fenr 1.7.2

• Stopped using cache in tests, as it might lead to failures in case of a corrupted cache.

fenr 1.7.1

• Fixed argument "on_error" is missing, with no default error in fetch_wiki().

fenr 1.5.2

• Added evidence code column to GO-term mapping table. It can be used to filter mapping based on their quality. See https://geneontology.org/docs/guide-go-evidence-codes for explanation.

fenr 1.5.1

• Attempted to fix a bizarre error message on Bioconductor's test machines with older version of MacOS. Windows and Linux are not affected; my laptop running Sequoia 5.2 does not show show errors. I suspect a memory leak in older systems. The error vector memory limit of 64.0 Gb reached, see mem.maxVSize() happened in the function parse_kegg_genes(), a flat-file parser for KEGG. It occurred around the call tidyr::separate(), which I replaced with an alternative approach. Will see if the error is fixed.

fenr 1.3.1

• Go term namespace added to the information extracted by fetch_go.

fenr 1.1.11

• Fixing a mixup in the vignette (mixed up old and new versions - don't ask how).

fenr 1.1.10

• Changed the way assert_url_path() handles some remote files - it turns out every time it was called, the entire file was unnecessary downloaded, leading to duplication. Now we only assert top directories. Should speed things up!
• Increased default timeout to 30 s.
• Due to recurring issues with build and check on Bioconductor's machines, I have removed all database downloads from the vignette. Any glitch in the GO server, or simply an internet problem would cause the vignette build to crash. The GO-term information is now attached as data and loaded in the vignette.
• Made sure the package passes BUILD and CHECK with no internet connection.
• Correction in vignette: using yeast genome for topGO, instead of human (somehow it was not applied in 1.0.5).

fenr 1.1.8

• Further improvements to error handling with unresponsive servers

fenr 1.1.7

• Improved error handling with unresponsive servers

fenr 1.1.6

• Changed the Ensembl mapping file downloaded from Reactome to "Physical entity" mapping, as it contains gene symbols, in addition to the Ensembl IDs.
• Changed the name of GAF column DB Object Synonym from gene_synonym to gene_id for consistency with other methods.
• Changed Ensembl column ensembl_gene_id to gene_id for consistency.
• Corrected Reactome test as it failed with multiple gene symbols per gene id.
• Replaced biomaRt with a single RESTful XML call; as biomaRt is used only once to obtain GO terms, this replacement reduced dependency footprint of the package