CRAN Package Check Results for Package karyotapR

Last updated on 2025-10-09 13:49:45 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.1 36.66 321.47 358.13 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.1 28.70 235.32 264.02 ERROR
r-devel-linux-x86_64-fedora-clang 1.0.1 602.27 ERROR
r-devel-linux-x86_64-fedora-gcc 1.0.1 542.08 NOTE
r-devel-windows-x86_64 1.0.1 37.00 269.00 306.00 ERROR
r-patched-linux-x86_64 1.0.1 38.58 332.18 370.76 NOTE
r-release-linux-x86_64 1.0.1 33.84 329.00 362.84 NOTE
r-release-macos-arm64 1.0.1 141.00 NOTE
r-release-macos-x86_64 1.0.1 316.00 NOTE
r-release-windows-x86_64 1.0.1 40.00 300.00 340.00 NOTE
r-oldrel-macos-arm64 1.0.1 146.00 OK
r-oldrel-macos-x86_64 1.0.1 245.00 OK
r-oldrel-windows-x86_64 1.0.1 54.00 399.00 453.00 OK

Check Details

Version: 1.0.1
Check: DESCRIPTION meta-information
Result: NOTE Missing dependency on R >= 4.1.0 because package code uses the pipe |> or function shorthand \(...) syntax added in R 4.1.0. File(s) using such syntax: ‘GaussianMixtureCalls.R’ 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: 1.0.1
Check: examples
Result: ERROR Running examples in ‘karyotapR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getCytobands > ### Title: Add chromosome cytobands and chromosome arms to > ### 'TapestriExperiment' > ### Aliases: getCytobands > > ### ** Examples > > tap.object <- newTapestriExperimentExample() # example TapestriExperiment object ℹ Moving gRNA probe to `altExp` slot "grnaCounts". ℹ Moving barcode probe to `altExp` slot "barcodeCounts". ℹ Moving chrY probe(s) probe_231, probe_232, probe_233, probe_234, probe_235, probe_236, probe_237, probe_238, probe_239, and probe_240 to `altExp` slot "chrYCounts". > tap.object <- getCytobands(tap.object, genome = "hg19") ℹ Adding cytobands from hg19. Loading required namespace: GenomeInfoDb Failed with error: ‘there is no package called ‘GenomeInfoDb’’ Error in .requirePackage(package) : unable to load required package ‘GenomeInfoDb’ Calls: getCytobands ... vapply -> FUN -> is -> getClassDef -> .requirePackage Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed calcSmoothCopyNumber 4.349 0.165 5.316 assayHeatmap 4.463 0.020 5.726 Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.1
Check: tests
Result: ERROR Running ‘testthat.R’ [13s/17s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(karyotapR) Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: Seqinfo Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("karyotapR") Failed with error: 'there is no package called 'GenomeInfoDb'' [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-normalization.R:16:5'): NA in normalization input triggers message ── Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb' Backtrace: ▆ 1. ├─base::suppressMessages(newDummyTapestriExperiment()) at test-normalization.R:16:5 2. │ └─base::withCallingHandlers(...) 3. └─karyotapR:::newDummyTapestriExperiment() 4. └─karyotapR::getCytobands(tapestri.object) 5. └─karyotapR:::.GetCytobands.df(amplicon.df, return.genomic.ranges = TRUE) 6. ├─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges) 7. └─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges) 8. └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...) 9. └─GenomicRanges:::findOverlaps_GNCList(...) 10. ├─base::merge(seqinfo(query), seqinfo(subject)) 11. └─Seqinfo::merge(seqinfo(query), seqinfo(subject)) 12. └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...) 13. └─base::vapply(args, function(arg) is(arg, class(x)), logical(1)) 14. └─Seqinfo (local) FUN(X[[i]], ...) 15. └─methods::is(arg, class(x)) 16. └─methods::getClassDef(class1) 17. └─methods:::.requirePackage(package) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.1
Check: examples
Result: ERROR Running examples in ‘karyotapR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getCytobands > ### Title: Add chromosome cytobands and chromosome arms to > ### 'TapestriExperiment' > ### Aliases: getCytobands > > ### ** Examples > > tap.object <- newTapestriExperimentExample() # example TapestriExperiment object ℹ Moving gRNA probe to `altExp` slot "grnaCounts". ℹ Moving barcode probe to `altExp` slot "barcodeCounts". ℹ Moving chrY probe(s) probe_231, probe_232, probe_233, probe_234, probe_235, probe_236, probe_237, probe_238, probe_239, and probe_240 to `altExp` slot "chrYCounts". > tap.object <- getCytobands(tap.object, genome = "hg19") ℹ Adding cytobands from hg19. Loading required namespace: GenomeInfoDb Failed with error: ‘there is no package called ‘GenomeInfoDb’’ Error in .requirePackage(package) : unable to load required package ‘GenomeInfoDb’ Calls: getCytobands ... vapply -> FUN -> is -> getClassDef -> .requirePackage Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.1
Check: tests
Result: ERROR Running ‘testthat.R’ [10s/13s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(karyotapR) Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: Seqinfo Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("karyotapR") Failed with error: 'there is no package called 'GenomeInfoDb'' [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-normalization.R:16:5'): NA in normalization input triggers message ── Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb' Backtrace: ▆ 1. ├─base::suppressMessages(newDummyTapestriExperiment()) at test-normalization.R:16:5 2. │ └─base::withCallingHandlers(...) 3. └─karyotapR:::newDummyTapestriExperiment() 4. └─karyotapR::getCytobands(tapestri.object) 5. └─karyotapR:::.GetCytobands.df(amplicon.df, return.genomic.ranges = TRUE) 6. ├─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges) 7. └─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges) 8. └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...) 9. └─GenomicRanges:::findOverlaps_GNCList(...) 10. ├─base::merge(seqinfo(query), seqinfo(subject)) 11. └─Seqinfo::merge(seqinfo(query), seqinfo(subject)) 12. └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...) 13. └─base::vapply(args, function(arg) is(arg, class(x)), logical(1)) 14. └─Seqinfo (local) FUN(X[[i]], ...) 15. └─methods::is(arg, class(x)) 16. └─methods::getClassDef(class1) 17. └─methods:::.requirePackage(package) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.1
Check: examples
Result: ERROR Running examples in ‘karyotapR-Ex.R’ failed The error most likely occurred in: > ### Name: getCytobands > ### Title: Add chromosome cytobands and chromosome arms to > ### 'TapestriExperiment' > ### Aliases: getCytobands > > ### ** Examples > > tap.object <- newTapestriExperimentExample() # example TapestriExperiment object ℹ Moving gRNA probe to `altExp` slot "grnaCounts". ℹ Moving barcode probe to `altExp` slot "barcodeCounts". ℹ Moving chrY probe(s) probe_231, probe_232, probe_233, probe_234, probe_235, probe_236, probe_237, probe_238, probe_239, and probe_240 to `altExp` slot "chrYCounts". > tap.object <- getCytobands(tap.object, genome = "hg19") ℹ Adding cytobands from hg19. Loading required namespace: GenomeInfoDb Failed with error: ‘there is no package called ‘GenomeInfoDb’’ Error in .requirePackage(package) : unable to load required package ‘GenomeInfoDb’ Calls: getCytobands ... vapply -> FUN -> is -> getClassDef -> .requirePackage Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64

