NEWS

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BiocFileCache 2.11

BUG FIX

• (2.11.1) Merge PR to fix dbplyr compatibility issue

BiocFileCache 2.9

USER VISIBLE CHANGE

• (2.9.1) Add documentation for operating behind a proxy

BiocFileCache 2.7

USER VISIBLE CHANGE

• (2.7.1) Remove rappdirs officially from package after deprecating functionality and moving to using default R tools caching location.

BUG FIX

• (2.7.2) Fix mismatch of arguments from function to generic for bfcupdate

BiocFileCache 2.5

ENHANCEMENT

• (2.5.2) Add option to override unique identifer when adding files to the cache. This will allow exact match of original file name.

BUG FIX

• (2.5.1) ERROR if interactively decide not to removebfc

BiocFileCache 2.3

ENHANCEMENT

• (2.3.4) Add instructions for a shared cache across multiple users of a system
• (2.3.2) Add direct SQL calls for certain retrieval functions to speed up access time. This will speed up the bfcquery function as well as any function tha utilized the underlying .sql_get_field, .get_all_rids or .get_all_web_rids.
• (2.3.1) Add @LTLA solution for making bfcrpath thread safe

BiocFileCache 2.1

MAJOR UPDATES

• (2.1.1) Change caching location warning/deprecation to an ERROR in preparation for removal of dependency next release.

BiocFileCache 1.99

MAJOR UPDATES

• (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.
• (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.
• (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.
• (1.99.0) Fixes partial argument matching error in SQL function SQLExecute
• (1.15.1) Added file locking for thread-safe SQL operations. Thanks for the PR @LTLA

BUG FIX

• (1.99.6) cleanbfc() incorrect format string; see https://github.com/Bioconductor/BiocFileCache/issues/31

BiocFileCache 1.11

BUG FIX

• (1.11.5) Update dplyr functions for dplyr_1.0.0 release
• (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

• (1.11.1) Add makeCachedActiveBinding(). Allows data to be cached during ActiveBinding call. Avoids callback function executing data retrieval everytime.
• (1.11.3) Only asks for / reports use of temporary cache once per session. https://github.com/Bioconductor/TENxBrainData/issues/7

BiocFileCache 1.7

BUG FIX

• (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.
• (1.7.9) Make creation of database atomic commits
• (1.7.8) Make adding resource to database atomic commits
• (1.7.4) Limit where possible opening database in RW mode. Use read-only mode whereever possible to avoid database locking
• (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
• (1.7.1) Fix man documentation example. Interactive vs non interactive session

BiocFileCache 1.5

NEW FEATURES

• (v. 1.5.1) Add 'exact = ' for exact matching in bfcquery(), bfcrpath(). (v. 1.5.2) defaults to TRUE for bfcrpath()

BUG FIX

• (v. 1.5.2) bfcrpath() more robust when adding regular expression rnames.

USER-VISIBLE CHANGES

• (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.

BiocFileCache 1.3

NEW FEATURES

• (v. 1.3.35) Save a post download processed file to cache.
• (v. 1.3.28) Add ask = TRUE argument to BiocFileCache().
• (v. 1.3.24) Add function makeBiocFileCacheFromDataFrame to convert data.frame to BiocFileCache
• (v. 1.3.19) etag now checked in addition to last modified time to determine if local version of file is current
• (v. 1.3.16) importbfc to load output of exportbfc
• (v. 1.3.15) exportbfc allows users to create exportable archive of bfc related files
• (v. 1.3.11) bfcisrelative checks for rtype='local' in addition to relative
• (v. 1.3.11) Helper function to check rtype for local but relative, and web and update if necessary
• (v. 1.3.10) Add function to check portability of BiocFileCache: bfcisrelative
• (v. 1.3.10) Add function to convert rpaths for portability: bfcrelative
• (v. 1.3.9) Optionally download web resource when adding to cache bfcadd(download=TRUE)

SCHEMA CHANGE

• (v. 1.3.36) expires added
• (v. 1.3.19) etag added
• (v. 1.3.9) Last modified time default is NA

USER-VISIBLE CHANGES

• (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.
• (v. 1.3.30) bfcnew(), bfcadd(), accept vector arguments; performance improvements and
• (v. 1.3.25) bfcinfo and bfcquery will show full rpaths even if stored as relative
• (v. 1.3.22) prompt user only once when using default cache
• (v. 1.3.17) prompt user when overwriting exisiting file
• (v. 1.3.16) add importbfc to extract output of exportbfc and load bfc object
• (v. 1.3.16) added exportbfc to export bfc or subset of bfc
• (v. 1.3.16) bfcisportblae and bfcportbale removed for exportbfc
• (v. 1.3.14) upon bfc creation, option to update to most current schema
• (v. 1.3.13) bfcportable operates over all offending ids instead of asking individually
• (v. 1.3.12) bfcisrelative/bfcrelative changed to bfcisportbale/bfcportable
• (v. 1.3.11) web resource rpaths are stored as relative links
• (v. 1.3.9) If web resource was not downloaded, bfcneedsupdate is TRUE
• (v. 1.3.9) Local and non downloaded web will have last modified time as NA
• (v. 1.3.6) Update how default cache location is determined
• (v. 1.3.1) Expose GET::config argument to web resource functions

BUG CORRECTION

• (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
• (v. 1.3.37) correct which functions update access_time
• (v. 1.3.26) patch for cache_info after returning etag and last_modified
• (v. 1.3.4) patch for cache_info bug

BiocFileCache 1.1

NEW FEATURES

• (v. 1.1.7) bfcmeta() and friends allows arbitrary metadata on records and ability to query bfcmeta data.

USER-VISIBLE CHANGES

• (v. 1.1.16) if httr::HEAD fails don't try httr::GET, just report not available
• (v. 1.1.7) bfcquery() syntax changed to grep(), rather than SQL 'LIKE'.
• (v. 1.1.7) bfcquery() supports user-specified 'fields='.
• (v. 1.1.5) queryCount renamed to bfccount
• (v. 1.1.2) Add user specified extension to file in cache
• (v. 1.1.2) Use dbExecute/dbSendStatement rather than pasting query
• Files in cache retain basename and extension of original file

BiocFileCache 0.99.0

SIGNIFICANT NEW FEATURES

• First Bioconductor release.