Update R packages for macOS and Windows.

source/R-Portable-Mac/library/AnnotationDbi/DBschemas/SchemaGuidelines.txt

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+SchemaGuidelines
+================
+
+We want our schemas to be as portable as possible. In particular they should
+be compatible with SQLite, MySQL, PostgreSQL and Oracle.
+All the current schemas (i.e. the *_DB.sql files in schemas_0.9/ and
+schemas_1.0/) have been successfully tested (i.e. imported) with SQLite
+(3.4.1), MySQL+InnoDB (5.0.26) and PostgreSQL (8.1.9) on a 64-bit openSUSE
+10.2 system. They have not been tested on Oracle yet.
+
+o All of the *_DB.sql files must define a "metadata" table (with cols "name"
+  and "value") and all the *.sqlite files using one of these schemas must
+  have a 'DBSCHEMA' and a 'DBSCHEMAVERSION' entry in their "metadata" table.
+
+o Make explicit use of the NULL or NOT NULL constraint on every column (except
+  on PRIMARY KEY cols that are implicitly NOT NULL).
+
+o Centralize all the data type definitions in the DataTypes.txt file and use
+  them consistently across all the *_DB.sql files.
+
+o Use preferably CHAR(n) or VARCHAR(n) types instead of non-standard TEXT type
+  for character columns. Note that n must be <= 255 for compatibility with
+  MySQL. Don't define an INDEX (or try to put a UNIQUE constraint, which
+  implicitly creates an INDEX) on a TEXT column since this is not portable.
+  Also don't define an INDEX on a CHAR(n) or VARCHAR(n) column where n is
+  large (i.e. > 80) since this is not portable either. Doing so when n <= 80
+  should be safe though.
+
+o Always use a character type for "external" (aka "real world") ids even for
+  ids like Entrez Gene IDs, PubMed IDs or OMIM IDs that are in fact integers.
+
+o Put PRIMARY KEY and UNIQUE definitions "in line" at the end of the column
+  definition (after the SQL type and the NULL/NOT NULL constraint for UNIQUE).
+
+o Make the PRIMARY KEY column the first column in the CREATE TABLE statement.
+
+o Put "regular" (i.e. non PRIMARY KEY, non UNIQUE) INDEX definitions all
+  together at the end of the *_DB.sql file.
+
+o Make sure that referenced tables are created before referencing tables.
+
+o Make the FOREIGN KEYs portable. This means that:
+    - Use portable syntax. Putting 
+        FOREIGN KEY (col) REFERENCES table (col)
+      inside the CREATE TABLE statement but at the end of it (after all the
+      column definitions) is compatible with SQLite (which will just ignore
+      it), MySQL+InnoDB and PostgreSQL.
+    - There must be NOT NULL and UNIQUE constraints on the referenced column
+      (typically a PRIMARY KEY).
+    - The referencing and referenced columns must have the same type.
+
+o Prefix with an underscore the column names that store "internal" ids.
+

source/R-Portable-Mac/library/AnnotationDbi/DBschemas/schemas_0.9/00README.TXT

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+This directory contains version 0.9 of the full set of schemas used in the
+sqlite-based annotation data packages.
+
+Version 0.9 is our target for the BioC 2.1 release i.e. it is the version
+that we plan to use in the data packages that will be released with
+Bioconductor 2.1 (AnnotationDbi 1.0.0).
+
+Version 0.9 has been successfully tested (i.e. imported) with SQLite
+(3.4.1), MySQL+InnoDB (5.0.26) and PostgreSQL (8.1.9) on a 64-bit openSUSE
+10.2 system. It has not been tested on Oracle yet.
+
+All the *.sqlite files using one of the 0.9 schemas must set DBSCHEMAVERSION
+to 0.9 in their "metadata" table.
+
+See the DataTypes.txt file for all the data types used across the 0.9 schemas.
+

source/R-Portable-Mac/library/AnnotationDbi/DBschemas/schemas_0.9/ARABIDOPSISCHIP_DB.sql

