NEWS

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OmnipathR 4.1.3

Technical

• Downloads from rest.uniprot.org use HTTP/1.1. Over HTTP/2, UniProt sometimes resets slow transfers, and the download fails with "HTTP/2 stream 1 was not closed cleanly". The new option omnipathr.http1_hosts lists the hosts that use HTTP/1.1
• UniProt queries (all_uniprots and the functions built on it): on build servers, if UniProt fails, they give a warning and an empty table, and skip UniProt for the rest of the session
• Faster examples on build servers: kinasephos and the deprecated NicheNet network functions do not download in the checks of OmnipathR

OmnipathR 4.1.2

Deprecated

• The NicheNet functions (nichenet_*) are deprecated, and the NicheNet vignette is removed. A new version will retrieve the NicheNet prior knowledge built by the OmniPath server. The resource clients written for NicheNet (e.g. EVEX, Harmonizome, ReMap) stay
• static_table and static_tables are deprecated. The regular query functions try the plain HTTP server if the HTTPS server fails
• The packages mlrMBO, parallelMap, ParamHelpers and smoof are not in Suggests any more. nichenet_optimization asks for them if they are not installed

Bug fixes

• static_table: works again for interaction tables. Before, it stopped with "argument is of length zero" in unnest_evidences
• Slow functions return their full result when another package calls them on a build server. Before, they returned NULL in the checks of dependent packages, such as wppi

Technical

• The downloader accepts fallback URLs (mirrors). Each round of attempts tries all URLs once, then the next round starts after a short wait
• HTTP errors: the log shows the status, the final URL and the response headers. After HTTP 429 or 503, the wait follows the Retry-After header, but it is never longer than the new option omnipathr.retry_downloads_max_wait (30 s)
• biomart_query: tries the US East and Asia mirrors of Ensembl if the main site fails. On build servers, if all mirrors fail, it gives a warning and an empty table, and skips Ensembl for the rest of the session

OmnipathR 4.1.1

Bug fixes

• KEGG: the organism list comes from the list/genome endpoint, because list/organism returns 400
• oma_organisms: reads the new OMA header, and downloads the table again when the cached copy is malformed
• subnetwork: selects the vertices with igraph::V()
• omnipath_cache_remove: with max_age or min_age, it removes only the matching versions. Before, it removed all versions when status was not given
• resources: the category filter works again

Technical

• resources: downloads with retries, and keeps the list in the cache for one hour at most
• The environment variable OMNIPATHR_BUILDSERVER marks a build server
• Vignettes build when a third-party server does not answer; the chunk shows the error
• Tests of the live web service do not run on Bioconductor build machines
• Runnable examples for 32 more manual pages
• CITATION file in ASCII

OmnipathR 4.0.0

Features

• ID translation ambiguity analysis
• KEGG REST API client
• New metabolomics resources: HMDB, RaMP, Chalmers Sysbio GEMs, STITCH,
• Metabolite-protein interactions from MetalinksDB
• Metabolite ID translation using RaMP and HMDB data

Technical

• Rewritten and improved parameter processing for OmniPath queries
• Rewritten downloaders based on curl and httr2
• Fine control over curl handlers
• Detailed log messages about HTTP requests
• Diagnostic log messages: session info, libraries, versions, platform info, curl options, HTTP timings, headers
• Option to include curl debug log in the log file
• Robust TCP keep-alive parameters that hopefully fix rest.uniprot.org dowloads

OmnipathR 3.2.0

• New resource: PrePPI
• Configuration option to completely disable logging to file
• New vignettes: Path reconstruction, and Bioconductor 2021 Workshop
• Many minor bugfixes and improvements

OmnipathR 2.99.19

• NicheNet pipeline works
• Fixed an error which resulted value 1 in the n_references columns even for records without references

OmnipathR 2.99.17

• Improved quality filtering of intercell networks

OmnipathR 2.99.16

• Improved API for translate_ids
• Quality filtering of intercell networks

OmnipathR 2.99.13

• Functions to access KEGG Pathways
• More robust access to UniProt (in case of network failures)

OmnipathR 2.99.11

• Improved downloader backends

OmnipathR 2.99.8

• OBO parser
• Gene Ontology access, functions to work with ontology trees
• Database manager

OmnipathR 2.99.7

• New interactions query parameter: loops
• Fixed many caching bugs

OmnipathR 2.99.6

• All downloaders attempt 3 times
• New resources: Human Phenotype Ontology and Gene Ontology annotations

OmnipathR 2.99.0 (2021-03-08)

• Many new resources besides OmniPath: BioPlex, ConsensusPathDB, EVEX, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, InWeb InBioMap, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011
• Methods for converting network elements to Bio Model Analyzer (BMA) motifs
• NicheNet workflow
• Some igraph related methods: finding all paths up to certain length; extracting the giant component of a graph
• Caching
• Logging
• Configuration handling

OmnipathR 1.99.0 (2020-10-03)

• New tests
• Many little bugfixes
• Updated package metadata
• Preparation for Bioconductor 3.12

OmnipathR 1.3.4 (2020-08-04)

• License and password handling
• Can be directed to different server by options

OmnipathR 1.3.1 (2020-06-05)

• Addition of the package website.
• Modification of the pdf vignette for an html one.
• Major refactoring of functions.
• Addition of the intercellular network function.
• Modification for the intercellular categories.

OmnipathR 1.1.4 (2020-03-28)

• Refactored the import_annotations method

OmnipathR 0.99.12 (2019-10-10)

• Modification in the separation between genes within a complex (from dash to underscore)

OmnipathR 0.99.0 (2019-10-10)

• Submitted to Bioconductor