variantspark
A 'Sparklyr' Extension for 'VariantSpark'
Description
This is a 'sparklyr' extension integrating 'VariantSpark' and R. 'VariantSpark' is a framework based on 'scala' and 'spark' to analyze genome datasets, see <https://bioinformatics.csiro.au/>. It was tested on datasets with 3000 samples each one containing 80 million features in either unsupervised clustering approaches and supervised applications, like classification and regression. The genome datasets are usually writing in VCF, a specific text file format used in bioinformatics for storing gene sequence variations. So, 'VariantSpark' is a great tool for genome research, because it is able to read VCF files, run analyses and return the output in a 'spark' data frame.
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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
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
package dependencies
Package required but not available: ‘sparklyr’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026
NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
LazyData
'LazyData' is specified without a 'data' directory
LazyData
'LazyData' is specified without a 'data' directory
LazyData
'LazyData' is specified without a 'data' directory
Code
Structure
Lines of code
117,517
Files
39
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
7
Internal functions
3
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
444.86
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
85.7%
\dontrun example ratio
85.7%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
No
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
100%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
Apache License 2.0 | file LICENSE
License flags
SPDX valid, not OSI
History
Versions
1
First release
2019-06-13
Latest release
2019-06-13
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.
Dependency Network
Version History
1 trackedR Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN Jun 13, 2019. Releases before tracking aren’t shown.