Version: 1.0.1
Check: tests
Result: ERROR Running ‘testthat.R’ [21s/63s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(karyotapR) Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: Seqinfo Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("karyotapR") Failed with error: 'there is no package called 'GenomeInfoDb'' [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-normalization.R:16:5'): NA in normalization input triggers message ── Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb' Backtrace: ▆ 1. ├─base::suppressMessages(newDummyTapestriExperiment()) at test-normalization.R:16:5 2. │ └─base::withCallingHandlers(...) 3. └─karyotapR:::newDummyTapestriExperiment() 4. └─karyotapR::getCytobands(tapestri.object) 5. └─karyotapR:::.GetCytobands.df(amplicon.df, return.genomic.ranges = TRUE) 6. ├─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges) 7. └─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges) 8. └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...) 9. └─GenomicRanges:::findOverlaps_GNCList(...) 10. ├─base::merge(seqinfo(query), seqinfo(subject)) 11. └─Seqinfo::merge(seqinfo(query), seqinfo(subject)) 12. └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...) 13. └─base::vapply(args, function(arg) is(arg, class(x)), logical(1)) 14. └─Seqinfo (local) FUN(X[[i]], ...) 15. └─methods::is(arg, class(x)) 16. └─methods::getClassDef(class1) 17. └─methods:::.requirePackage(package) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.1
Check: tests
Result: ERROR Running 'testthat.R' [11s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(karyotapR) Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: Seqinfo Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("karyotapR") Failed with error: 'there is no package called 'GenomeInfoDb'' [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-normalization.R:16:5'): NA in normalization input triggers message ── Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb' Backtrace: ▆ 1. ├─base::suppressMessages(newDummyTapestriExperiment()) at test-normalization.R:16:5 2. │ └─base::withCallingHandlers(...) 3. └─karyotapR:::newDummyTapestriExperiment() 4. └─karyotapR::getCytobands(tapestri.object) 5. └─karyotapR:::.GetCytobands.df(amplicon.df, return.genomic.ranges = TRUE) 6. ├─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges) 7. └─GenomicRanges::findOverlaps(amplicon.gr, cytoband.hg19.genomicRanges) 8. └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...) 9. └─GenomicRanges:::findOverlaps_GNCList(...) 10. ├─base::merge(seqinfo(query), seqinfo(subject)) 11. └─Seqinfo::merge(seqinfo(query), seqinfo(subject)) 12. └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...) 13. └─base::vapply(args, function(arg) is(arg, class(x)), logical(1)) 14. └─Seqinfo (local) FUN(X[[i]], ...) 15. └─methods::is(arg, class(x)) 16. └─methods::getClassDef(class1) 17. └─methods:::.requirePackage(package) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted Flavor: r-devel-windows-x86_64

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