CRAN Package Check Results for Package SATS

Last updated on 2026-09-21 11:51:56 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.0.11	21.73	225.02	246.75	OK
r-devel-linux-x86_64-debian-gcc	1.0.11	17.61	158.88	176.49	OK
r-devel-linux-x86_64-fedora-clang	1.0.11	17.00	152.46	169.46	OK
r-devel-linux-x86_64-fedora-gcc	1.0.11	16.00	147.52	163.52	OK
r-devel-windows-x86_64	1.0.11	29.00	281.00	310.00	OK
r-patched-linux-x86_64	1.0.10	21.93	192.05	213.98	OK
r-release-linux-x86_64	1.0.11	21.48	206.24	227.72	OK
r-release-macos-arm64	1.0.11	6.00	51.00	57.00	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	45.00	51.00	ERROR
r-oldrel-macos-x86_64	1.0.11	17.00	159.00	176.00	ERROR
r-oldrel-windows-x86_64	1.0.11	37.00	269.00	306.00	OK

Check Details

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