Last updated on 2026-09-16 09:58:16 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.10 | 21.04 | 207.66 | 228.70 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.10 | 15.75 | 150.03 | 165.78 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.10 | 16.00 | 144.45 | 160.45 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.11 | 16.00 | 152.67 | 168.67 | OK | |
| r-devel-windows-x86_64 | 1.0.10 | 26.00 | 261.00 | 287.00 | OK | |
| r-patched-linux-x86_64 | 1.0.10 | 21.17 | 194.91 | 216.08 | OK | |
| r-release-linux-x86_64 | 1.0.10 | 20.69 | 192.99 | 213.68 | OK | |
| r-release-macos-arm64 | 1.0.10 | 7.00 | 55.00 | 62.00 | OK | |
| r-release-macos-x86_64 | 1.0.11 | 17.00 | 198.00 | 215.00 | OK | |
| r-release-windows-x86_64 | 1.0.10 | 24.00 | 182.00 | 206.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.11 | 6.00 | 56.00 | 62.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.0.11 | 18.00 | 163.00 | 181.00 | ERROR | |
| r-oldrel-windows-x86_64 | 1.0.10 | 35.00 | 249.00 | 284.00 | OK |
Version: 1.0.11
Check: examples
Result: ERROR
Running examples in ‘SATS-Ex.R’ failed
The error most likely occurred in:
> ### Name: GenerateLMatrix
> ### Title: Generate a sample-level panel-context matrix
> ### Aliases: GenerateLMatrix
>
> ### ** Examples
>
> data(SimData, package="SATS")
>
> keep <- match(SimData$PatientInfo$SEQ_ASSAY_ID,
+ unique(SimData$PanelEx$SEQ_ASSAY_ID), nomatch=0) > 0
> PatientInfo <- SimData$PatientInfo[keep, ]
>
> L_mat <- GenerateLMatrix(SimData$PanelEx, PatientInfo, Class="SBS",
+ SBS_order="COSMIC", ref.genome="hg19")
Error in (function (cond) :
error in evaluating the argument 'x' in selecting a method for function 'getSeq': there is no package called ‘BSgenome.Hsapiens.UCSC.hg19’
Calls: GenerateLMatrix ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.0.11
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(SATS)
>
> test_check("SATS")
Saving _problems/test-GeneratePanelSize-14.R
Saving _problems/test-GenerateVMatrix-18.R
Saving _problems/test-GenerateVMatrix-27.R
Saving _problems/test-GenerateVMatrix-42.R
Saving _problems/test-GenerateVMatrix-62.R
Saving _problems/test-GenerateVMatrix-78.R
Saving _problems/test-input-conversion-63.R
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 45 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-GeneratePanelSize.R:14:1'): (code run outside of `test_that()`) ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'BSgenome.Hsapiens.UCSC.hg19'", call = loadNamespace(x), package = "BSgenome.Hsapiens.UCSC.hg19", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'x' in selecting a method for function 'getSeq': there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
Backtrace:
▆
1. ├─SATS::GeneratePanelSize(...) at test-GeneratePanelSize.R:14:1
2. │ └─SATS:::GeneratePanelSize_SBS(...)
