Last updated on 2026-02-08 19:51:28 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.8.7 | 28.09 | 296.43 | 324.52 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.8.7 | 16.83 | 202.24 | 219.07 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.8.7 | 48.00 | 351.95 | 399.95 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.8.7 | 45.00 | 466.69 | 511.69 | ERROR | |
| r-devel-windows-x86_64 | 0.8.7 | 29.00 | 269.00 | 298.00 | ERROR | |
| r-patched-linux-x86_64 | 0.8.7 | 27.42 | 275.38 | 302.80 | ERROR | |
| r-release-linux-x86_64 | 0.8.7 | 26.20 | 274.09 | 300.29 | ERROR | |
| r-release-macos-arm64 | 0.8.7 | OK | ||||
| r-release-macos-x86_64 | 0.8.7 | 19.00 | 213.00 | 232.00 | OK | |
| r-release-windows-x86_64 | 0.8.7 | 28.00 | 262.00 | 290.00 | OK | |
| r-oldrel-macos-arm64 | 0.8.7 | OK | ||||
| r-oldrel-macos-x86_64 | 0.8.7 | 19.00 | 259.00 | 278.00 | OK | |
| r-oldrel-windows-x86_64 | 0.8.7 | 40.00 | 352.00 | 392.00 | ERROR |
Version: 0.8.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [23s/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-devel-linux-x86_64-debian-clang
Version: 0.8.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [16s/19s]
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’ [20s/20s]
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/36s]
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' [18s]
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/25s]
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
Version: 0.8.7
Check: tests
Result: ERROR
Running 'testthat.R' [25s]
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-oldrel-windows-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.