scaper
Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation
v0.2.0
·
Apr 16, 2025
·
GPL (>= 2)
Description
Generates cell-level cytokine activity estimates using relevant information from gene sets constructed with the 'CytoSig' and the 'Reactome' databases and scored using the modified 'Variance-adjusted Mahalanobis (VAM)' framework for single-cell RNA-sequencing (scRNA-seq) data. 'CytoSig' database is described in: Jiang at al., (2021) <doi:10.1038/s41592-021-01274-5>. 'Reactome' database is described in: Gillespie et al., (2021) <doi:10.1093/nar/gkab1028>. The 'VAM' method is outlined in: Frost (2020) <doi:10.1093/nar/gkaa582>.
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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 'scaper-vignette-CytoSig.Rmd' using rmarkdown Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| ! Package pdftex.def Error: File `ec02dfd7afbdbf34ecb6fab00197a77435fd302a.pdf' not found: using draft setting. Error: processing vignette 'scaper-vignette-CytoSig.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/scaper.Rcheck/vign_test/scaper/vignettes/scaper-vignette-CytoSig.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See scaper-vignette-CytoSig.log for more info. --- failed re-building 'scaper-vignette-CytoSig.Rmd' --- re-building 'scaper-vignette-Reactome.Rmd' using rmarkdown Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| ! Package pdftex.def Error: File `f12efb46c3c7a4b66080cfdde11b7d9ebad2fad9.pdf' not found: using draft setting. Error: processing vignette 'scaper-vignette-Reactome.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/scaper.Rcheck/vign_test/scaper/vignettes/scaper-vignette-Reactome.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See scaper-vignette-Reactome.log for more info. --- failed re-building 'scaper-vignette-Reactome.Rmd' SUMMARY: processing the following files failed: 'scaper-vignette-CytoSig.Rmd' 'scaper-vignette-Reactome.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 'scaper-vignette-CytoSig.Rmd' using rmarkdown Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ***************** ...[truncated]... te-Reactome.log for more info. --- failed re-building 'scaper-vignette-Reactome.Rmd' SUMMARY: processing the following files failed: 'scaper-vignette-CytoSig.Rmd' 'scaper-vignette-Reactome.Rmd' Error: Vignette re-building failed. Execution halted