ssw
Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD
Description
Provides an R interface for 'SSW' (Striped Smith-Waterman) via its 'Python' binding 'ssw-py'. 'SSW' is a fast 'C' and 'C++' implementation of the Smith-Waterman algorithm for pairwise sequence alignment using Single-Instruction-Multiple-Data (SIMD) instructions. 'SSW' enhances the standard algorithm by efficiently returning alignment information and suboptimal alignment scores. The core 'SSW' library offers performance improvements for various bioinformatics tasks, including protein database searches, short-read alignments, primary and split-read mapping, structural variant detection, and read-overlap graph generation. These features make 'SSW' particularly useful for genomic applications. Zhao et al. (2013) <doi:10.1371/journal.pone.0082138> developed the original 'C' and 'C++' implementation.
Downloads
521
Last 30 days
7497th
1.6K
Last 90 days
6.3K
Last year
Trend: +0.8% (30d vs prior 30d)
0
Last 30 days
25
Last 90 days
86
Last year
Trend: -100% (30d vs prior 30d)
3
Last 7 days
12
Last 30 days
0
All-time
autoCRAN-only: this name is served only by autoCRAN, so the count is exact.
CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
WARNING 12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE Jun 8, 2026
whether the namespace can be loaded with stated dependencies
Fatal error: cannot create 'R_TempDir' A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file.
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
Code
Structure
Lines of code
909
Files
31
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
6
Internal functions
2
Recent export changes
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
100%
\dontrun example ratio
0%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
2
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2024-09-05
Latest release
2024-09-18
Avg cadence
13 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.