NEWS

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AnnotationHub 3.13.0

BUG CORRECTION

• (3.13.1) merged @votti PR for not checking connection if localhub is selected

NEW FEATURES

• (3.13.2) Add auto clean of cache if corrupt index file
• (3.13.3) Add auto redownload once if resource is not loading in R, if localHub is not selected and internet available.

AnnotationHub 3.11.0

BUG CORRECTION

• (3.11.4) Correct subsetting. Didn't account for multiple files associated with single entry (ie. bam/bai).

AnnotationHub 3.9.0

NEW FEATURES

• (3.9.1) Remove the defunct 'display' method for AnnotationHub.
• (3.9.1) Rename vignette from TroubleshootingTheCache to TroubleshootingTheHubs

AnnotationHub 3.7.0

NEW FEATURES

• (3.7.4) Suppress snapshot date unless interactive session
• (3.7.1) Add DispatchClass for keras model weights

DEPRECATED

• (3.7.2) Deprecate display in favor of BiocHubsShiny; see vignette

AnnotationHub 3.5.0

NEW FEATURES

• (3.5.2) Add dcf dispatchclass
• (3.5.1) Add CompDb dispatchclass

AnnotationHub 3.3.0

NEW FEATURES

• (3.3.6) Serialized S4 hub resources (AnnotationHub and ExperimentHub) are now passed thru updateObject() at load-time

USER-VISIBLE MODIFICATIONS

• (3.3.8) Add instructions for creating a hub shared across multiple users
• (3.3.2) Remove TESTING option as only needed to expose devel orgdb
• (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

• (3.1.9) Fix broken test. Identical not appropriate. all present appropriate

AnnotationHub 3.1.0

MAJOR UPDATES

• (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

• (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.
• (3.1.3) Fix typo in message display
• (3.1.5) Deprecate the 'display,Hub-method'

BUG CORRECTION

• (3.1.7) Fix ERROR message for out-dated orgDbs

AnnotationHub 2.99.0

MAJOR UPDATES

• (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.
• (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.

AnnotationHub 2.23.0

USER-VISIBLE MODIFICATIONS

• (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

• (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.

AnnotationHub 2.21.0

BUG FIX

• (2.21.5) Fix documentation for setting AnnotationHubOptions
• (2.21.3) Fix printing of proxy when present

USER-VISIBLE MODIFICATIONS

• (2.21.6) Make internet connection test less stringent
• (2.21.4) Add link to github for reporting issues
• (2.21.2) Update to reference [email protected] for help
• (2.21.1) Update .tidyGRanges to account for incorrect or missing genomes

AnnotationHub 2.19.0

BUG FIX

• (2.19.12) change has_internet to nslookup to avoid locations that do not have access to google dns.

NEW FEATURES

• (2.19.8) Fixed messages to be more informative
• (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.
• (2.19.4) trycatch around bfcneedsupdate call will prevent error when internet is spotty and resource cannot be checked for a newer version.
• (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.
• (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

• (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.

AnnotationHub 2.17.0

NEW FEATURES

• (2.17.6) remove debugging message of loading resource ('AH: 1')
• (2.17.5) system environment variable to control localHub option for creating hub based only on previously downloaded resources
• (2.17.9) Allow force redownload of Hub sqlite file with refreshHub
• (2.17.12) Only display download message when something to download.
• (2.17.13) The output list of files is the AH/EH id not AHid:resourceid

BUG FIXES

• (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
• (2.17.8) On chance of very first download of hub failure, next call to construtor will redownload
• (2.17.10) Fix ability to use hubs when offline
• (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.

AnnotationHub 2.15.0

SIGNIFICANT USER-VISIBLE CHANGES

• (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

• (2.15.15) Added BamFile Resource method
• (2.15.9) Add helper function to get additional information on resources. getInfoOnIds
• (2.15.2) Add function to list currently available DispatchClass

USER-VISIBLE MODIFICATIONS

• (2.15.3) Bioconductor will no longer accept random, Individual resources without an accompanied package.
• (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.
• (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

• (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

AnnotationHub 2.12.0

MODIFICATIONS

• Updated code from BiocInstaller to BiocManager
• Moved readMetadataFromCsv back to AnnotationHubData.
• Use AnnotationHubData::makeAnnotationHubMetadata to validate metadata.csv

BUG FIXES

• Prompt for permission when downloading many (more than AnnotationHubOption("MAX_DOWNLOADS")) resources.

