Last updated on 2021-02-13 04:47:46 CET.

Flavor | Version | T_{install} | T_{check} | T_{total} | Status | Flags |
---|---|---|---|---|---|---|

r-devel-linux-x86_64-debian-clang | 0.1.17 | 26.23 | 222.18 | 248.41 | WARN | |

r-devel-linux-x86_64-debian-gcc | 0.1.17 | 23.53 | 163.97 | 187.50 | WARN | |

r-devel-linux-x86_64-fedora-clang | 0.1.17 | 302.89 | WARN | |||

r-devel-linux-x86_64-fedora-gcc | 0.1.17 | 273.72 | WARN | |||

r-devel-windows-ix86+x86_64 | 0.1.17 | 65.00 | 200.00 | 265.00 | WARN | |

r-patched-linux-x86_64 | 0.1.17 | 18.17 | 209.16 | 227.33 | WARN | |

r-patched-solaris-x86 | 0.1.17 | 429.30 | WARN | |||

r-release-linux-x86_64 | 0.1.17 | 17.39 | 212.42 | 229.81 | WARN | |

r-release-macos-x86_64 | 0.1.17 | OK | ||||

r-release-windows-ix86+x86_64 | 0.1.17 | 64.00 | 274.00 | 338.00 | WARN | |

r-oldrel-macos-x86_64 | 0.1.17 | ERROR |

Version: 0.1.17

Check: re-building of vignette outputs

Result: WARN

Error(s) in re-building vignettes:

...

--- re-building 'figures_article.Rmd' using knitr

--- finished re-building 'figures_article.Rmd'

--- re-building 'introduction.Rmd' using knitr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

filter, lag

The following objects are masked from 'package:base':

intersect, setdiff, setequal, union

Attaching package: 'magrittr'

The following object is masked from 'package:purrr':

set_names

The following object is masked from 'package:tidyr':

extract

Attaching SeuratObject

Attaching package: 'tidyseurat'

The following object is masked from 'package:SeuratObject':

pbmc_small

The following object is masked from 'package:magrittr':

extract

The following objects are masked from 'package:dplyr':

bind_cols, bind_rows, count

The following object is masked from 'package:stats':

filter

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

tidyseurat says: A data frame is returned for independent data analysis.

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in irlba(A = t(x = object), nv = npcs, ...) :

You're computing too large a percentage of total singular values, use a standard svd instead.

tidyseurat says: A data frame is returned for independent data analysis.

Calculating cluster 0

For a more efficient implementation of the Wilcoxon Rank Sum Test,

(default method for FindMarkers) please install the limma package

--------------------------------------------

install.packages('BiocManager')

BiocManager::install('limma')

--------------------------------------------

After installation of limma, Seurat will automatically use the more

efficient implementation (no further action necessary).

This message will be shown once per session

Calculating cluster 1

Calculating cluster 2

Calculating cluster 3

Quitting from lines 219-232 (./../man/fragments/intro.Rmd)

Quitting from lines 50-51 (./../man/fragments/intro.Rmd)

Error: processing vignette 'introduction.Rmd' failed with diagnostics:

Problem with `filter()` input `..1`.

x object 'avg_logFC' not found

i Input `..1` is `top_n_rank(10, avg_logFC)`.

i The error occurred in group 1: cluster = "0".

--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:

'introduction.Rmd'

Error: Vignette re-building failed.

Execution halted

Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.17

Check: re-building of vignette outputs

Result: WARN

Error(s) in re-building vignettes:

...

--- re-building ‘figures_article.Rmd’ using knitr

--- finished re-building ‘figures_article.Rmd’

--- re-building ‘introduction.Rmd’ using knitr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

filter, lag

The following objects are masked from 'package:base':

intersect, setdiff, setequal, union

Attaching package: 'magrittr'

The following object is masked from 'package:purrr':

set_names

The following object is masked from 'package:tidyr':

extract

Attaching SeuratObject

Attaching package: 'tidyseurat'

The following object is masked from 'package:SeuratObject':

pbmc_small

The following object is masked from 'package:magrittr':

extract

The following objects are masked from 'package:dplyr':

bind_cols, bind_rows, count

The following object is masked from 'package:stats':

filter

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

tidyseurat says: A data frame is returned for independent data analysis.

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in irlba(A = t(x = object), nv = npcs, ...) :

You're computing too large a percentage of total singular values, use a standard svd instead.

tidyseurat says: A data frame is returned for independent data analysis.

Calculating cluster 0

For a more efficient implementation of the Wilcoxon Rank Sum Test,

(default method for FindMarkers) please install the limma package

--------------------------------------------

install.packages('BiocManager')

BiocManager::install('limma')

--------------------------------------------

After installation of limma, Seurat will automatically use the more

efficient implementation (no further action necessary).

This message will be shown once per session

Calculating cluster 1

Calculating cluster 2

Calculating cluster 3

Quitting from lines 219-232 (./../man/fragments/intro.Rmd)

Quitting from lines 50-51 (./../man/fragments/intro.Rmd)

Error: processing vignette 'introduction.Rmd' failed with diagnostics:

Problem with `filter()` input `..1`.

✖ object ‘avg_logFC’ not found

ℹ Input `..1` is `top_n_rank(10, avg_logFC)`.

ℹ The error occurred in group 1: cluster = "0".

--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:

‘introduction.Rmd’

Error: Vignette re-building failed.