3. │ └─Biostrings::getSeq(BSgenome.Hsapiens.UCSC.hg19::Hsapiens, Seq_assay_GRanges)
4. ├─base::loadNamespace(x)
5. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
7. │ │ └─base (local) doWithOneRestart(return(expr), restart)
8. │ └─base::stop(cond)
9. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-GenerateVMatrix.R:18:3'): GenerateVMatrix returns COSMIC-ordered SBS counts ──
Error in `get_reference_genome(ref.genome)`: Make sure package BSgenome.Hsapiens.UCSC.hg19 is loaded
Backtrace:
▆
1. └─SATS::GenerateVMatrix(sbs_mut, Class = "SBS", ref.genome = "hg19") at test-GenerateVMatrix.R:18:3
2. └─SATS:::GenerateVMatrix_SBS(mutation_record, ref.genome, mutation_order)
3. └─SATS:::get_reference_genome(ref.genome)
── Error ('test-GenerateVMatrix.R:27:3'): GenerateVMatrix returns DBS78-ordered DBS counts ──
Error in `get_reference_genome(ref.genome)`: Make sure package BSgenome.Hsapiens.UCSC.hg19 is loaded
Backtrace:
▆
1. └─SATS::GenerateVMatrix(dbs_mut, Class = "DBS", ref.genome = "hg19") at test-GenerateVMatrix.R:27:3
2. └─SATS:::GenerateVMatrix_DBS(mutation_record, ref.genome, mutation_order)
3. └─SATS:::get_reference_genome(ref.genome)
── Error ('test-GenerateVMatrix.R:42:3'): GenerateVMatrix and GenerateLMatrix align SBS V and L matrices ──
Error in `get_reference_genome(ref.genome)`: Make sure package BSgenome.Hsapiens.UCSC.hg19 is loaded
Backtrace:
▆
1. └─SATS::GenerateVMatrix(sbs_mut, Class = "SBS", ref.genome = "hg19") at test-GenerateVMatrix.R:42:3
2. └─SATS:::GenerateVMatrix_SBS(mutation_record, ref.genome, mutation_order)
3. └─SATS:::get_reference_genome(ref.genome)
── Error ('test-GenerateVMatrix.R:62:3'): GenerateVMatrix and GenerateLMatrix align DBS V and L matrices ──
Error in `get_reference_genome(ref.genome)`: Make sure package BSgenome.Hsapiens.UCSC.hg19 is loaded
Backtrace:
▆
1. └─SATS::GenerateVMatrix(dbs_mut, Class = "DBS", ref.genome = "hg19") at test-GenerateVMatrix.R:62:3
2. └─SATS:::GenerateVMatrix_DBS(mutation_record, ref.genome, mutation_order)
3. └─SATS:::get_reference_genome(ref.genome)
── Error ('test-GenerateVMatrix.R:76:3'): GenerateLMatrix direct genomic-information input matches low-level workflow ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'BSgenome.Hsapiens.UCSC.hg19'", call = loadNamespace(x), package = "BSgenome.Hsapiens.UCSC.hg19", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'x' in selecting a method for function 'getSeq': there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
Backtrace:
▆
1. ├─SATS::GeneratePanelSize(...) at test-GenerateVMatrix.R:76:3
2. │ └─SATS:::GeneratePanelSize_SBS(...)
3. │ └─Biostrings::getSeq(BSgenome.Hsapiens.UCSC.hg19::Hsapiens, Seq_assay_GRanges)
4. ├─base::loadNamespace(x)
5. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
7. │ │ └─base (local) doWithOneRestart(return(expr), restart)
8. │ └─base::stop(cond)
9. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-input-conversion.R:63:3'): VCF and BED converters feed GenerateVMatrix and GenerateLMatrix ──
Error in `get_reference_genome(ref.genome)`: Make sure package BSgenome.Hsapiens.UCSC.hg19 is loaded
Backtrace:
▆
1. └─SATS::GenerateVMatrix(mut, Class = "SBS", ref.genome = "hg19") at test-input-conversion.R:63:3
2. └─SATS:::GenerateVMatrix_SBS(mutation_record, ref.genome, mutation_order)
3. └─SATS:::get_reference_genome(ref.genome)
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 45 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 1.0.11
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(SATS)
>
> test_check("SATS")
Saving _problems/test-GeneratePanelSize-14.R
Saving _problems/test-GenerateVMatrix-18.R
Saving _problems/test-GenerateVMatrix-27.R
Saving _problems/test-GenerateVMatrix-42.R
Saving _problems/test-GenerateVMatrix-62.R
Saving _problems/test-GenerateVMatrix-78.R
Saving _problems/test-input-conversion-63.R
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 45 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-GeneratePanelSize.R:14:1'): (code run outside of `test_that()`) ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'BSgenome.Hsapiens.UCSC.hg19'", call = loadNamespace(x), package = "BSgenome.Hsapiens.UCSC.hg19", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'x' in selecting a method for function 'getSeq': there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
Backtrace:
▆
1. ├─SATS::GeneratePanelSize(...) at test-GeneratePanelSize.R:14:1
2. │ └─SATS:::GeneratePanelSize_SBS(...)