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+--
+-- ARABIDOPSISCHIP_DB schema
+-- =========================
+--
+
+-- The "genes" table is the central table.
+CREATE TABLE genes (
+  id INTEGER PRIMARY KEY,
+  gene_id CHAR(9) NOT NULL UNIQUE               -- AGI locus ID
+);
+
+-- Data linked to the "genes" table.
+CREATE TABLE probes (
+  id INTEGER NULL,                              -- REFERENCES genes
+  probe_id VARCHAR(80) NOT NULL,                -- manufacturer ID
+  is_multiple SMALLINT NOT NULL,                -- a silly and useless field
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+CREATE TABLE aracyc (
+  id INTEGER NOT NULL,                          -- REFERENCES genes
+  pathway_name VARCHAR(255) NOT NULL,           -- AraCyc pathway name
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+CREATE TABLE chromosome_locations (
+  id INTEGER NOT NULL,                          -- REFERENCES genes
+  chromosome CHAR(1) NOT NULL,                  -- Arabidopsis chromosome
+  start_location INTEGER NOT NULL,
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+CREATE TABLE ec (                               --    Table
+  id INTEGER NOT NULL,                          -- 
+  ec_number VARCHAR(13) NOT NULL,               --    NOT
+  FOREIGN KEY (id) REFERENCES genes (id)        -- 
+);                                              --    used!
+CREATE TABLE enzyme (
+  id INTEGER NOT NULL,                          -- REFERENCES genes
+  ec_name VARCHAR(255) NOT NULL,                -- EC name
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+-- Note that the "gene_info" table differs from other schemas:
+--   o no UNIQUE constraint on col "id"
+--   o no NOT NULL constraints on cols "gene_name" and "symbol"
+--   o one additional col "chromosome"
+CREATE TABLE gene_info (
+  id INTEGER NOT NULL,                          -- REFERENCES genes
+  gene_name VARCHAR(255) NULL,                  -- gene name
+  symbol VARCHAR(80) NULL,                      -- gene symbol
+  chromosome CHAR(1) NULL,                      -- Arabidopsis chromosome
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+CREATE TABLE go_bp (
+  id INTEGER NOT NULL,                          -- REFERENCES genes
+  go_id CHAR(10) NOT NULL,                      -- GO ID
+  evidence CHAR(3) NOT NULL,                    -- GO evidence code
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+CREATE TABLE go_bp_all (
+  id INTEGER NOT NULL,                          -- REFERENCES genes
+  go_id CHAR(10) NOT NULL,                      -- GO ID
+  evidence CHAR(3) NOT NULL,                    -- GO evidence code
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+CREATE TABLE go_cc (
+  id INTEGER NOT NULL,                          -- REFERENCES genes
+  go_id CHAR(10) NOT NULL,                      -- GO ID
+  evidence CHAR(3) NOT NULL,                    -- GO evidence code
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+CREATE TABLE go_cc_all (
+  id INTEGER NOT NULL,                          -- REFERENCES genes
+  go_id CHAR(10) NOT NULL,                      -- GO ID
+  evidence CHAR(3) NOT NULL,                    -- GO evidence code
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+CREATE TABLE go_mf (
+  id INTEGER NOT NULL,                          -- REFERENCES genes
+  go_id CHAR(10) NOT NULL,                      -- GO ID
+  evidence CHAR(3) NOT NULL,                    -- GO evidence code
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+CREATE TABLE go_mf_all (
+  id INTEGER NOT NULL,                          -- REFERENCES genes
+  go_id CHAR(10) NOT NULL,                      -- GO ID
+  evidence CHAR(3) NOT NULL,                    -- GO evidence code
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+CREATE TABLE kegg (
+  id INTEGER NOT NULL,                          -- REFERENCES genes
+  kegg_id CHAR(5) NOT NULL,                     -- KEGG pathway short ID
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+CREATE TABLE pubmed (
+  id INTEGER NOT NULL,                          -- REFERENCES genes
+  pubmed_id VARCHAR(10) NOT NULL,               -- PubMed ID
+  FOREIGN KEY (id) REFERENCES genes (id)
+);
+
+-- Metadata tables.
+CREATE TABLE metadata (
+  name VARCHAR(80) PRIMARY KEY,
+  value VARCHAR(255)
+);
+CREATE TABLE qcdata (
+  map_name VARCHAR(80) PRIMARY KEY,
+  count INTEGER NOT NULL
+);
+CREATE TABLE map_metadata (
+  map_name VARCHAR(80) NOT NULL,
+  source_name VARCHAR(80) NOT NULL,
+  source_url VARCHAR(255) NOT NULL,
+  source_date VARCHAR(20) NOT NULL
+);
+
+-- Explicit index creation on the referencing column of all the foreign keys.
+-- Note that this is only needed for SQLite: PostgreSQL and MySQL create those
+-- indexes automatically.
+CREATE INDEX Fprobes ON probes (id);
+CREATE INDEX Faracyc ON aracyc (id);
+CREATE INDEX Fchromosome_locations ON chromosome_locations (id);
+CREATE INDEX Fec ON ec (id);
+CREATE INDEX Fenzyme ON enzyme (id);
+CREATE INDEX Fgene_info ON gene_info (id);
+CREATE INDEX Fgo_bp ON go_bp (id);
+CREATE INDEX Fgo_bp_all ON go_bp_all (id);
+CREATE INDEX Fgo_cc ON go_cc (id);
+CREATE INDEX Fgo_cc_all ON go_cc_all (id);
+CREATE INDEX Fgo_mf ON go_mf (id);
+CREATE INDEX Fgo_mf_all ON go_mf_all (id);
+CREATE INDEX Fkegg ON kegg (id);
+CREATE INDEX Fpubmed ON pubmed (id);
+
+-- Other indexes.
+CREATE INDEX Lprobes ON probes (probe_id);
+