Execution halted

Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.1.17

Check: re-building of vignette outputs

Result: WARN

Error(s) in re-building vignettes:

--- re-building ‘figures_article.Rmd’ using knitr

--- finished re-building ‘figures_article.Rmd’

--- re-building ‘introduction.Rmd’ using knitr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

filter, lag

The following objects are masked from 'package:base':

intersect, setdiff, setequal, union

Attaching package: 'magrittr'

The following object is masked from 'package:purrr':

set_names

The following object is masked from 'package:tidyr':

extract

Attaching SeuratObject

Attaching package: 'tidyseurat'

The following object is masked from 'package:SeuratObject':

pbmc_small

The following object is masked from 'package:magrittr':

extract

The following objects are masked from 'package:dplyr':

bind_cols, bind_rows, count

The following object is masked from 'package:stats':

filter

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

tidyseurat says: A data frame is returned for independent data analysis.

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in irlba(A = t(x = object), nv = npcs, ...) :

You're computing too large a percentage of total singular values, use a standard svd instead.

tidyseurat says: A data frame is returned for independent data analysis.

Calculating cluster 0

For a more efficient implementation of the Wilcoxon Rank Sum Test,

(default method for FindMarkers) please install the limma package

--------------------------------------------

install.packages('BiocManager')

BiocManager::install('limma')

--------------------------------------------

After installation of limma, Seurat will automatically use the more

efficient implementation (no further action necessary).

This message will be shown once per session

Calculating cluster 1

Calculating cluster 2

Calculating cluster 3

Quitting from lines 219-232 (./../man/fragments/intro.Rmd)

Quitting from lines 50-51 (./../man/fragments/intro.Rmd)

Error: processing vignette 'introduction.Rmd' failed with diagnostics:

Problem with `filter()` input `..1`.

✖ object 'avg_logFC' not found

ℹ Input `..1` is `top_n_rank(10, avg_logFC)`.

ℹ The error occurred in group 1: cluster = "0".

--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:

‘introduction.Rmd’

Error: Vignette re-building failed.

Execution halted

Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.17

Check: re-building of vignette outputs

Result: WARN

Error(s) in re-building vignettes:

--- re-building ‘figures_article.Rmd’ using knitr

--- finished re-building ‘figures_article.Rmd’

--- re-building ‘introduction.Rmd’ using knitr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

filter, lag

The following objects are masked from 'package:base':

intersect, setdiff, setequal, union

Attaching package: 'magrittr'

The following object is masked from 'package:purrr':

set_names

The following object is masked from 'package:tidyr':

extract

Attaching SeuratObject

Attaching package: 'tidyseurat'

The following object is masked from 'package:SeuratObject':

pbmc_small

The following object is masked from 'package:magrittr':

extract

The following objects are masked from 'package:dplyr':

bind_cols, bind_rows, count

The following object is masked from 'package:stats':

filter

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

tidyseurat says: A data frame is returned for independent data analysis.

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in irlba(A = t(x = object), nv = npcs, ...) :

You're computing too large a percentage of total singular values, use a standard svd instead.

tidyseurat says: A data frame is returned for independent data analysis.

Calculating cluster 0

Calculating cluster 1

Calculating cluster 2

Calculating cluster 3

Quitting from lines 219-232 (./../man/fragments/intro.Rmd)

Quitting from lines 50-51 (./../man/fragments/intro.Rmd)

Error: processing vignette 'introduction.Rmd' failed with diagnostics:

Problem with `filter()` input `..1`.

✖ object 'avg_logFC' not found

ℹ Input `..1` is `top_n_rank(10, avg_logFC)`.

ℹ The error occurred in group 1: cluster = "0".

--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:

‘introduction.Rmd’

Error: Vignette re-building failed.

Execution halted

Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.1.17

Check: re-building of vignette outputs

Result: WARN

Error(s) in re-building vignettes:

--- re-building 'figures_article.Rmd' using knitr

--- finished re-building 'figures_article.Rmd'

--- re-building 'introduction.Rmd' using knitr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

filter, lag

The following objects are masked from 'package:base':

intersect, setdiff, setequal, union

Attaching package: 'magrittr'

The following object is masked from 'package:purrr':

set_names

The following object is masked from 'package:tidyr':

extract

Attaching SeuratObject

Attaching package: 'tidyseurat'

The following object is masked from 'package:SeuratObject':

pbmc_small

The following object is masked from 'package:magrittr':

extract

The following objects are masked from 'package:dplyr':

bind_cols, bind_rows, count

The following object is masked from 'package:stats':

filter

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

tidyseurat says: A data frame is returned for independent data analysis.

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in sqrt(1/i) : NaNs produced

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

Warning in irlba(A = t(x = object), nv = npcs, ...) :

You're computing too large a percentage of total singular values, use a standard svd instead.

tidyseurat says: A data frame is returned for independent data analysis.

Calculating cluster 0

For a more efficient implementation of the Wilcoxon Rank Sum Test,

(default method for FindMarkers) please install the limma package

--------------------------------------------

install.packages('BiocManager')

BiocManager::install('limma')

--------------------------------------------

After installation of limma, Seurat will automatically use the more

efficient implementation (no further action necessary).

This message will be shown once per session

Calculating cluster 1

Calculating cluster 2

Calculating cluster 3

Quitting from lines 219-232 (./../man/fragments/intro.Rmd)

Quitting from lines 50-51 (./../man/fragments/intro.Rmd)

Error: processing vignette 'introduction.Rmd' failed with diagnostics:

Problem with `filter()` input `..1`.

x object 'avg_logFC' not found

i Input `..1` is `top_n_rank(10, avg_logFC)`.

i The error occurred in group 1: cluster = "0".

--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:

'introduction.Rmd'

Error: Vignette re-building failed.

Execution halted

Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.1.17

Check: whether package can be installed

Result: ERROR

Installation failed.

Flavor: r-oldrel-macos-x86_64