CHANGES IN VERSION 2.1
----------------------
MAJOR UPDATES
o (2.1.1) Change caching location warning/deprecation to an ERROR in
preparation for removal of dependency next release.
CHANGES IN VERSION 1.99
----------------------
MAJOR UPDATES
o (1.99.0) The default caching location has changed. Instead of
rappdirs::user_cache_dir using tools::R_user_dir. To avoid conflicting
caches, a user will have to manage an old cache location before
proceeding. Information for handling an old cache location is provided in
the vignette.
o (1.99.0) Another major change, a default caching location is automatically
created in a non interactive session instead of using a temporary
location. In an interactive session, a user is still prompted for
permission.
o (1.99.0) An enviornment variable may be set system wide or user wide to
control the default caching location: BFC_CACHE. Note: do not use R
variables or command line export to set this variable. It must be set system
wide or user wide for reproducibility in future R sessions or else it must
be specified upon ever usage. It must be set before calling
library(BiocFileCache) to take effect.
o (1.99.0) Fixes partial argument matching error in SQL function SQLExecute
o (1.15.1) Added file locking for thread-safe SQL operations. Thanks for the PR @LTLA
BUG FIX
o (1.99.6) cleanbfc() incorrect format string; see
https://github.com/Bioconductor/BiocFileCache/issues/31
CHANGES IN VERSION 1.11
----------------------
BUG FIX
o (1.11.5) Update dplyr functions for dplyr_1.0.0 release
o (1.11.2) Fixes run of examples. Different result manual vs interactive so
have conditional that will allow complete example if run by user rather than
run automatically through the checks.
NEW FEATURES
o (1.11.1) Add makeCachedActiveBinding(). Allows data to be cached during
ActiveBinding call. Avoids callback function executing data retrieval
everytime.
o (1.11.3) Only asks for / reports use of temporary cache once per
session. https://github.com/Bioconductor/TENxBrainData/issues/7
CHANGES IN VERSION 1.7
----------------------
BUG FIX
o (1.7.10) Fix date comparison to use as.POSIXlt instead of as.Date. This
catches the rare edge case if a remote resource is updated twice in a day
and a download happened in between the two.
o (1.7.9) Make creation of database atomic commits
o (1.7.8) Make adding resource to database atomic commits
o (1.7.4) Limit where possible opening database in RW mode. Use read-only
mode whereever possible to avoid database locking
o (1.7.2) Fix bug in multi path addition through bfcadd/bfcrpaths. The
function was assuming all files had same rtype and action. Now can
vectorize
o (1.7.1) Fix man documentation example. Interactive vs non interactive
session
CHANGES IN VERSION 1.5
----------------------
NEW FEATURES
o (v. 1.5.1) Add 'exact = ' for exact matching in bfcquery(),
bfcrpath(). (v. 1.5.2) defaults to TRUE for bfcrpath()
BUG FIX
o (v. 1.5.2) bfcrpath() more robust when adding regular expression
rnames.
USER-VISIBLE CHANGES
o (v. 1.5.4) bfcpath() implementation change. Only displays rpath and can
work with multiple rids. bfcpath only for rpath access while bfcrpath is the
option to get or add.
CHANGES IN VERSION 1.3
----------------------
NEW FEATURES
o (v. 1.3.35) Save a post download processed file to cache.
o (v. 1.3.28) Add ask = TRUE argument to BiocFileCache().
o (v. 1.3.24) Add function makeBiocFileCacheFromDataFrame to
convert data.frame to BiocFileCache
o (v. 1.3.19) etag now checked in addition to last modified time to
determine if local version of file is current
o (v. 1.3.16) importbfc to load output of exportbfc
o (v. 1.3.15) exportbfc allows users to create exportable archive of bfc
related files
o (v. 1.3.11) bfcisrelative checks for rtype='local' in addition to relative
o (v. 1.3.11) Helper function to check rtype for local but
relative, and web and update if necessary
o (v. 1.3.10) Add function to check portability of BiocFileCache:
bfcisrelative
o (v. 1.3.10) Add function to convert rpaths for portability: bfcrelative
o (v. 1.3.9) Optionally download web resource when adding to cache
bfcadd(download=TRUE)
SCHEMA CHANGE
o (v. 1.3.36) expires added
o (v. 1.3.19) etag added
o (v. 1.3.9) Last modified time default is NA
USER-VISIBLE CHANGES
o (v. 1.3.38) ... argument exposed and pased to GET, this includes bfcadd
which original ... was pasesed to file.copy. This use of ... is used in bfc
functions bfcadd(), bfcupdate() and bfcdownload() which could potential
download the file.
o (v. 1.3.30) bfcnew(), bfcadd(), accept vector arguments;
performance improvements and
o (v. 1.3.25) bfcinfo and bfcquery will show full rpaths even if
stored as relative
o (v. 1.3.22) prompt user only once when using default cache
o (v. 1.3.17) prompt user when overwriting exisiting file
o (v. 1.3.16) add importbfc to extract output of exportbfc and
load bfc object
o (v. 1.3.16) added exportbfc to export bfc or subset of bfc
o (v. 1.3.16) bfcisportblae and bfcportbale removed for exportbfc
o (v. 1.3.14) upon bfc creation, option to update to most current schema
o (v. 1.3.13) bfcportable operates over all offending ids instead
of asking individually
o (v. 1.3.12) bfcisrelative/bfcrelative changed to
bfcisportbale/bfcportable
o (v. 1.3.11) web resource rpaths are stored as relative links
o (v. 1.3.9) If web resource was not downloaded, bfcneedsupdate is TRUE
o (v. 1.3.9) Local and non downloaded web will have last modified
time as NA
o (v. 1.3.6) Update how default cache location is determined
o (v. 1.3.1) Expose GET::config argument to web resource functions
BUG CORRECTION
o (v. 1.3.40) correct trycatch with cache_info. cache_info bug workaround
orginally output NA even if present, now manually grab values if present
o (v. 1.3.37) correct which functions update access_time
o (v. 1.3.26) patch for cache_info after returning etag and last_modified
o (v. 1.3.4) patch for cache_info bug
CHANGES IN VERSION 1.1
----------------------
NEW FEATURES
o (v. 1.1.7) bfcmeta() and friends allows arbitrary metadata on
records and ability to query bfcmeta data.
USER-VISIBLE CHANGES
o (v. 1.1.16) if httr::HEAD fails don't try httr::GET, just report not
available
o (v. 1.1.7) bfcquery() syntax changed to grep(), rather than SQL
'LIKE'.
o (v. 1.1.7) bfcquery() supports user-specified 'fields='.
o (v. 1.1.5) queryCount renamed to bfccount
o (v. 1.1.2) Add user specified extension to file in cache
o (v. 1.1.2) Use dbExecute/dbSendStatement rather than pasting query
o Files in cache retain basename and extension of original file
CHANGES IN VERSION 0.99.0
-------------------------
SIGNIFICANT NEW FEATURES
o First Bioconductor release.