c("GO:0018075","GO:0018075"),GOTERM) bug (the problem was in the .toListOfLists() function which was affecting the "as.list" method for GOTermsAnnDbBimap objects). Version bump.

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AnnotationDbi
Fixed slowdown bugs
These bugs only impacts the speed at which SQLForge does it's job.
The results will be the same. But if you are building ~ 700 packages,
you might appreciate this change.
Bug fix for increased AnnBuilder file format compatibility
This fix makes things more compatible for people who are using classic
AnnBuilder style files.

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AnnotationDbi
Fixed bug where wrong type of ID causes ins. of spaces
This fixed a bug where R was automatically casting numeric IDs to be
numbers which would cause spaces to be inserted downstream when these
data would be stuck into the database.

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AnnotationDbi
Fixed bad but subtle bug in SQLforge.
This fixes a bad bug in SQLforge that would under certain rare
circumstances, map the wrong type of indentifier into the entrez gene
field. Now the code does a better job of making sure that when it has
an alternate ID, to find a correct entrez gene id if one can be found
and stick that into the entrez gene field.

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AnnotationDbi
Fixes map_counts bug for org.Sc.eg.db packages.

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AnnotationDbi
Fixed rare bug that can happen when an ID is a very long integer
Fixed a rare bug that can happen where a very long integer is the ID.
When this happens R can promote this to a double before passing it to
SQLite which will then add an unwanted .0 extension onto the end of
it. Now Sqlforge will check for such IDs and cast them (but only if
needed).

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AnnotationDbi
Modifications to Plasmodium falciparum man pages.
Corrects bugs that would otherwise be found in the Plasmodium
falciparum man pages for packages that get produced using this.

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AnnotationDbi
These changes add support for Plasmodium falciparum
These changes add support to make databases and organism level
packages for the malaria parasite Plasmodium falciparum.

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AnnotationDbi
Updates to Documentation.
This updates the main vignette for AnnotationDbi with more examples,
and also updates the man pages for the homology package so that users
will in future know where the inparanoid abbreviations come from.

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AnnotationDbi
Removed code for redundant indices.
This removes many redundant indices from the SQLForge code. This
should reduce the size of the databases somewhat while not impacting
performance.

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AnnotationDbi
Adds a vignette for SQLForge, and some bug fixes.
This checkin adds a vignette for the newer SQLForge functions as well
as some bug fixes for some of the populate functions so that they can
correctly build their databases in the specified directories. Also, a
much shorter example file was added to cut down on the time needed to
check the new vignette.

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AnnotationDbi
Fixes a bad bug in SQLForge introduced by Refseq vers. #s
This adds some debug code, and also fixes a bad bug introduced when I
added code that attempts to automatically scrub version numbers from

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AnnotationDbi
Cleans up the parameter names and input for SQLForge.
The param "ll" has been changed to "eg" for SQLForge since they are
not called locus link IDs anymore (so why name parameters after a name
people are forgetting in new code?). Also there is an issue that can
crop up with refseq IDs if the user is not paying attention and leaves
on the version numbers to these IDs. For Refseq IDs, only the
accession part of the ID is actually matched to a gene, and some
vendors give IDs that do have the version number attached while others
trim them off. Therefore our DBs always deal with these IDs with the
extraneous stuff removed. However since none of the databases use
these IDs, it also becomes impossible for any database to match on
them if the version numbers have not already been not clipped off by
the user (when the IDs have been provided by a vendor who leaves them
on), so there is now some "auto-cleanup" that SQLForge will do if the
user feeds refseq IDs as a primary ID that are still not trimmed of
their version numbers.

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AnnotationDbi
Updates to SQLForge and a better error msg for mget.
Part of this update just changes the AnnotationDbi mget message to
look more like what is expected based on what its parents msg looked
like. The other part overhauls the part of the code that does the
initial mapping for SQLForge so that it will not write out
indermediate files. This step was uneccessary and generally just a bad
idea that was causing bugs on the windows platform. The new code
should be more robust to cross platform issues.

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AnnotationDbi
Just the documentation.
This check in adds some more documentation to the man pages to better
describe some of the new helper functions used in AnnotationDbi.

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AnnotationDbi
adding to the TODO list

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AnnotationDbi
adding to the TODO list
started a TODO list here

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AnnotationDbi
started a TODO list here

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AnnotationDbi
Directory checking and refseq bug.
Fixed bug that happened when refseq IDs were uses as the primary
ID. And also added checking to wrapper functions to let users know if
they are trying to write a database into a place that does not exist
yet. These changes only affect SQLForge.

