Last updated on 2026-02-27 04:52:09 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.8.7 | 29.43 | 294.38 | 323.81 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.8.7 | 19.44 | 203.61 | 223.05 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.8.7 | 48.00 | 465.83 | 513.83 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.8.7 | 45.00 | 450.08 | 495.08 | ERROR | |
| r-devel-macos-arm64 | 0.8.10 | 7.00 | 73.00 | 80.00 | OK | |
| r-devel-windows-x86_64 | 0.8.7 | 29.00 | 264.00 | 293.00 | ERROR | |
| r-patched-linux-x86_64 | 0.8.7 | 26.68 | 277.36 | 304.04 | ERROR | |
| r-release-linux-x86_64 | 0.8.7 | 23.78 | 273.63 | 297.41 | ERROR | |
| r-release-macos-arm64 | 0.8.10 | 7.00 | 78.00 | 85.00 | OK | |
| r-release-macos-x86_64 | 0.8.10 | 22.00 | 410.00 | 432.00 | OK | |
| r-release-windows-x86_64 | 0.8.10 | 29.00 | 248.00 | 277.00 | OK | |
| r-oldrel-macos-arm64 | 0.8.10 | 7.00 | 76.00 | 83.00 | OK | |
| r-oldrel-macos-x86_64 | 0.8.10 | 22.00 | 407.00 | 429.00 | OK | |
| r-oldrel-windows-x86_64 | 0.8.10 | 29.00 | 259.00 | 288.00 | OK |
Version: 0.8.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidyseurat)
Loading required package: ttservice
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
========================================
tidyseurat version 0.8.7
If you use TIDYSEURAT in published research, please cite:
Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021.
This message can be suppressed by:
suppressPackageStartupMessages(library(tidyseurat))
To restore the Seurat default display use options("restore_Seurat_show" = TRUE)
========================================
Attaching package: 'tidyseurat'
The following object is masked from 'package:ttservice':
plot_ly
>
> test_check("tidyseurat")
Saving _problems/test-dplyr-208.R
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-dplyr.R:205:3'): add_count ─────────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `.drop` argument of `add_count()` was deprecated in dplyr 1.0.0 and
is now defunct.
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(add_count(pbmc_small, groups)), length(rownames(pbmc_small))) at test-dplyr.R:205:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(add_count(pbmc_small, groups))
5. ├─dplyr::add_count(pbmc_small, groups)
6. ├─tidyseurat:::add_count.Seurat(pbmc_small, groups)
7. │ └─... %>% as_meta_data(x)
8. ├─tidyseurat:::as_meta_data(., x)
9. │ └─... %>% column_to_rownames(c_(seurat_object)$name)
10. ├─tibble::column_to_rownames(., c_(seurat_object)$name)
11. │ ├─base::stopifnot(is.data.frame(.data))
12. │ └─base::is.data.frame(.data)
13. ├─dplyr::select_if(., !colnames(.) %in% col_to_exclude)
14. │ └─rlang::is_logical(.predicate)
15. ├─colnames(.) %in% col_to_exclude
16. ├─base::colnames(.)
17. │ └─base::is.data.frame(x)
18. ├─dplyr::add_count(...)
19. └─dplyr:::add_count.data.frame(...)
20. └─dplyr:::add_count_impl(...)
21. └─lifecycle::deprecate_stop("1.0.0", "add_count(.drop = )", env = error_call)
22. └─lifecycle:::deprecate_stop0(msg)
23. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.8.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [16s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidyseurat)
Loading required package: ttservice
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
========================================
tidyseurat version 0.8.7
If you use TIDYSEURAT in published research, please cite:
Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021.
This message can be suppressed by:
suppressPackageStartupMessages(library(tidyseurat))
To restore the Seurat default display use options("restore_Seurat_show" = TRUE)
========================================
Attaching package: 'tidyseurat'
The following object is masked from 'package:ttservice':
plot_ly
>
> test_check("tidyseurat")
Saving _problems/test-dplyr-208.R
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-dplyr.R:205:3'): add_count ─────────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `.drop` argument of `add_count()` was deprecated in dplyr 1.0.0 and
is now defunct.
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(add_count(pbmc_small, groups)), length(rownames(pbmc_small))) at test-dplyr.R:205:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(add_count(pbmc_small, groups))
5. ├─dplyr::add_count(pbmc_small, groups)
6. ├─tidyseurat:::add_count.Seurat(pbmc_small, groups)
7. │ └─... %>% as_meta_data(x)
8. ├─tidyseurat:::as_meta_data(., x)
9. │ └─... %>% column_to_rownames(c_(seurat_object)$name)
10. ├─tibble::column_to_rownames(., c_(seurat_object)$name)
11. │ ├─base::stopifnot(is.data.frame(.data))
12. │ └─base::is.data.frame(.data)
13. ├─dplyr::select_if(., !colnames(.) %in% col_to_exclude)
14. │ └─rlang::is_logical(.predicate)
15. ├─colnames(.) %in% col_to_exclude
16. ├─base::colnames(.)
17. │ └─base::is.data.frame(x)
18. ├─dplyr::add_count(...)