AnnotationHub 2.10.0

NEW FEATURES

• AnnotationHub will now work offline utilizing argument 'localHub'; will also use this option automatically if no internet connection is detected.
• Added new GDSResource class
• Added documentation for creating an AnnotationHub package

MODIFICATIONS

• Modified tags vector when passed to display to improve speed of display querying
• Moved readMetadataFromCsv from AnnotationHubData.
• Removed listResources and loadResource from AnnotationHub; not implemented and only valid in ExperimentHub

BUG FIXES

• Expose snapshot less than or equal to release date
• Force rebuild of index if index file corrput or out of date

AnnotationHub 2.8.0

NEW FEATURES

• add .get1,RDSResource-method
• add RdsResource class
• add EnsDb dispatch class
• expose rdatapath in metadata

MODIFICATIONS

• modify records exposed as metadata - expose records added <= snapshot date - expose a single OrgDb per organism per BioC version
• edits to .get1,GenomicScores-method and .get1,GenomicScoresResource-method
• work on biocVersion and snapshotDate relationship: - snapshotDate() must be <= biocVersion() release date - possibleDates() are now filtered by snapshotDate()
• remove GenomicScoresResource; Robert Castelo will handle loading these resources in his GenomicScores software package
• Changed show method for hub object - removed sourcelastmodifieddate - added rdatadateadded

BUG FIXES

• fix bug in ordering of output from .uid0()
• fix bugs in 'snapshotDate<-' method

AnnotationHub 2.6.0

NEW FEATURES

• add vignette section on sharing resources on clusters
• add 'preparerclass' to index.rda to allow search by package name for ExperimentHub objects
• add GenomicScoresResource class for Robert Castelo

MODIFICATIONS

• return 'tags' metadata as list instead of comma-separated character vector
• move AnnotationHubRecipes vignette to AnnotationHubData
• move listResources() and loadResources() from ExperimentHub
• expose additional fields in .DB_RESOURCE_FIELDS()
• modify cache path to avoid creating a '~' directory on Mac
• use https: NCBI rul in documentation
• modify .get1,EpiExpressionTextResource-method to use 'gene_id' column as row names

AnnotationHub 2.4.0

NEW FEATURES

• add new status codes '4' and '5' to 'statuses' mysql table; change 'status_id' field to '4' for all removed records to date
• add getRecordStatus() generic
• add package() generic
• 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
• add 'EpigenomeRoadmapNarrowAllPeaks' and 'EpigenomeRoadmapNarrowFDR' classes

MODIFICATIONS

• distinguish between broad and narrow peak files in EpigenomeRoadmapFileResource dispatch class
• 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
• snapshotDate now uses timestamp (last date any row was modified) instead of rdatadateadded
• .require fails rather than emits warning - unit test on .require() - also, cache(hub[FALSE]) does not create spurious error
• 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

• Work around httr() progress() bug by disabling progress bar

AnnotationHub 2.2.0

SIGNIFICANT USER-VISIBLE CHANGES

• seqinfo(GRanges) for all genomes supported by GenomeInfoDb now contain seqlengths.

AnnotationHub 2.1.21

SIGNIFICANT USER-VISIBLE CHANGES

• fileName() returns the cache path on the disk for a file that has been cached and NA for files which have not been cached.
• The error message (when file is not downloaded from the hub) displays the AnnotationHub name, title, and reason for failure.

AnnotationHub 2.1

NEW FEATURES

• as.list() splits AnnotationHub instances into a list of instances, each with a single record. c() concatenates hubs.

BUG FIXES

• cache<- now behaves as documented, e.g., removing the cached version of the file.

AnnotationHub 2.0.0

NEW FEATURES

• AnnotationHub is all new. We basically rewrote the entire thing.
• The back end is new (new database, new way of tracking/routing data etc.)
• The front end is new (new AnnotationHub object, new methods, new behaviors, new ways of finding and downloading data)
• The metadata has also been cleaned up and made more consistent/searchable
• The recipes that are used to populate these data have also been cleaned up.
• There is also a new vignette to explain how to use the new AnnotationHub in detail

IMPROVEMENTS SINCE LAST TIME

• 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.
• 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.
• 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.