CHANGES IN VERSION 3.13.0
-------------------------
BUG CORRECTION
o (3.13.1) merged @votti PR for not checking connection if localhub is selected
NEW FEATURES
o (3.13.2) Add auto clean of cache if corrupt index file
o (3.13.3) Add auto redownload once if resource is not loading in R, if localHub
is not selected and internet available.
CHANGES IN VERSION 3.11.0
-------------------------
BUG CORRECTION
o (3.11.4) Correct subsetting. Didn't account for multiple files associated
with single entry (ie. bam/bai).
CHANGES IN VERSION 3.9.0
-------------------------
NEW FEATURES
o (3.9.1) Remove the defunct `display` method for AnnotationHub.
o (3.9.1) Rename vignette from TroubleshootingTheCache to TroubleshootingTheHubs
CHANGES IN VERSION 3.7.0
-------------------------
NEW FEATURES
o (3.7.4) Suppress snapshot date unless interactive session
o (3.7.1) Add DispatchClass for keras model weights
DEPRECATED
o (3.7.2) Deprecate display in favor of BiocHubsShiny; see vignette
CHANGES IN VERSION 3.5.0
-------------------------
NEW FEATURES
o (3.5.2) Add dcf dispatchclass
o (3.5.1) Add CompDb dispatchclass
CHANGES IN VERSION 3.3.0
-------------------------
NEW FEATURES
o (3.3.6) Serialized S4 hub resources (AnnotationHub and ExperimentHub)
are now passed thru updateObject() at load-time
USER-VISIBLE MODIFICATIONS
o (3.3.8) Add instructions for creating a hub shared across multiple users
o (3.3.2) Remove TESTING option as only needed to expose devel orgdb
o (3.3.2) Change filter for orgdbs. orgdbs at release time will be stamped
with devel (to be release) and then manually have biocversion added for the
upcoming new devel. Filtering then based on biocversion number. This will
expose devel orgdbs as soon as generated
BUG CORRECTION
o (3.1.9) Fix broken test. Identical not appropriate. all present appropriate
CHANGES IN VERSION 3.1.0
-------------------------
MAJOR UPDATES
o (3.1.2) In accordance with the deprecated caching location, upgraded to
error/defunct from warning/deprecated in preparaion for removal of
dependency next release
USER-VISIBLE MODIFICATIONS
o (3.1.1) If there is a duplicate entry in the hub cache for a resource, hub
code will no longer produce an ERROR. If the duplicate resource was not
requested the duplicate is ignored. If the duplicate resource is requested,
produce a warning for corrupt cache and continue with first found entry.
o (3.1.3) Fix typo in message display
o (3.1.5) Deprecate the `display,Hub-method`
BUG CORRECTION
o (3.1.7) Fix ERROR message for out-dated orgDbs
CHANGES IN VERSION 2.99.0
-------------------------
MAJOR UPDATES
o (2.99.0) 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 (2.99.0) 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.
CHANGES IN VERSION 2.23.0
-------------------------
USER-VISIBLE MODIFICATIONS
o (2.23.2) Create a new all encompassing vignette that references both
ExpeirmentHub and AnnotationHub. Reference this one vignette in all four
related packages instead of trying to maintain multiple vigenttes that were
essentially the same. This also involves removing CreateAnAnnotationPackage
MODIFICATIONS
o (2.23.1) Fixed ERROR message to better indicate vignette troubleshooting
document and fixed reference in Troubleshooting vignette. These ERRORs are
triggered by both AnnotationHub and ExperimentHub so clarified the
Troubleshooting document is in AnnotationHub.
CHANGES IN VERSION 2.21.0
-------------------------
BUG FIX
o (2.21.5) Fix documentation for setting AnnotationHubOptions
o (2.21.3) Fix printing of proxy when present
USER-VISIBLE MODIFICATIONS
o (2.21.6) Make internet connection test less stringent
o (2.21.4) Add link to github for reporting issues
o (2.21.2) Update to reference hubs@bioconductor.org for help
o (2.21.1) Update .tidyGRanges to account for incorrect or missing genomes
CHANGES IN VERSION 2.19.0
-------------------------
BUG FIX
o (2.19.12) change has_internet to nslookup to avoid locations that do not
have access to google dns.
