Last updated on 2023-11-20 09:49:34 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.1 | ERROR | ||||
| r-devel-linux-x86_64-debian-gcc | 0.1.1 | 24.48 | 188.21 | 212.69 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.1 | 370.17 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.1 | 347.91 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.1 | 25.00 | 181.00 | 206.00 | ERROR | |
| r-patched-linux-x86_64 | 0.1.1 | 23.53 | 246.90 | 270.43 | ERROR | |
| r-release-linux-x86_64 | 0.1.1 | 17.75 | 242.81 | 260.56 | ERROR | |
| r-release-macos-arm64 | 0.1.1 | 121.00 | OK | |||
| r-release-macos-x86_64 | 0.1.1 | 234.00 | OK | |||
| r-release-windows-x86_64 | 0.1.1 | 32.00 | 224.00 | 256.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.1.1 | 108.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.1.1 | 153.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.1.1 | 34.00 | 225.00 | 259.00 | ERROR |
Version: 0.1.1
Check: examples
Result: ERROR
Running examples in ‘scAnnotate-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scAnnotate
> ### Title: scAnnotate
> ### Aliases: scAnnotate
>
> ### ** Examples
>
> data(pbmc1)
> data(pbmc2)
> predict_label=scAnnotate(train=pbmc1,
+ test=pbmc2[,-1],
+ distribution="normal",
+ correction ="harmony",
+ screening ="wilcox",
+ threshold=0,
+ lognormalized=TRUE)
Warning: Data is of class matrix. Coercing to dgCMatrix.
Finding variable features for layer counts
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Warning: No layers found matching search pattern provided
Error in `ScaleData()`:
! No layer matching pattern 'data' found. Please run NormalizeData and retry
Backtrace:
▆
1. └─scAnnotate::scAnnotate(...)
2. └─scAnnotate:::br_harmony(...)
3. ├─Seurat::ScaleData(obj.pc)
4. └─Seurat:::ScaleData.Seurat(obj.pc)
5. ├─Seurat::ScaleData(...)
6. └─Seurat:::ScaleData.StdAssay(...)
7. └─rlang::abort(paste0("No layer matching pattern '", olayer, "' found. Please run NormalizeData and retry"))
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: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scAnnotate)
>
> test_check("scAnnotate")
Finding variable features for layer counts
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
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 2 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_scAnnotate.R:7:1'): (code run outside of `test_that()`) ────────
Error in `br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)`: no slot of name "counts" for this object of class "Assay5"
Backtrace:
▆
1. └─scAnnotate::scAnnotate(...) at test_scAnnotate.R:7:1
2. └─scAnnotate:::br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Introduction.Rmd’ using rmarkdown
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Quitting from lines 58-65 [unnamed-chunk-4] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
no slot of name "counts" for this object of class "Assay5"
--- 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-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scAnnotate)
>
> test_check("scAnnotate")
Finding variable features for layer counts
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
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 2 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_scAnnotate.R:7:1'): (code run outside of `test_that()`) ────────
Error in `br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)`: no slot of name "counts" for this object of class "Assay5"
Backtrace:
▆
1. └─scAnnotate::scAnnotate(...) at test_scAnnotate.R:7:1
2. └─scAnnotate:::br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.1
Check: examples
Result: ERROR
Running examples in ‘scAnnotate-Ex.R’ failed
The error most likely occurred in:
> ### Name: scAnnotate
> ### Title: scAnnotate
> ### Aliases: scAnnotate
>
> ### ** Examples
>
> data(pbmc1)
> data(pbmc2)
> predict_label=scAnnotate(train=pbmc1,
+ test=pbmc2[,-1],
+ distribution="normal",
+ correction ="harmony",
+ screening ="wilcox",
+ threshold=0,
+ lognormalized=TRUE)
Warning: Data is of class matrix. Coercing to dgCMatrix.
Finding variable features for layer counts
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Warning: No layers found matching search pattern provided
Error in `ScaleData()`:
! No layer matching pattern 'data' found. Please run NormalizeData and retry
Backtrace:
▆
1. └─scAnnotate::scAnnotate(...)
2. └─scAnnotate:::br_harmony(...)
3. ├─Seurat::ScaleData(obj.pc)
4. └─Seurat:::ScaleData.Seurat(obj.pc)
5. ├─Seurat::ScaleData(...)
6. └─Seurat:::ScaleData.StdAssay(...)
7. └─rlang::abort(paste0("No layer matching pattern '", olayer, "' found. Please run NormalizeData and retry"))
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: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [18s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scAnnotate)
>
> test_check("scAnnotate")
Finding variable features for layer counts
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
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 2 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_scAnnotate.R:7:1'): (code run outside of `test_that()`) ────────
Error in `br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)`: no slot of name "counts" for this object of class "Assay5"
Backtrace:
▆
1. └─scAnnotate::scAnnotate(...) at test_scAnnotate.R:7:1
2. └─scAnnotate:::br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Introduction.Rmd’ using rmarkdown
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Quitting from lines 58-65 [unnamed-chunk-4] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
no slot of name "counts" for this object of class "Assay5"
--- 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-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: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [16s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scAnnotate)
>
> test_check("scAnnotate")
Finding variable features for layer counts
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
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 2 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_scAnnotate.R:7:1'): (code run outside of `test_that()`) ────────
Error in `br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)`: no slot of name "counts" for this object of class "Assay5"
Backtrace:
▆
1. └─scAnnotate::scAnnotate(...) at test_scAnnotate.R:7:1
2. └─scAnnotate:::br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(scAnnotate)
>
> test_check("scAnnotate")
Finding variable features for layer counts
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
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 2 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_scAnnotate.R:7:1'): (code run outside of `test_that()`) ────────
Error in `br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)`: no slot of name "counts" for this object of class "Assay5"
Backtrace:
▆
1. └─scAnnotate::scAnnotate(...) at test_scAnnotate.R:7:1
2. └─scAnnotate:::br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scAnnotate)
>
> test_check("scAnnotate")
Finding variable features for layer counts
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
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 2 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_scAnnotate.R:7:1'): (code run outside of `test_that()`) ────────
Error in `br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)`: no slot of name "counts" for this object of class "Assay5"
Backtrace:
▆
1. └─scAnnotate::scAnnotate(...) at test_scAnnotate.R:7:1
2. └─scAnnotate:::br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(scAnnotate)
>
> test_check("scAnnotate")
Finding variable features for layer counts
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
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 2 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_scAnnotate.R:7:1'): (code run outside of `test_that()`) ────────
Error in `br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)`: no slot of name "counts" for this object of class "Assay5"
Backtrace:
▆
1. └─scAnnotate::scAnnotate(...) at test_scAnnotate.R:7:1
2. └─scAnnotate:::br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(scAnnotate)
>
> test_check("scAnnotate")
Finding variable features for layer counts
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
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 2 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_scAnnotate.R:7:1'): (code run outside of `test_that()`) ────────
Error in `br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)`: no slot of name "counts" for this object of class "Assay5"
Backtrace:
▆
1. └─scAnnotate::scAnnotate(...) at test_scAnnotate.R:7:1
2. └─scAnnotate:::br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(scAnnotate)
>
> test_check("scAnnotate")
Finding variable features for layer counts
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
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 2 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_scAnnotate.R:7:1'): (code run outside of `test_that()`) ────────
Error in `br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)`: no slot of name "counts" for this object of class "Assay5"
Backtrace:
▆
1. └─scAnnotate::scAnnotate(...) at test_scAnnotate.R:7:1
2. └─scAnnotate:::br_seurat(train.xx = train[, -1], test = test, lognormalized = lognormalized)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64