19. └─dplyr:::add_count.data.frame(...)
20. └─dplyr:::add_count_impl(...)
21. └─lifecycle::deprecate_stop("1.0.0", "add_count(.drop = )", env = error_call)
22. └─lifecycle:::deprecate_stop0(msg)
23. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.8.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [36s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidyseurat)
Loading required package: ttservice
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
========================================
tidyseurat version 0.8.7
If you use TIDYSEURAT in published research, please cite:
Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021.
This message can be suppressed by:
suppressPackageStartupMessages(library(tidyseurat))
To restore the Seurat default display use options("restore_Seurat_show" = TRUE)
========================================
Attaching package: 'tidyseurat'
The following object is masked from 'package:ttservice':
plot_ly
>
> test_check("tidyseurat")
Saving _problems/test-dplyr-208.R
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-dplyr.R:205:3'): add_count ─────────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `.drop` argument of `add_count()` was deprecated in dplyr 1.0.0 and
is now defunct.
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(add_count(pbmc_small, groups)), length(rownames(pbmc_small))) at test-dplyr.R:205:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(add_count(pbmc_small, groups))
5. ├─dplyr::add_count(pbmc_small, groups)
6. ├─tidyseurat:::add_count.Seurat(pbmc_small, groups)
7. │ └─... %>% as_meta_data(x)
8. ├─tidyseurat:::as_meta_data(., x)
9. │ └─... %>% column_to_rownames(c_(seurat_object)$name)
10. ├─tibble::column_to_rownames(., c_(seurat_object)$name)
11. │ ├─base::stopifnot(is.data.frame(.data))
12. │ └─base::is.data.frame(.data)
13. ├─dplyr::select_if(., !colnames(.) %in% col_to_exclude)
14. │ └─rlang::is_logical(.predicate)
15. ├─colnames(.) %in% col_to_exclude
16. ├─base::colnames(.)
17. │ └─base::is.data.frame(x)
18. ├─dplyr::add_count(...)
19. └─dplyr:::add_count.data.frame(...)
20. └─dplyr:::add_count_impl(...)
21. └─lifecycle::deprecate_stop("1.0.0", "add_count(.drop = )", env = error_call)
22. └─lifecycle:::deprecate_stop0(msg)
23. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.8.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [33s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidyseurat)
Loading required package: ttservice
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
========================================
tidyseurat version 0.8.7
If you use TIDYSEURAT in published research, please cite:
Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021.
This message can be suppressed by:
suppressPackageStartupMessages(library(tidyseurat))
To restore the Seurat default display use options("restore_Seurat_show" = TRUE)
========================================
Attaching package: 'tidyseurat'
The following object is masked from 'package:ttservice':
plot_ly
>
> test_check("tidyseurat")
Saving _problems/test-dplyr-208.R
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-dplyr.R:205:3'): add_count ─────────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `.drop` argument of `add_count()` was deprecated in dplyr 1.0.0 and
is now defunct.
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(add_count(pbmc_small, groups)), length(rownames(pbmc_small))) at test-dplyr.R:205:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(add_count(pbmc_small, groups))
5. ├─dplyr::add_count(pbmc_small, groups)
6. ├─tidyseurat:::add_count.Seurat(pbmc_small, groups)
7. │ └─... %>% as_meta_data(x)
8. ├─tidyseurat:::as_meta_data(., x)
9. │ └─... %>% column_to_rownames(c_(seurat_object)$name)
10. ├─tibble::column_to_rownames(., c_(seurat_object)$name)
11. │ ├─base::stopifnot(is.data.frame(.data))
12. │ └─base::is.data.frame(.data)
13. ├─dplyr::select_if(., !colnames(.) %in% col_to_exclude)
14. │ └─rlang::is_logical(.predicate)
15. ├─colnames(.) %in% col_to_exclude
16. ├─base::colnames(.)
17. │ └─base::is.data.frame(x)
18. ├─dplyr::add_count(...)
19. └─dplyr:::add_count.data.frame(...)
20. └─dplyr:::add_count_impl(...)
21. └─lifecycle::deprecate_stop("1.0.0", "add_count(.drop = )", env = error_call)
22. └─lifecycle:::deprecate_stop0(msg)
23. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.8.7
Check: tests
Result: ERROR
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(tidyseurat)
Loading required package: ttservice
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
========================================
tidyseurat version 0.8.7
If you use TIDYSEURAT in published research, please cite:
Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021.
This message can be suppressed by:
suppressPackageStartupMessages(library(tidyseurat))
To restore the Seurat default display use options("restore_Seurat_show" = TRUE)
========================================
Attaching package: 'tidyseurat'
The following object is masked from 'package:ttservice':
plot_ly
>
> test_check("tidyseurat")
Saving _problems/test-dplyr-208.R
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-dplyr.R:205:3'): add_count ─────────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `.drop` argument of `add_count()` was deprecated in dplyr 1.0.0 and
is now defunct.