NEW FEATURES
o (2.19.8) Fixed messages to be more informative
o (2.19.8) trycatch around bfcneedsupdate/bfcdownload for sqlite database to
prevent error when internet is spotty and databse source cannot be checked
for a newer version.
o (2.19.4) trycatch around bfcneedsupdate call will prevent error when
internet is spotty and resource cannot be checked for a newer version.
o (2.19.3) New function removeResources for removing locally downloaded
cached resources. Nicer interface than using cache. Improved documentation
on use of setting a cache to NULL to also remove resources.
o (2.19.2) Adds option ask to constructor. Default: True. Ask will ask user
to create default AnnotationHub location and if in an non interactive
session utilize a temporary directory. If False, the default directory is
created and utilized without prompting.
USER-VISIBLE MODIFICATIONS
o (2.19.1) Improve ERROR message when resource isn't found. Also involved
updating RecordStatus function. If resource hasn't been completely removed
from database, gives when the resource was removed. If the resource is
available but after the snapshot date being utilized, specialized message.
CHANGES IN VERSION 2.17.0
-------------------------
NEW FEATURES
o (2.17.6) remove debugging message of loading resource (`AH: 1`)
o (2.17.5) system environment variable to control localHub option for
creating hub based only on previously downloaded resources
o (2.17.9) Allow force redownload of Hub sqlite file with refreshHub
o (2.17.12) Only display download message when something to download.
o (2.17.13) The output list of files is the AH/EH id not AHid:resourceid
BUG FIXES
o (2.17.4) Fix localHub when no internet connection. The internal use of
isDevel was preventing Hub creation when no internet connection. Fixed by
checking connection. This code pretained to orgDb filters
o (2.17.8) On chance of very first download of hub failure, next call to
construtor will redownload
o (2.17.10) Fix ability to use hubs when offline
o (2.17.11) Add BiocVersion to Imports. Fixes bug with R CMD check when
testing if library can be loaded off search path. BiocManager doesn't Import
BiocVersions and this is needed to get the correct BiocManager version of
the snapshot date.
CHANGES IN VERSION 2.15.0
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o (2.15.9) The Hubs have been updated to use BiocFileCache as a backend
utility for managing and downloading resources. This allows for file
specific caching mechanism. This change is a significant user change as it
changed the default directories for the Hubs (AnnotationHub/ExperimentHub)
as well as the base directory no longer being hidden.
NEW FEATURES
o (2.15.15) Added BamFile Resource method
o (2.15.9) Add helper function to get additional information on
resources. getInfoOnIds
o (2.15.2) Add function to list currently available DispatchClass
USER-VISIBLE MODIFICATIONS
o (2.15.3) Bioconductor will no longer accept random, Individual resources
without an accompanied package.
o (2.15.4) We also encourage the use of AnnotationHub rather than very
large annotation packages. We added sections for users wishing to convert
existing packages to use AnnotationHub as well.
o (2.15.7) There were substantial updates to Rsamtools. Rsamtools no longer
supports razip files. These files have been removed from the hub and
vignette updated to use the twobit and gff files
BUG FIXES
o (2.15.5) Fixed bug. If resources are removed from the hub, this should
only be reflected in the devel branch but still be available in release
branch. The filter for exposed resources was refined to respect
datadateremoved
CHANGES IN VERSION 2.12.0
-------------------------
MODIFICATIONS
o Updated code from BiocInstaller to BiocManager
CHANGES IN VERSION 2.12.0
-------------------------
BUG FIXES
o Prompt for permission when downloading many (more than
AnnotationHubOption("MAX_DOWNLOADS")) resources.
MODIFICATIONS
o Moved readMetadataFromCsv back to AnnotationHubData.
o Use AnnotationHubData::makeAnnotationHubMetadata to validate metadata.csv
CHANGES IN VERSION 2.10.0
------------------------
NEW FEATURES
o AnnotationHub will now work offline utilizing argument 'localHub'; will
also use this option automatically if no internet connection is detected.
o Added new GDSResource class
o Added documentation for creating an AnnotationHub package
MODIFICATIONS
o Modified tags vector when passed to display to improve speed of display
querying
o Moved readMetadataFromCsv from AnnotationHubData.
