CHANGES IN VERSION 1.18.0
------------------------
MODIFICATIONS
o RSQLite deprecated dbGetPreparedQuery/dbSendPreparedQuery; Updated with
dbGetQuery/dbSendQuery/dbBind/dbFetch
o update for building BioC 3.5
BUG FIXES
o Resolve tmp issue, change outputDir to NCBIFilesDir
o Fixed a bug in makeOrgPackageFromNCBI when there are no GO terms
CHANGES IN VERSION 1.16.0
------------------------
NEW FEATURES
o add check that required db0 package is installed in makeDBPackage()
o add script to create viableIDs data file
MODIFICATIONS
o remove outdated unit test and deprecate MAPCOUNTS in ChipDb
package templates
o update ChipDb package templates to load DBI in unit tests
o allow build without --keep-empty-dirs flag
o misc code cleanup
- No duplicate dependencies in DESCRIPTION
- resolve symbols in name space
- re-usable unit tests (new rather than reuse of temporary files)
- avoid unnecesary paste(), e.g, message(paste())
- use of loadNamespace() rather than require()
- avoid 1:n iterations
- formatting, e.g., of SQL and if () {} else {}
o remove unused tests/runalltests.Rout.save file in
AnnDbPkg-templates
o use https: rather than http: for NCBI access
o rename R code and man page files consistent with high level functions
o bump OrgDb version for 3.4 release
o add explicit AnnotationDbi:::NCBIORG_DB_SeedGenerator()
BUG FIXES
o getFastaSpeciesDirs() trims '\r' on Windows
CHANGES IN VERSION 1.14.0
------------------------
NEW FEATURES
o build 'alias' table in OrgDbs sqlite db for frog, chimp, rhesus and
mosquito
MODIFICATIONS
o update AnnDbPkg template man to reference select() interface
o work on makeOrgPackageFromNCBI:
- error early when tax id is not found in gene_info.gz
- add 'rebuildCache' arg to control repeated downloads
- remove old code and comments
- update man page
o add PFAM and PROSITE man pages to NCBICHIP and NCBIORG package
templates
o allow passing of directory location in wrapBaseDBPackages()
o change format of licence; report current version of AnnotationDbi
o modify appendArabidopsisGenes() to check for null 'gene_id'
o add DBI to 'Suggests'; load DBI in _dbconn man page
o load SQLite in vignettes; no longer free from
AnnotationDbi::dbFileConnect()
CHANGES IN VERSION 1.8.0
------------------------
NEW FEATURES
o Adds support for making orgDb objects/databases for all NCBI
taxIDs where there is sufficient data (for adding to
AnnotationHub). This makes objects for 1100 organisms.
CHANGES IN VERSION 1.6.0
------------------------
NEW FEATURES
o Adds support for a generalized makeChipPackage() function so
that users with a probe that maps to an ID can make a chip package
providing only that they have access to an org package (no .db0
package required).
o Adds support for making new inparanoid8 databases (for loading
into AnnotationHub)
CHANGES IN VERSION 1.4.0
------------------------
NEW FEATURES
o adds more general mechanism for creating organism packages.
makeOrgPackage() will now allow users to pass in a series of
data.frames, and (provided that they are formatted correctly) will
compile those into a gene-centric organism package. The aim is to
provide a more general mechanism for people who are working on
organisms that are off the beaten path.
o updates to the documentation (new vignettes) to better clarify
how users who need to make new organism packages should do so.
CHANGES IN VERSION 1.0.0
------------------------
o All of the code that used to live in AnnotationDbi but was
primarily involved in the creation of new annotation packages
now lives here.
NEW FEATURES
o New biocViews tags have been added to the code that generates all
the new Annotation packages. These allow users to search
annotation packages by the type of annotation package that they
are. So for example you can now quickly list only the
TranscriptDb packages by using the web site.