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(add_count(pbmc_small, groups)), length(rownames(pbmc_small))) at test-dplyr.R:205:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(add_count(pbmc_small, groups))
5. ├─dplyr::add_count(pbmc_small, groups)
6. ├─tidyseurat:::add_count.Seurat(pbmc_small, groups)
7. │ └─... %>% as_meta_data(x)
8. ├─tidyseurat:::as_meta_data(., x)
9. │ └─... %>% column_to_rownames(c_(seurat_object)$name)
10. ├─tibble::column_to_rownames(., c_(seurat_object)$name)
11. │ ├─base::stopifnot(is.data.frame(.data))
12. │ └─base::is.data.frame(.data)
13. ├─dplyr::select_if(., !colnames(.) %in% col_to_exclude)
14. │ └─rlang::is_logical(.predicate)
15. ├─colnames(.) %in% col_to_exclude
16. ├─base::colnames(.)
17. │ └─base::is.data.frame(x)
18. ├─dplyr::add_count(...)
19. └─dplyr:::add_count.data.frame(...)
20. └─dplyr:::add_count_impl(...)
21. └─lifecycle::deprecate_stop("1.0.0", "add_count(.drop = )", env = error_call)
22. └─lifecycle:::deprecate_stop0(msg)
23. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.8.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidyseurat)
Loading required package: ttservice
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
========================================
tidyseurat version 0.8.7
If you use TIDYSEURAT in published research, please cite:
Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021.
This message can be suppressed by:
suppressPackageStartupMessages(library(tidyseurat))
To restore the Seurat default display use options("restore_Seurat_show" = TRUE)
========================================
Attaching package: 'tidyseurat'
The following object is masked from 'package:ttservice':
plot_ly
>
> test_check("tidyseurat")
Saving _problems/test-dplyr-208.R
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-dplyr.R:205:3'): add_count ─────────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `.drop` argument of `add_count()` was deprecated in dplyr 1.0.0 and
is now defunct.
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(add_count(pbmc_small, groups)), length(rownames(pbmc_small))) at test-dplyr.R:205:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(add_count(pbmc_small, groups))
5. ├─dplyr::add_count(pbmc_small, groups)
6. ├─tidyseurat:::add_count.Seurat(pbmc_small, groups)
7. │ └─... %>% as_meta_data(x)
8. ├─tidyseurat:::as_meta_data(., x)
9. │ └─... %>% column_to_rownames(c_(seurat_object)$name)
10. ├─tibble::column_to_rownames(., c_(seurat_object)$name)
11. │ ├─base::stopifnot(is.data.frame(.data))
12. │ └─base::is.data.frame(.data)
13. ├─dplyr::select_if(., !colnames(.) %in% col_to_exclude)
14. │ └─rlang::is_logical(.predicate)
15. ├─colnames(.) %in% col_to_exclude
16. ├─base::colnames(.)
17. │ └─base::is.data.frame(x)
18. ├─dplyr::add_count(...)
19. └─dplyr:::add_count.data.frame(...)
20. └─dplyr:::add_count_impl(...)
21. └─lifecycle::deprecate_stop("1.0.0", "add_count(.drop = )", env = error_call)
22. └─lifecycle:::deprecate_stop0(msg)
23. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
Error:
! Test failures.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.8.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidyseurat)
Loading required package: ttservice
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
========================================
tidyseurat version 0.8.7
If you use TIDYSEURAT in published research, please cite:
Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021.
This message can be suppressed by:
suppressPackageStartupMessages(library(tidyseurat))
To restore the Seurat default display use options("restore_Seurat_show" = TRUE)
========================================
Attaching package: 'tidyseurat'
The following object is masked from 'package:ttservice':
plot_ly
>
> test_check("tidyseurat")
Saving _problems/test-dplyr-208.R
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-dplyr.R:205:3'): add_count ─────────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `.drop` argument of `add_count()` was deprecated in dplyr 1.0.0 and
is now defunct.
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(add_count(pbmc_small, groups)), length(rownames(pbmc_small))) at test-dplyr.R:205:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(add_count(pbmc_small, groups))
5. ├─dplyr::add_count(pbmc_small, groups)
6. ├─tidyseurat:::add_count.Seurat(pbmc_small, groups)
7. │ └─... %>% as_meta_data(x)
8. ├─tidyseurat:::as_meta_data(., x)
9. │ └─... %>% column_to_rownames(c_(seurat_object)$name)
10. ├─tibble::column_to_rownames(., c_(seurat_object)$name)
11. │ ├─base::stopifnot(is.data.frame(.data))
12. │ └─base::is.data.frame(.data)
13. ├─dplyr::select_if(., !colnames(.) %in% col_to_exclude)
14. │ └─rlang::is_logical(.predicate)
15. ├─colnames(.) %in% col_to_exclude
16. ├─base::colnames(.)
17. │ └─base::is.data.frame(x)
18. ├─dplyr::add_count(...)
19. └─dplyr:::add_count.data.frame(...)
20. └─dplyr:::add_count_impl(...)
21. └─lifecycle::deprecate_stop("1.0.0", "add_count(.drop = )", env = error_call)
22. └─lifecycle:::deprecate_stop0(msg)
23. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 11 | SKIP 0 | PASS 75 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64