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AnnotationDbi
Minor bug fixes for cross platform compatibility of sqlForge
These minor fixes should ensure that sqlForge will work better across
OS platforms when looking for the standard DB packages.
Fixed mget(c("969","969"),org.Hs.egGO) bug (was in "as.list" method for GoAnnDbBimap objects). Version bump.

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AnnotationDbi
Addition of code to package up intermediate DBs.
This checkin adds the code that will be used to make biannual updates
of the intermediate databases. These databases will be shipped out to
developers as very large R packages, and will allow us to ensure that
everyone has the correct intermediate database installed in the
correct place. One package is planned per supported organism. The
sqlForge code has been modified to find these databases as a default
parameter so that everyone should be able to just use biocLite to get
the latest intermediate DBs (if they want to make annotation packages)
and then to just use the wrapper functions to crank out .db packages
for supported organisms.

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AnnotationDbi
Major overhaul of PFAM.db
These changes reflect a major overhaul of the new PFAM.db package to
squash bugs in there so that they won't burn users and also to provide
proper documentation.

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AnnotationDbi
Major overhaul of PFAM.db
These changes reflect a major overhaul of the new PFAM.db package to
squash bugs in there so that they won't burn users and also to provide
proper documentation.

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AnnotationDbi
Bug fixes for sqlForge involving primarily fly and arabidopsis.
These bug fixes only affect the sqlForge portion of the codebase and
primarily are concerned with getting the output perfect for the sqlite
files generarted for flies and arabidposis.
Updating the license reference to reflect R standards.

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AnnotationDbi
Changes and bug fixes for making chip based pkgs.
These changes and bug fixes allow things to work properly for making
chip based databases and bundling these into packages. There is still
a minor issue with arabidopsis to fix. And then the intermediate
databases need to be bundled into packages for easy distribution and
the default paths set for these helper functions.
Wrapper functions for chip packages
This update adds wrapper functions for chip packages along with man
pages. This code still needs to be much more thoroughly tested and
there are still problems here with support for Yeast and Arabidopsis
which both still need to have the portion of their code that maps data
set up for the mapping of non-affy packages. But at least now it
should be possible to call a function, and have it make a database,
and then wrap that up into a chip based package. Organism based
packages are more monolithic and so are not really expected to need a
wrapper package. Although the code to make the sqlite files and the
packages for these is already here.

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AnnotationDbi
Don't want to forget the version bump.
Bumped to 1.1.11
Remove limitation of metaDataSrc.sqlite
There are a number of bug fixes in this patch, but the most important
change is that there is no longer a requirement that a sqlite database
have an entry in the local metaDataSrc.sqlite file. This change is
critical to allowing users to make custom packages.

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AnnotationDbi
Adds support to make most chip and organism sqlite files
This update adds many new functions to add functionality to make many
new kinds of organism and chip based sqlite files. In general there
is a master function for each schema that adds the ability to make
sqlite files of that type (with correct parameters). These functions
will later be wrapped in another function that should call these
functions and then also call makeAnnDbPkg() to make the sqlite file
and then wrap it up in a new package.

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AnnotationDbi
Fixes a bug in the display of chrlengths vectors
There was a bug in the creation of the chrlengths vectors that was
introduced with the 1.0 schema changes. Bug only affected the display
of the data and not the underlying data, so only AnnotationDbi needs
to be updated to clear this up.

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AnnotationDbi
Minor bug fixes for release of candidate 1.1.8
These include some small typo fixes to the .Rd files, corrections to
the author lists on some new packages and the usual required update to
the version numbers across the board.

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AnnotationDbi
Added Marc to the Author field. Updated dependencies. Version bump.
Clean up of the code in showQCdata()
Bug fix for shoqQCdata()
This time the bug fixes are actually in.
Fixed bugs in showQCdata()
This change just fixes the showQCdata function so that the counts are
displayed correctly.
Fixes a bug in the new shoqQCData function.
This function needs further work to get the mapped keys to be counted
correctly.
Cosmetic change only.
This adds a news section to the AnnotationDbi
This adds a news section to AnnotationDbi which will be used to
announce MAJOR "bullet point" changes that have been made to the
package since the last revision.
Modifications to schemas.
These are changes to the schema documentation so that they more
precisely align with what was in the sqlite files that are feeding
into AnnotationDbi. Also, code was added to
AnnotationDbi-internals.Rd so that it will not complain about the man
pages being in a sub-template within AnnotationDbi for the new
packages.
Applied Marc's big patch: switch to version 1.0 of the schemas + support for the Inparanoid packages + support for new PFAM.db + pkgname() function for displaying QC information. No version bump for now. inst/NEWS file is in preparation and will be added later.

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