Last updated on 2025-12-28 01:49:11 CET.
| Package | ERROR | OK |
|---|---|---|
| CACIMAR | 9 | 4 |
Current CRAN status: ERROR: 9, OK: 4
Version: 1.0.0
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Junyao Jiang <jiangjunyao789@163.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Junyao",
family = "Jiang",
role = c("aut", "cre"),
email = "jiangjunyao789@163.com")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘CACIMAR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Format_Markers_Frac
> ### Title: Format marker genes for plotting
> ### Aliases: Format_Markers_Frac
>
> ### ** Examples
>
> data("pbmc_small")
> all.markers <- Identify_Markers(pbmc_small)
Calculating cluster 0
Calculating cluster 1
Calculating cluster 2
[1] "0"
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
▆
1. └─CACIMAR::Identify_Markers(pbmc_small)
2. └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)
3. └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)
4. └─CACIMAR:::Markertest(...)
5. ├─Seurat::GetAssayData(object = object, slot = "data")
6. └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")
7. └─SeuratObject::.Deprecate(...)
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [16s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(CACIMAR)
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
>
> test_check("CACIMAR")
mm_zf_0T1 mm_zf_1T0 mm_zf_1T1 mm_zf_1TN mm_zf_NT1 mm_zf_NTN
14207 37432 10353 3238 273 128
[1] "mm_zf_0T1"
[1] "mm_zf_1T0"
[1] "mm_zf_1T1"
[1] "mm_zf_1TN"
[1] "mm_zf_NT1"
[1] "mm_zf_NTN"
Using NCS as value column: use value.var to override.
Calculating cluster 0
Calculating cluster 1
Calculating cluster 2
[1] "0"
Saving _problems/test-test1-10.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-test1.R:10:3'): test CACIMAR ───────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. └─CACIMAR::Identify_Markers(pbmc_small) at test-test1.R:10:3
2. └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)
3. └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)
4. └─CACIMAR:::Markertest(...)
5. ├─Seurat::GetAssayData(object = object, slot = "data")
6. └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")
7. └─SeuratObject::.Deprecate(...)
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [11s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(CACIMAR)
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
>
> test_check("CACIMAR")
mm_zf_0T1 mm_zf_1T0 mm_zf_1T1 mm_zf_1TN mm_zf_NT1 mm_zf_NTN
14207 37432 10353 3238 273 128
[1] "mm_zf_0T1"
[1] "mm_zf_1T0"
[1] "mm_zf_1T1"
[1] "mm_zf_1TN"
[1] "mm_zf_NT1"
[1] "mm_zf_NTN"
Using NCS as value column: use value.var to override.
Calculating cluster 0
Calculating cluster 1
Calculating cluster 2
[1] "0"
Saving _problems/test-test1-10.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-test1.R:10:3'): test CACIMAR ───────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. └─CACIMAR::Identify_Markers(pbmc_small) at test-test1.R:10:3
2. └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)
3. └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)
4. └─CACIMAR:::Markertest(...)
5. ├─Seurat::GetAssayData(object = object, slot = "data")
6. └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")
7. └─SeuratObject::.Deprecate(...)
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘CACIMAR-Ex.R’ failed
The error most likely occurred in:
> ### Name: Format_Markers_Frac
> ### Title: Format marker genes for plotting
> ### Aliases: Format_Markers_Frac
>
> ### ** Examples
>
> data("pbmc_small")
> all.markers <- Identify_Markers(pbmc_small)
Calculating cluster 0
Calculating cluster 1
Calculating cluster 2
[1] "0"
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
▆
1. └─CACIMAR::Identify_Markers(pbmc_small)
2. └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)
3. └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)
4. └─CACIMAR:::Markertest(...)
5. ├─Seurat::GetAssayData(object = object, slot = "data")
6. └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")
7. └─SeuratObject::.Deprecate(...)
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [27s/91s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(CACIMAR)
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
>
> test_check("CACIMAR")
mm_zf_0T1 mm_zf_1T0 mm_zf_1T1 mm_zf_1TN mm_zf_NT1 mm_zf_NTN
14207 37432 10353 3238 273 128
[1] "mm_zf_0T1"
[1] "mm_zf_1T0"
[1] "mm_zf_1T1"
[1] "mm_zf_1TN"
[1] "mm_zf_NT1"
[1] "mm_zf_NTN"
Using NCS as value column: use value.var to override.
Calculating cluster 0
Calculating cluster 1
Calculating cluster 2
[1] "0"
Saving _problems/test-test1-10.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-test1.R:10:3'): test CACIMAR ───────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. └─CACIMAR::Identify_Markers(pbmc_small) at test-test1.R:10:3
2. └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)
3. └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)
4. └─CACIMAR:::Markertest(...)
5. ├─Seurat::GetAssayData(object = object, slot = "data")
6. └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")
7. └─SeuratObject::.Deprecate(...)