3. │ └─Biostrings::getSeq(BSgenome.Hsapiens.UCSC.hg19::Hsapiens, Seq_assay_GRanges)
4. ├─base::loadNamespace(x)
5. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
7. │ │ └─base (local) doWithOneRestart(return(expr), restart)
8. │ └─base::stop(cond)
9. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-GenerateVMatrix.R:18:3'): GenerateVMatrix returns COSMIC-ordered SBS counts ──
Error in `get_reference_genome(ref.genome)`: Make sure package BSgenome.Hsapiens.UCSC.hg19 is loaded
Backtrace:
▆
1. └─SATS::GenerateVMatrix(sbs_mut, Class = "SBS", ref.genome = "hg19") at test-GenerateVMatrix.R:18:3
2. └─SATS:::GenerateVMatrix_SBS(mutation_record, ref.genome, mutation_order)
3. └─SATS:::get_reference_genome(ref.genome)
── Error ('test-GenerateVMatrix.R:27:3'): GenerateVMatrix returns DBS78-ordered DBS counts ──
Error in `get_reference_genome(ref.genome)`: Make sure package BSgenome.Hsapiens.UCSC.hg19 is loaded
Backtrace:
▆
1. └─SATS::GenerateVMatrix(dbs_mut, Class = "DBS", ref.genome = "hg19") at test-GenerateVMatrix.R:27:3
2. └─SATS:::GenerateVMatrix_DBS(mutation_record, ref.genome, mutation_order)
3. └─SATS:::get_reference_genome(ref.genome)
── Error ('test-GenerateVMatrix.R:42:3'): GenerateVMatrix and GenerateLMatrix align SBS V and L matrices ──
Error in `get_reference_genome(ref.genome)`: Make sure package BSgenome.Hsapiens.UCSC.hg19 is loaded
Backtrace:
▆
1. └─SATS::GenerateVMatrix(sbs_mut, Class = "SBS", ref.genome = "hg19") at test-GenerateVMatrix.R:42:3
2. └─SATS:::GenerateVMatrix_SBS(mutation_record, ref.genome, mutation_order)
3. └─SATS:::get_reference_genome(ref.genome)
── Error ('test-GenerateVMatrix.R:62:3'): GenerateVMatrix and GenerateLMatrix align DBS V and L matrices ──
Error in `get_reference_genome(ref.genome)`: Make sure package BSgenome.Hsapiens.UCSC.hg19 is loaded
Backtrace:
▆
1. └─SATS::GenerateVMatrix(dbs_mut, Class = "DBS", ref.genome = "hg19") at test-GenerateVMatrix.R:62:3
2. └─SATS:::GenerateVMatrix_DBS(mutation_record, ref.genome, mutation_order)
3. └─SATS:::get_reference_genome(ref.genome)
── Error ('test-GenerateVMatrix.R:76:3'): GenerateLMatrix direct genomic-information input matches low-level workflow ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'BSgenome.Hsapiens.UCSC.hg19'", call = loadNamespace(x), package = "BSgenome.Hsapiens.UCSC.hg19", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'x' in selecting a method for function 'getSeq': there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
Backtrace:
▆
1. ├─SATS::GeneratePanelSize(...) at test-GenerateVMatrix.R:76:3
2. │ └─SATS:::GeneratePanelSize_SBS(...)
3. │ └─Biostrings::getSeq(BSgenome.Hsapiens.UCSC.hg19::Hsapiens, Seq_assay_GRanges)
4. ├─base::loadNamespace(x)
5. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
7. │ │ └─base (local) doWithOneRestart(return(expr), restart)
8. │ └─base::stop(cond)
9. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-input-conversion.R:63:3'): VCF and BED converters feed GenerateVMatrix and GenerateLMatrix ──
Error in `get_reference_genome(ref.genome)`: Make sure package BSgenome.Hsapiens.UCSC.hg19 is loaded
Backtrace:
▆
1. └─SATS::GenerateVMatrix(mut, Class = "SBS", ref.genome = "hg19") at test-input-conversion.R:63:3
2. └─SATS:::GenerateVMatrix_SBS(mutation_record, ref.genome, mutation_order)
3. └─SATS:::get_reference_genome(ref.genome)
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 45 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-x86_64