Last updated on 2023-10-01 23:03:58 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.1 | 65.29 | 572.51 | 637.80 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.2.1 | 48.83 | 337.23 | 386.06 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.1 | 636.31 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.1 | 773.34 | NOTE | |||
| r-devel-windows-x86_64 | 1.2.1 | 51.00 | 421.00 | 472.00 | NOTE | |
| r-patched-linux-x86_64 | 1.2.1 | 47.31 | 549.00 | 596.31 | NOTE | |
| r-release-linux-x86_64 | 1.2.1 | 44.89 | 425.02 | 469.91 | ERROR | |
| r-release-macos-arm64 | 1.2.1 | 233.00 | NOTE | |||
| r-release-macos-x86_64 | 1.2.1 | 311.00 | NOTE | |||
| r-release-windows-x86_64 | 1.2.1 | 68.00 | 409.00 | 477.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.2.1 | 154.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.2.1 | 253.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.2.1 | 69.00 | 490.00 | 559.00 | OK |
Version: 1.2.1
Check: C++ specification
Result: NOTE
Specified C++11: please drop specification unless essential
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 1.2.1
Check: examples
Result: ERROR
Running examples in ‘scoper-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hierarchicalClones
> ### Title: Hierarchical clustering method for clonal partitioning
> ### Aliases: hierarchicalClones
>
> ### ** Examples
>
> # Find clonal groups
> results <- hierarchicalClones(ExampleDb, threshold=0.15)
Error in groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL, :
The column locus was not found
Calls: hierarchicalClones -> defineClonesScoper -> prepare_db -> groupGenes
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [18s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
>
> test_check("scoper")
Loading required package: scoper
Loading required package: ggplot2
As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
A description of the standard is available at https://docs.airr-community.org.
The legacy Change-O format is supported through arguments to each function
that allow the input column names to be explicitly defined.
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 14 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_clone.R:29:5'): Test identicalClones ───────────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::identicalClones(...) at test_clone.R:29:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
── Error ('test_clone.R:53:5'): Test hierarchicalClones ────────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::hierarchicalClones(...) at test_clone.R:53:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
── Error ('test_clone.R:82:5'): Test spectralClones - novj ─────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::spectralClones(...) at test_clone.R:82:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
── Error ('test_clone.R:110:5'): Test spectralClones - vj ──────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::spectralClones(...) at test_clone.R:110:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 14 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Scoper-Vignette.Rmd’ using rmarkdown
Quitting from lines 75-81 [unnamed-chunk-2] (Scoper-Vignette.Rmd)
Error: processing vignette 'Scoper-Vignette.Rmd' failed with diagnostics:
The column locus was not found
--- failed re-building ‘Scoper-Vignette.Rmd’
SUMMARY: processing the following file failed:
‘Scoper-Vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64
Version: 1.2.1
Check: examples
Result: ERROR
Running examples in ‘scoper-Ex.R’ failed
The error most likely occurred in:
> ### Name: hierarchicalClones
> ### Title: Hierarchical clustering method for clonal partitioning
> ### Aliases: hierarchicalClones
>
> ### ** Examples
>
> # Find clonal groups
> results <- hierarchicalClones(ExampleDb, threshold=0.15)
Error in groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL, :
The column locus was not found
Calls: hierarchicalClones -> defineClonesScoper -> prepare_db -> groupGenes
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-windows-x86_64
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [29s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
>
> test_check("scoper")
Loading required package: scoper
Loading required package: ggplot2
As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
A description of the standard is available at https://docs.airr-community.org.
The legacy Change-O format is supported through arguments to each function
that allow the input column names to be explicitly defined.
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 14 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_clone.R:29:5'): Test identicalClones ───────────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::identicalClones(...) at test_clone.R:29:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
── Error ('test_clone.R:53:5'): Test hierarchicalClones ────────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::hierarchicalClones(...) at test_clone.R:53:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
── Error ('test_clone.R:82:5'): Test spectralClones - novj ─────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::spectralClones(...) at test_clone.R:82:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
── Error ('test_clone.R:110:5'): Test spectralClones - vj ──────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::spectralClones(...) at test_clone.R:110:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 14 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Scoper-Vignette.Rmd’ using rmarkdown
Quitting from lines 75-81 [unnamed-chunk-2] (Scoper-Vignette.Rmd)
Error: processing vignette 'Scoper-Vignette.Rmd' failed with diagnostics:
The column locus was not found
--- failed re-building ‘Scoper-Vignette.Rmd’
SUMMARY: processing the following file failed:
‘Scoper-Vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-windows-x86_64
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [24s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
>
> test_check("scoper")
Loading required package: scoper
Loading required package: ggplot2
As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
A description of the standard is available at https://docs.airr-community.org.
The legacy Change-O format is supported through arguments to each function
that allow the input column names to be explicitly defined.
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 14 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_clone.R:29:5'): Test identicalClones ───────────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::identicalClones(...) at test_clone.R:29:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
── Error ('test_clone.R:53:5'): Test hierarchicalClones ────────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::hierarchicalClones(...) at test_clone.R:53:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
── Error ('test_clone.R:82:5'): Test spectralClones - novj ─────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::spectralClones(...) at test_clone.R:82:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
── Error ('test_clone.R:110:5'): Test spectralClones - vj ──────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::spectralClones(...) at test_clone.R:110:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 14 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.2.1
Check: tests
Result: ERROR
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
>
> test_check("scoper")
Loading required package: scoper
Loading required package: ggplot2
As of v1.0.0 the AIRR Rearrangement schema is now the default file format.
A description of the standard is available at https://docs.airr-community.org.
The legacy Change-O format is supported through arguments to each function
that allow the input column names to be explicitly defined.
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 14 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_clone.R:29:5'): Test identicalClones ───────────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::identicalClones(...) at test_clone.R:29:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
── Error ('test_clone.R:53:5'): Test hierarchicalClones ────────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::hierarchicalClones(...) at test_clone.R:53:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
── Error ('test_clone.R:82:5'): Test spectralClones - novj ─────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::spectralClones(...) at test_clone.R:82:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
── Error ('test_clone.R:110:5'): Test spectralClones - vj ──────────────────────
Error in `groupGenes(db, v_call = v_call, j_call = j_call, junc_len = NULL,
cell_id = cell_id, locus = locus, only_heavy = only_heavy,
first = first)`: The column locus was not found
Backtrace:
▆
1. └─scoper::spectralClones(...) at test_clone.R:110:4
2. └─scoper:::defineClonesScoper(...)
3. └─scoper:::prepare_db(...)
4. └─alakazam::groupGenes(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 14 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64