NEWS

AnnotationForge 1.41.0

1.41.5 Add RUnit to Suggest
1.41.3 Update viableID.rda for upcoming release
1.41.2 Use dbExecute() instead of dbGetQuery() or dbSendQuery() to avoid warnings

1.41.4 Knoknok Optimizations and allow specification of the desired Ensembl release
1.41.1 James MacDonald Fixed makeOrgPackageFromNCBI to use existing downloaded files

Removed UniGene from OrgDb and ChipDb packages
Added Gene Type table to OrgDb and ChipDb packages
Added functionality to build Orthology.eg.db package which maps NCBI Gene IDs between species
RSQLite deprecated usage of dbGetQuery for database altering statements; updated to use dbExecute instead

RSQLite deprecated dbGetPreparedQuery/dbSendPreparedQuery; Updated with dbGetQuery/dbSendQuery/dbBind/dbFetch
update for building BioC 3.5

remove outdated unit test and deprecate MAPCOUNTS in ChipDb package templates
update ChipDb package templates to load DBI in unit tests
allow build without --keep-empty-dirs flag
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 {}
remove unused tests/runalltests.Rout.save file in AnnDbPkg-templates
use https: rather than http: for NCBI access
rename R code and man page files consistent with high level functions
bump OrgDb version for 3.4 release
add explicit AnnotationDbi:::NCBIORG_DB_SeedGenerator()

update AnnDbPkg template man to reference select() interface
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
add PFAM and PROSITE man pages to NCBICHIP and NCBIORG package templates
allow passing of directory location in wrapBaseDBPackages()
change format of licence; report current version of AnnotationDbi
modify appendArabidopsisGenes() to check for null 'gene_id'
add DBI to 'Suggests'; load DBI in _dbconn man page
load SQLite in vignettes; no longer free from AnnotationDbi::dbFileConnect()

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.

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).
Adds support for making new inparanoid8 databases (for loading into AnnotationHub)

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.
updates to the documentation (new vignettes) to better clarify how users who need to make new organism packages should do so.

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
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.