alakazam
Immunoglobulin Clonal Lineage and Diversity Analysis
v1.4.2
·
Dec 15, 2025
·
AGPL-3
Description
Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>, Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
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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 'AminoAcids-Vignette.Rmd' using rmarkdown ! Package pdftex.def Error: File `d78ec05f7921cb6bfe19e213b65debc7ae30c211.pdf' not found: using draft setting. Error: processing vignette 'AminoAcids-Vignette.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/alakazam.Rcheck/vign_test/alakazam/vignettes/AminoAcids-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See AminoAcids-Vignette.log for more info. --- failed re-building 'AminoAcids-Vignette.Rmd' --- re-building 'Diversity-Vignette.Rmd' using rmarkdown ! Package pdftex.def Error: File `f3a1fa47197dbace2ee75fe1f172909219ffc617.pdf' not found: using draft setting. Error: processing vignette 'Diversity-Vignette.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/alakazam.Rcheck/vign_test/alakazam/vignettes/Diversity-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. S ...[truncated]... nettes/Fastq-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Fastq-Vignette.log for more info. --- failed re-building 'Fastq-Vignette.Rmd' --- re-building 'Files-Vignette.Rmd' using rmarkdown --- finished re-building 'Files-Vignette.Rmd' --- re-building 'GeneUsage-Vignette.Rmd' using rmarkdown ! Package pdftex.def Error: File `5222ff49d8b70fbf45e02aba0ea6e1afdc7d4b81.pdf' not found: using draft setting. Error: processing vignette 'GeneUsage-Vignette.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/alakazam.Rcheck/vign_test/alakazam/vignettes/GeneUsage-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See GeneUsage-Vignette.log for more info. --- failed re-building 'GeneUsage-Vignette.Rmd' SUMMARY: processing the following files failed: 'AminoAcids-Vignette.Rmd' 'Diversity-Vignette.Rmd' 'Fastq-Vignette.Rmd' 'GeneUsage-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
ERROR
r-oldrel-windows-x86_64
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'AminoAcids-Vignette.Rmd' using rmarkdown ! Package pdftex.def Error: File `d78ec05f7921cb6bfe19e213b65debc7ae30c211.pdf' not found: using draft setting. Error: processing vignette 'AminoAcids-Vign ...[truncated]... -- failed re-building 'GeneUsage-Vignette.Rmd' SUMMARY: processing the following files failed: 'AminoAcids-Vignette.Rmd' 'Diversity-Vignette.Rmd' 'Fastq-Vignette.Rmd' 'GeneUsage-Vignette.Rmd' Error: Vignette re-building failed. Execution halted
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
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1.4.2
Mar 10, 2026