NEWS
QuickBLAST 2026-07-13 (2026-07-13)
Updated:
- Preparing for Bioconductor submission
Added:
QuickBLAST 2026-07-11 (2026-07-11)
Updated:
- Reduced warnings entirely
- Moved CMakeLists.txt to tools/
- Moved compiled makeblastdb executable to bin/
- pragma to compile cloudflare-zlib and suppress warnings
Removed:
- install.libs.R - libs are copied in respective Makevars
- O3 optimization
QuickBLAST 2026-07-08 (2026-07-08)
Fixed:
- Parquet threads crashing vignettes on windows. Single thread enforced for parquet writers.
Updated:
- Vignette block for outputformats
- RccpThread::R* wherever necessary
Added:
- CSV and IPC output format support
- O3 optimization
QuickBLAST 2026-07-01 (2026-07-01)
Updated:
- Included CMake variables to prevent home folder usage for CRAN policy compliance.
QuickBLAST 2026-06-30 (2026-06-30)
Updated:
- [Windows] Fix for MakeBLASTDB()
- Checked for cross-platform builds using r-hub
- CRAN friendly build
QuickBLAST 2026-04-12 (2026-04-12)
Updated:
- CXX STD to CXX20
- Package directory structure
- Startup message moved to .OnAttach()
- manpages and vignettes
Added:
- Patch fix to arrow for timezone format with GCC > 14 and C++20
- QuickBLAST logo
Removed:
- Non-portable flags: -fPIC -O3 -Wall
- pkgdown site files
QuickBLAST 2026-04-09 (2026-04-09)
Updated:
- README
- vignettes
- R doc site
Fixed:
- roxygen //' tags
- File existence check for file BLAST
- Race conditions and corruptions in file BLAST when the no. of threads was greater than the input sequence count
- When return_values==F and writing to output file, return of empty record batch is not erroreous.
QuickBLAST 2026-04-08 (2026-04-08)
Updated:
- Static dependencies + Shared R library as imposed by the R package policy - Shared libs are not built and copied over anymore
- C std=gnu2x, CXX std=gnu++20
- [Windows] Using source built sqlite3 due to missing aux functions
- [Windows] Toolchain injection provides 40+ patches to compile ncbi-cxx-toolkit with Rtools45 toolchain
- Seperated *nix and Windows build flow using preprocessor directives and build vars
- BLAST_dbs() parallelization
- [Windows] OpenMP Support
Fixed:
- Windows build
- iconv for multi-UTF support & unbounded file mapping and finish of dangling file writer thread in arrow wrapper
Added:
- [Windows] Dependencies provided as external projects to be compiled by CMake
- multi-os memory mapping, parquet and csv format support to arrow wrapper
- Chunking of large sequences to support genome scale megablast - blast does not work for some reason
Removed:
- patchelf, R source compilation
QuickBLAST 2026-03-25 (2026-03-25)
Updated:
- Added optimal Visit() functions that uses the visitor pattern of Arrow to flatten arrow types to R lists
QuickBLAST 2026-03-13 (2026-03-13)
Updated:
- Considerable optimizations
- Attempt to set $ORIGIN through linker flags failed for ncbi-toolkit
- Tweaking windows build system for r-cran winbuilder
- Removing '-fdiagnostics-color=always'
- Clear verbosity
- shared lib trimming failed but stripping works
Added:
- Using boost headers for quick vector access in RecordBatch to R List conversion
- auto-joining safe_jthread implementation wherever necessary
- Support for genomes through sequence chunking
- Seperate stuct to simplify arrow container storage
QuickBLAST 2026-03-08 (2026-03-08)
Bug
- There is a known bug with RStudio due to libc++ library collisions between QuickBLAST and RStudio