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [25s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(CACIMAR)
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
>
> test_check("CACIMAR")
mm_zf_0T1 mm_zf_1T0 mm_zf_1T1 mm_zf_1TN mm_zf_NT1 mm_zf_NTN
14207 37432 10353 3238 273 128
[1] "mm_zf_0T1"
[1] "mm_zf_1T0"
[1] "mm_zf_1T1"
[1] "mm_zf_1TN"
[1] "mm_zf_NT1"
[1] "mm_zf_NTN"
Using NCS as value column: use value.var to override.
Calculating cluster 0
Calculating cluster 1
Calculating cluster 2
[1] "0"
Saving _problems/test-test1-10.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-test1.R:10:3'): test CACIMAR ───────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. └─CACIMAR::Identify_Markers(pbmc_small) at test-test1.R:10:3
2. └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)
3. └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)
4. └─CACIMAR:::Markertest(...)
5. ├─Seurat::GetAssayData(object = object, slot = "data")
6. └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")
7. └─SeuratObject::.Deprecate(...)
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(CACIMAR)
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
>
> test_check("CACIMAR")
mm_zf_0T1 mm_zf_1T0 mm_zf_1T1 mm_zf_1TN mm_zf_NT1 mm_zf_NTN
14207 37432 10353 3238 273 128
[1] "mm_zf_0T1"
[1] "mm_zf_1T0"
[1] "mm_zf_1T1"
[1] "mm_zf_1TN"
[1] "mm_zf_NT1"
[1] "mm_zf_NTN"
Using NCS as value column: use value.var to override.
Calculating cluster 0
Calculating cluster 1
Calculating cluster 2
[1] "0"
Saving _problems/test-test1-10.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-test1.R:10:3'): test CACIMAR ───────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. └─CACIMAR::Identify_Markers(pbmc_small) at test-test1.R:10:3
2. └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)
3. └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)
4. └─CACIMAR:::Markertest(...)
5. ├─Seurat::GetAssayData(object = object, slot = "data")
6. └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")
7. └─SeuratObject::.Deprecate(...)
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
Error:
! Test failures.
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(CACIMAR)
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
>
> test_check("CACIMAR")
mm_zf_0T1 mm_zf_1T0 mm_zf_1T1 mm_zf_1TN mm_zf_NT1 mm_zf_NTN
14207 37432 10353 3238 273 128
[1] "mm_zf_0T1"
[1] "mm_zf_1T0"
[1] "mm_zf_1T1"
[1] "mm_zf_1TN"
[1] "mm_zf_NT1"
[1] "mm_zf_NTN"
Using NCS as value column: use value.var to override.
Calculating cluster 0
Calculating cluster 1
Calculating cluster 2
[1] "0"
Saving _problems/test-test1-10.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-test1.R:10:3'): test CACIMAR ───────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. └─CACIMAR::Identify_Markers(pbmc_small) at test-test1.R:10:3
2. └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)
3. └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)
4. └─CACIMAR:::Markertest(...)
5. ├─Seurat::GetAssayData(object = object, slot = "data")
6. └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")
7. └─SeuratObject::.Deprecate(...)
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
Error:
! Test failures.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(CACIMAR)
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
>
> test_check("CACIMAR")
mm_zf_0T1 mm_zf_1T0 mm_zf_1T1 mm_zf_1TN mm_zf_NT1 mm_zf_NTN
14207 37432 10353 3238 273 128
[1] "mm_zf_0T1"
[1] "mm_zf_1T0"
[1] "mm_zf_1T1"
[1] "mm_zf_1TN"
[1] "mm_zf_NT1"
[1] "mm_zf_NTN"
Using NCS as value column: use value.var to override.
Calculating cluster 0
Calculating cluster 1
Calculating cluster 2
[1] "0"
Saving _problems/test-test1-10.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-test1.R:10:3'): test CACIMAR ───────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. └─CACIMAR::Identify_Markers(pbmc_small) at test-test1.R:10:3
2. └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)
3. └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)
4. └─CACIMAR:::Markertest(...)
5. ├─Seurat::GetAssayData(object = object, slot = "data")
6. └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")
7. └─SeuratObject::.Deprecate(...)
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(CACIMAR)
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following objects are masked from 'package:base':
intersect, t
>
> test_check("CACIMAR")
mm_zf_0T1 mm_zf_1T0 mm_zf_1T1 mm_zf_1TN mm_zf_NT1 mm_zf_NTN
14207 37432 10353 3238 273 128
[1] "mm_zf_0T1"
[1] "mm_zf_1T0"
[1] "mm_zf_1T1"
[1] "mm_zf_1TN"
[1] "mm_zf_NT1"
[1] "mm_zf_NTN"
Using NCS as value column: use value.var to override.
Calculating cluster 0
Calculating cluster 1
Calculating cluster 2
[1] "0"
Saving _problems/test-test1-10.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-test1.R:10:3'): test CACIMAR ───────────────────────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
i Please use the `layer` argument instead.
Backtrace:
▆
1. └─CACIMAR::Identify_Markers(pbmc_small) at test-test1.R:10:3
2. └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)
3. └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)
4. └─CACIMAR:::Markertest(...)
5. ├─Seurat::GetAssayData(object = object, slot = "data")
6. └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")
7. └─SeuratObject::.Deprecate(...)
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64
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