Last updated on 2025-05-22 05:51:19 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 6.64 | 102.78 | 109.42 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 4.98 | 77.88 | 82.86 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 157.96 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 189.17 | OK | |||
| r-devel-windows-x86_64 | 1.1.0 | 7.00 | 174.00 | 181.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 5.47 | 99.01 | 104.48 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 6.03 | 98.13 | 104.16 | OK | |
| r-release-macos-arm64 | 1.1.0 | 75.00 | OK | |||
| r-release-macos-x86_64 | 1.1.0 | 126.00 | OK | |||
| r-release-windows-x86_64 | 1.1.0 | 7.00 | 235.00 | 242.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 59.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.1.0 | 94.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.1.0 | 10.00 | 172.00 | 182.00 | OK |
Version: 1.1.0
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘H. Robert Frost <rob.frost@dartmouth.edu>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = c("H.", "Robert"),
family = "Frost",
role = c("aut", "cre"),
email = "rob.frost@dartmouth.edu")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘VAM_PBMC3K_Hallmark_LogNormalization.Rnw’ using Sweave
--- finished re-building ‘VAM_PBMC3K_Hallmark_LogNormalization.Rnw’
--- re-building ‘VAM_PBMC3K_LogNormalization.Rnw’ using Sweave
Error: processing vignette 'VAM_PBMC3K_LogNormalization.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'VAM_PBMC3K_LogNormalization.tex' failed.
Messages:
/usr/bin/texi2dvi: Your TeX installation appears to be broken - texi2dvi
cannot determine auxiliary files output from a TeX run.
You may need to install TeX, or change the values of your PATH, TEX
or PDFTEX environment variables in order to proceed.
--- failed re-building ‘VAM_PBMC3K_LogNormalization.Rnw’
--- re-building ‘VAM_PBMC3K_SCTransform.Rnw’ using Sweave
Error: processing vignette 'VAM_PBMC3K_SCTransform.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'VAM_PBMC3K_SCTransform.tex' failed.
Messages:
/usr/bin/texi2dvi: Your TeX installation appears to be broken - texi2dvi
cannot determine auxiliary files output from a TeX run.
You may need to install TeX, or change the values of your PATH, TEX
or PDFTEX environment variables in order to proceed.
--- failed re-building ‘VAM_PBMC3K_SCTransform.Rnw’
--- re-building ‘VAM_pbmc_small.Rnw’ using Sweave
Loading required package: MASS
Loading required package: Matrix
gene.weights not specified, defaulting all weights to 1
Computing VAM distances for 1 gene sets, 80 cells and 230 genes.
Min set size: 5, median size: 5
Computing VAM distances for 1 gene sets, 80 cells and 230 genes.
Min set size: 5, median size: 5
Warning: The `slot` argument of `FetchData()` is deprecated as of SeuratObject 5.0.0.
ℹ Please use the `layer` argument instead.
ℹ The deprecated feature was likely used in the Seurat package.
Please report the issue at <https://github.com/satijalab/seurat/issues>.
Error: processing vignette 'VAM_pbmc_small.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'VAM_pbmc_small.tex' failed.
Messages:
/usr/bin/texi2dvi: Your TeX installation appears to be broken - texi2dvi
cannot determine auxiliary files output from a TeX run.
You may need to install TeX, or change the values of your PATH, TEX
or PDFTEX environment variables in order to proceed.
--- failed re-building ‘VAM_pbmc_small.Rnw’
--- re-building ‘VAM_pbmc_small_sctransform.Rnw’ using Sweave
Loading required package: MASS
Loading required package: Matrix
Warning: The `slot` argument of `GetAssayData()` is deprecated as of SeuratObject 5.0.0.
ℹ Please use the `layer` argument instead.
ℹ The deprecated feature was likely used in the Seurat package.
Please report the issue at <https://github.com/satijalab/seurat/issues>.
`vst.flavor` is set to 'v2' but could not find glmGamPoi installed.
