shazam
Immunoglobulin Somatic Hypermutation Analysis
Description
Provides a computational framework for analyzing mutations in immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection pressure, mutational load quantification, building of somatic hypermutation (SHM) models, and model-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>, Yaari, et al (2012) <doi:10.1093/nar/gks457>, Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>, Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
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CRAN Check Status
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)
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'Baseline-Vignette.Rmd' using rmarkdown ! Package pdftex.def Error: File `556c7eaa9a3ab01287e3a0b70c3386bee0834b50.pdf' not found: using draft setting. Error: processing vignette 'Baseline-Vignette.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/shazam.Rcheck/vign_test/shazam/vignettes/Baseline-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Baseline-Vignette.log for more info. --- failed re-building 'Baseline-Vignette.Rmd' --- re-building 'DistToNearest-Vignette.Rmd' using rmarkdown ! Package pdftex.def Error: File `41eda445787879f32745fdb66ae06b7346991b1f.pdf' not found: using draft setting. Error: processing vignette 'DistToNearest-Vignette.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/shazam.Rcheck/vign_test/shazam/vignettes/DistToNearest-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Dis ...[truncated]... D:/RCompile/CRANpkg/local/4.4/shazam.Rcheck/vign_test/shazam/vignettes/Shmulate-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Shmulate-Vignette.log for more info. --- failed re-building 'Shmulate-Vignette.Rmd' --- re-building 'Targeting-Vignette.Rmd' using rmarkdown ! Package pdftex.def Error: File `ef4fd8e251794645eb423393fe44db92634a95f9.pdf' not found: using draft setting. Error: processing vignette 'Targeting-Vignette.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/shazam.Rcheck/vign_test/shazam/vignettes/Targeting-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Targeting-Vignette.log for more info. --- failed re-building 'Targeting-Vignette.Rmd' SUMMARY: processing the following files failed: 'Baseline-Vignette.Rmd' 'DistToNearest-Vignette.Rmd' 'Mutation-Vignette.Rmd' 'Shmulate-Vignette.Rmd' 'Targeting-Vignette.Rmd' Error: Vignette re-building failed. Execution halted
Check History
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 30, 2026
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'Baseline-Vignette.Rmd' using rmarkdown ! Package pdftex.def Error: File `556c7eaa9a3ab01287e3a0b70c3386bee0834b50.pdf' not found: using draft setting. Error: processing vignette 'Baseline-Vignette ...[truncated]... g-Vignette.Rmd' SUMMARY: processing the following files failed: 'Baseline-Vignette.Rmd' 'DistToNearest-Vignette.Rmd' 'Mutation-Vignette.Rmd' 'Shmulate-Vignette.Rmd' 'Targeting-Vignette.Rmd' Error: Vignette re-building failed. Execution halted