o Removed listResources and loadResource from AnnotationHub; not implemented
and only valid in ExperimentHub
BUG FIXES
o Expose snapshot less than or equal to release date
o Force rebuild of index if index file corrput or out of date
CHANGES IN VERSION 2.8.0
------------------------
NEW FEATURES
o add .get1,RDSResource-method
o add RdsResource class
o add EnsDb dispatch class
o expose rdatapath in metadata
MODIFICATIONS
o modify records exposed as metadata
- expose records added <= snapshot date
- expose a single OrgDb per organism per BioC version
o edits to .get1,GenomicScores-method and .get1,GenomicScoresResource-method
o work on biocVersion and snapshotDate relationship:
- snapshotDate() must be <= biocVersion() release date
- possibleDates() are now filtered by snapshotDate()
o remove GenomicScoresResource; Robert Castelo will handle loading these
resources in his GenomicScores software package
o Changed show method for hub object
- removed sourcelastmodifieddate
- added rdatadateadded
BUG FIXES
o fix bug in ordering of output from .uid0()
o fix bugs in 'snapshotDate<-' method
CHANGES IN VERSION 2.6.0
------------------------
NEW FEATURES
o add vignette section on sharing resources on clusters
o add 'preparerclass' to index.rda to allow search by package name for
ExperimentHub objects
o add GenomicScoresResource class for Robert Castelo
MODIFICATIONS
o return 'tags' metadata as list instead of comma-separated character
vector
o move AnnotationHubRecipes vignette to AnnotationHubData
o move listResources() and loadResources() from ExperimentHub
o expose additional fields in .DB_RESOURCE_FIELDS()
o modify cache path to avoid creating a '~' directory on Mac
o use https: NCBI rul in documentation
o modify .get1,EpiExpressionTextResource-method to use 'gene_id'
column as row names
CHANGES IN VERSION 2.4.0
------------------------
NEW FEATURES
o add new status codes '4' and '5' to 'statuses' mysql table;
change 'status_id' field to '4' for all removed records to date
o add getRecordStatus() generic
o add package() generic
o create 'Hub' VIRTUAL class
- add new .Hub() base constructor for all hubs
- add getAnnotationHubOption() and setAnnotationHubOption()
- promote cache() to generic
- add getHub() getter for AnnotationHubResource class
- add getUrl(), getCache(), getDate() getters
- export as few db helpers as possible
o add 'EpigenomeRoadmapNarrowAllPeaks' and
'EpigenomeRoadmapNarrowFDR' classes
MODIFICATIONS
o distinguish between broad and narrow peak files in
EpigenomeRoadmapFileResource dispatch class
o don't use cache for AnnotationHub SQLite connection
- originally introduced so could be closed if needed, but
creates complexity
- instead, open / close connection around individual queries (not a
performance concern)
- expose hub, cache, proxy in AnnotationHub constructor
- document dbconn,Hub-method, dbfile,Hub-method, .db_close
o snapshotDate now uses timestamp (last date any row was modified) instead
of rdatadateadded
o .require fails rather than emits warning
- unit test on .require()
- also, cache(hub[FALSE]) does not create spurious error
o work on removed records and biocVersion
- .uid0() was reorganized and no longer groups by record_id
- metadata is returned for records with
biocversion field <= current biocVersion
instead of an exact match with the current version
- metadata is not returned for removed records
BUG FIXES
o Work around httr() progress() bug by disabling progress bar
CHANGES IN VERSION 2.2.0
------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o seqinfo(GRanges) for all genomes supported by GenomeInfoDb now
contain seqlengths.
CHANGES IN VERSION 2.1.21
--------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o fileName() returns the cache path on the disk for a file that
has been cached and NA for files which have not been cached.
o The error message (when file is not downloaded from the hub)
displays the AnnotationHub name, title, and reason for failure.
CHANGES IN VERSION 2.1
----------------------
NEW FEATURES
o as.list() splits AnnotationHub instances into a list of
instances, each with a single record. c() concatenates hubs.
BUG FIXES
o cache<- now behaves as documented, e.g., removing the cached
version of the file.
CHANGES IN VERSION 2.0.0
------------------------
NEW FEATURES
o AnnotationHub is all new. We basically rewrote the entire thing.
o The back end is new (new database, new way of tracking/routing
data etc.)
o The front end is new (new AnnotationHub object, new methods, new
behaviors, new ways of finding and downloading data)
o The metadata has also been cleaned up and made more
consistent/searchable
o The recipes that are used to populate these data have also been
cleaned up.
o There is also a new vignette to explain how to use the new
AnnotationHub in detail
IMPROVEMENTS SINCE LAST TIME
o The old way of finding data (an enormous tree of paths), was not
really scalable to the amount of data we have to provide access
to. So we junked it. Now you have a number of better methods to
allow you to search for terms instead.
o The new hub interface can be searched using a new display
method, but it can *also* be searched entirely from the command
line. This allows you to use it in examples and scripts in a way
that is friendlier for reproducible research.
o For users who want to contribute valuable new annotation
resources to the AnnotationHub, it is now possible to write a
recipe and test that it works for yourself. Then once you are
happy with it, you can contact us and we can add data to the
AnnotationHub.