Please install the glmGamPoi package for much faster estimation.
--------------------------------------------
install.packages('BiocManager')
BiocManager::install('glmGamPoi')
--------------------------------------------
Falling back to native (slower) implementation.
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in glm.nb(formula = as.formula(new_formula), data = data) :
alternation limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in glm.nb(formula = as.formula(new_formula), data = data) :
alternation limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in glm.nb(formula = as.formula(new_formula), data = data) :
alternation limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in glm.nb(formula = as.formula(new_formula), data = data) :
alternation limit reached
Warning: glm.fit: algorithm did not converge
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in glm.nb(formula = as.formula(new_formula), data = data) :
alternation limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in glm.nb(formula = as.formula(new_formula), data = data) :
alternation limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace > :
iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning: The `slot` argument of `SetAssayData()` is deprecated as of SeuratObject 5.0.0.
ℹ Please use the `layer` argument instead.
ℹ The deprecated feature was likely used in the Seurat package.
Please report the issue at <https://github.com/satijalab/seurat/issues>.
PC_ 1
Positive: CST3, LYZ, HLA-DRA, S100A9, LST1, HLA-DPA1, HLA-DPB1, SAT1, AIF1, HLA-DRB1
IFITM3, S100A8, COTL1, TYROBP, TYMP, CTSS, LGALS1, HLA-DRB5, S100A11, FCN1
SERPINA1, FCER1G, CFD, LGALS2, IFI30, HLA-DQA1, HLA-DQB1, GRN, CFP, CD68
Negative: NKG7, CST7, CCL5, GZMA, IL32, CD3D, CTSW, PRF1, HNRNPF, GZMM
GNLY, FGFBP2, CD7, LCK, RARRES3, GZMB, CD3E, CRBN, CD247, EIF4A2
LAMP1, XBP1, LTB, SPON2, IL7R, GYPC, GZMH, LDHB, SSR2, LYAR
PC_ 2
Positive: PPBP, GPX1, SDPR, PF4, GNG11, CLU, SPARC, CD9, GP9, HIST1H2AC
TUBB1, NCOA4, NRGN, CCL5, CA2, TPM4, TREML1, NGFRAP1, PGRMC1, ITGA2B
RUFY1, PTCRA, FERMT3, MYL9, TMEM40, ODC1, ACRBP, PARVB, TSC22D1, TALDO1
Negative: IFITM2, HLA-DRA, HLA-DPB1, HNRNPF, HLA-DPA1, HLA-DRB1, TYROBP, LTB, LGALS1, CXCR4
LYZ, LST1, NKG7, EIF4A2, HLA-DRB5, AIF1, S100A11, CTSS, FCER1G, SRSF7
CD3D, CST3, FCGR3A, IL32, HSP90AA1, SSR2, CD79B, HLA-DQB1, LDHB, IFITM3
PC_ 3
Positive: LTB, HLA-DRA, HLA-DRB1, HLA-DQB1, MS4A1, CD79A, HLA-DPB1, CD79B, CXCR4, HLA-DRB5
HLA-DQA1, TCL1A, HLA-DPA1, HLA-DMB, SP100, HVCN1, TMEM123, SNHG7, LY86, NT5C
FCER2, LINC00926, BANK1, FCRLA, PPAPDC1B, NCF1, HLA-DQA2, PIK3IP1, LDHB, TNFAIP8
Negative: TYROBP, FCER1G, LGALS1, NKG7, FCGR3A, PRF1, GZMB, GNLY, FGFBP2, CST3
GZMA, CST7, LST1, S100A9, S100A8, AIF1, CTSW, SAT1, GZMM, IFITM3
CCL5, GZMH, CCL4, IGFBP7, S100A11, RHOC, FCN1, SPON2, PSAP, KLRD1
PC_ 4
Positive: HLA-DPB1, HLA-DRB1, HLA-DRA, FGFBP2, NKG7, HLA-DPA1, GZMB, GNLY, PRF1, CST7
HLA-DQB1, CTSW, HLA-DQA1, HLA-DRB5, GZMA, GZMH, MS4A1, CD79A, CCL4, HLA-DMB
