smartsnp
Fast Multivariate Analyses of Big Genomic Data
v1.2.0
·
Jun 9, 2025
·
MIT + file LICENSE
Description
Fast computation of multivariate analyses of small (10s to 100s markers) to big (1000s to 100000s) genotype data. Runs Principal Component Analysis allowing for centering, z-score standardization and scaling for genetic drift, projection of ancient samples to modern genetic space and multivariate tests for differences in group location (Permutation-Based Multivariate Analysis of Variance) and dispersion (Permutation-Based Multivariate Analysis of Dispersion).
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CRAN Check Status
1
ERROR
13
OK
Show all 14 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-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | ERROR |
| 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 details (1 non-OK)
ERROR
r-oldrel-windows-x86_64
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'Converting_VCF_and_PLINK_formats.Rmd' using rmarkdown File figure/data_transformation_example_plot-1.png not found in resource path Error: processing vignette 'Converting_VCF_and_PLINK_formats.Rmd' failed with diagnostics: pandoc document conversion failed with error 99 --- failed re-building 'Converting_VCF_and_PLINK_formats.Rmd' --- re-building 'aDNA_smartpca_analysis.Rmd' using rmarkdown File figure/lazaridis_plot-1.png not found in resource path Error: processing vignette 'aDNA_smartpca_analysis.Rmd' failed with diagnostics: pandoc document conversion failed with error 99 --- failed re-building 'aDNA_smartpca_analysis.Rmd' --- re-building 'mallard_smartpca_analysis.Rmd' using rmarkdown File figure/pca_plot_mallard-1.png not found in resource path Error: processing vignette 'mallard_smartpca_analysis.Rmd' failed with diagnostics: pandoc document conversion failed with error 99 --- failed re-building 'mallard_smartpca_analysis.Rmd' SUMMARY: processing the following files failed: 'Converting_VCF_and_PLINK_formats.Rmd' 'aDNA_smartpca_analysis.Rmd' 'mallard_smartpca_analysis.Rmd' Error: Vignette re-building failed. Execution halted
Check History
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 10, 2026
ERROR
r-oldrel-windows-x86_64
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'Converting_VCF_and_PLINK_formats.Rmd' using rmarkdown File figure/data_transformation_example_plot-1.png not found in resource path Error: processing vignette 'Converting_VCF_and_PLINK_formats.Rmd' ...[truncated]... re-building 'mallard_smartpca_analysis.Rmd' SUMMARY: processing the following files failed: 'Converting_VCF_and_PLINK_formats.Rmd' 'aDNA_smartpca_analysis.Rmd' 'mallard_smartpca_analysis.Rmd' Error: Vignette re-building failed. Execution halted