- Added early dependency checks for pwalign in functions that use pairwise alignment. If certain dependency conditions can't be met, the error is raised immediately, preventing unnecessary computation (#26).
- Replaced rjson with jsonlite to maintain compatibility with R < 4.4.0. The recent rjson update (v0.2.22 , 2024-08-20) requires R (>= 4.4.0), which would break builds on r-oldrel (#28).
-
Since Bioconductor 3.19 and Biostrings 2.72.0, the pairwise sequence alignment facilities have been moved from Biostrings into the pwalign package. For maximum compatibility, we now detect the installed Biostrings version at runtime and decide which package to use for pairwise alignment, without introducing pwalign as an additional hard dependency.
When calling
calcTwoProtSeqSim()andcalcParProtSeqSim(), if users have Biostrings >= 2.72.0 installed while pwalign is not installed, expect to see an explicit error in the results saying that pwalign is required and should be installed from Bioconductor.
- Replaced RCurl with httr2 and curl for retrieving molecular and sequence data from web APIs. Updated the outdated API endpoint URLs for DrugBank and RCSB PDB (#18).
inst/CITATIONnow usesbibentry()to replacecitEntry()(#19).- Fixed check notes on lost braces when running
R CMD checkunder R 4.4.x (#21).
- Migrate rcdk to a runtime soft dependency using rlang, to avoid build time issues.
- Migrate unit tests from using RUnit to testthat.
- Use GitHub Actions workflows for
R CMD checkand building the pkgdown website. - Fix URLs that are broken or moved in the documentation.
- Updated the endpoint URL of UniProt API to fix access issues (#14).
- Remove the
Enhancesfield inDESCRIPTIONto improve clarity.
- Fixed a build error on macOS in the
develbranch due to dependencies not available.
- Removed AppVeyor CI due to the frequent Bioconductor installation and dependency issues which are not related to the package itself.
- Updated GitHub repository links due to the recent handle change.
- Updated the vignette style.
- Fixed the issues in
calcTwoProtGOSim()andcalcParProtGOSim()to use the latest GOSemSim API for computing GO based semantic similarity.
- Fixed API endpoints that are not working due to their changes across time (#5).
- Fixed the vignette example for QSRR study (#6).
- Reformat vignette code with tidyverse style.
- Further remove all words related to the previous installation method per Bioconductor's request.
- Use the new
BiocManagerfor installation instructions.
- Resolved a critical bug due to improper
ifelseconditioning for the distribution descriptor in CTD.
- Fixed the ALOGP unit test to make it work under the recently updated CDK
- Added more unit tests for molecular descriptor calculation to improve code coverage
- Added Travis CI for continuous integration under Linux
- Added Appveyor for continuous integration under Windows
- Migrated from Sweave-based PDF vignette to knitr-based HTML vignette
- Better code formatting
- Minor fixes in function documentation and vignette
- Fixed some
R CMD checkerrors - ChemmineOB related fixes
- Fixed all drug molecule downloading utilities
- Fixed known problems in
extractProtfunctions - Fixed some build and dependency related problems
- Fixed some functions for downloading drug/chemical structures, such as
getMolFromPubChem()andgetMolFromChEMBL(). - General code style and documentation improvements
- Added the profile-based representation for proteins derived by PSSM
- Added a vignette which grouped similar functions into the same category. See vignette('Rcpi-quickref') . This makes the package structure clearer and enhances its usability.
- Other documentation improvements
- Initial release