CLIC3, AKR1C3, NT5C, ALOX5AP, C12orf75, SPON2, IGFBP7, KLRD1, CD79B, TTC38
Negative: CD3D, LDHB, IL7R, LTB, CD3E, NOSIP, TMEM123, MPHOSPH6, THYN1, TAGAP
COTL1, CD2, EIF4A2, AIF1, TAF7, ACAP1, DNAJB1, MAL, SAT1, CTSS
SAFB2, SRSF7, GYPC, ASNSD1, IFITM2, LST1, PIK3IP1, EPC1, TMUB1, TNFAIP8
PC_ 5
Positive: LYZ, S100A9, LGALS2, FCER1A, S100A8, GSTP1, CLEC10A, CD3D, CST3, GPX1
MS4A6A, IL1B, LDHB, HLA-DMA, LGALS3, RPL7L1, IL32, CD14, SRSF7, LCK
CD3E, IL7R, TYMP, RGS1, FCGRT, CFP, GRN, ASGR1, HLA-DQA1, SSR2
Negative: FCGR3A, CD79B, SAT1, IFITM2, AIF1, LST1, RHOC, RP11-290F20.3, FCER1G, EPC1
CTSS, IFITM3, TNFRSF1B, MS4A7, SERPINA1, MS4A1, CD68, RGS2, HNRNPF, HCK
PSAP, C5AR1, HVCN1, CD79A, S100A11, COTL1, WARS, IFI30, ADAR, CARD16
Warning: Number of dimensions changing from 19 to 10
Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session
18:49:12 UMAP embedding parameters a = 0.9922 b = 1.112
18:49:12 Read 80 rows and found 10 numeric columns
18:49:12 Using Annoy for neighbor search, n_neighbors = 30
18:49:12 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
18:49:13 Writing NN index file to temp file /tmp/RtmpJIivKB/working_dir/RtmpZimqyS/file9a0ad369dcced
18:49:13 Searching Annoy index using 1 thread, search_k = 3000
18:49:13 Annoy recall = 100%
18:49:13 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
18:49:14 Initializing from normalized Laplacian + noise (using RSpectra)
18:49:15 Commencing optimization for 500 epochs, with 1608 positive edges
18:49:15 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
18:49:15 Optimization finished
gene.weights not specified, defaulting all weights to 1
Computing VAM distances for 1 gene sets, 80 cells and 220 genes.
Min set size: 5, median size: 5
Warning: The `slot` argument of `FetchData()` is deprecated as of SeuratObject 5.0.0.
ℹ Please use the `layer` argument instead.
ℹ The deprecated feature was likely used in the Seurat package.
Please report the issue at <https://github.com/satijalab/seurat/issues>.
Error: processing vignette 'VAM_pbmc_small_sctransform.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'VAM_pbmc_small_sctransform.tex' failed.
Messages:
/usr/bin/texi2dvi: Your TeX installation appears to be broken - texi2dvi
cannot determine auxiliary files output from a TeX run.
You may need to install TeX, or change the values of your PATH, TEX
or PDFTEX environment variables in order to proceed.
--- failed re-building ‘VAM_pbmc_small_sctransform.Rnw’
SUMMARY: processing the following files failed:
‘VAM_PBMC3K_LogNormalization.Rnw’ ‘VAM_PBMC3K_SCTransform.Rnw’
‘VAM_pbmc_small.Rnw’ ‘VAM_pbmc_small_sctransform.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.0
Check: PDF version of manual
Result: WARN
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.0
Check: PDF version of manual without index
Result: ERROR
Re-running with no redirection of stdout/stderr.
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.0
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘VAM-manual.tex’
Flavor: r-devel-linux-x86_64-fedora-clang