CRAN Package Check Results for Package MOCHA

Last updated on 2024-12-25 05:48:39 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.0 21.01 248.70 269.71 OK
r-devel-linux-x86_64-debian-gcc 1.1.0 16.10 182.59 198.69 OK
r-devel-linux-x86_64-fedora-clang 1.1.0 416.37 OK
r-devel-linux-x86_64-fedora-gcc 1.1.0 436.87 OK
r-devel-windows-x86_64 1.1.0 24.00 406.00 430.00 OK
r-patched-linux-x86_64 1.1.0 20.34 237.82 258.16 NOTE
r-release-linux-x86_64 1.1.0 20.60 234.12 254.72 NOTE
r-release-macos-arm64 1.1.0 130.00 ERROR
r-release-macos-x86_64 1.1.0 236.00 ERROR
r-release-windows-x86_64 1.1.0 24.00 400.00 424.00 NOTE
r-oldrel-macos-arm64 1.1.0 121.00 ERROR
r-oldrel-macos-x86_64 1.1.0 245.00 ERROR
r-oldrel-windows-x86_64 1.1.0 26.00 566.00 592.00 NOTE

Additional issues

gcc-UBSAN noSuggests

Check Details

Version: 1.1.0
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘ArchR’ Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1.0
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19' Flavors: r-release-macos-arm64, r-release-macos-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [47s/56s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(MOCHA) > > test_check("MOCHA") Loading required package: chromVARmotifs harmonizing input: removing 1 sampleMap rows not in names(experiments) harmonizing input: removing 3 sampleMap rows not in names(experiments) [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ] ══ Skipped tests (23) ══════════════════════════════════════════════════════════ • On CRAN (20): 'test_COVID_data_pipeline.R:1:1', 'test_MotifEnrichment.R:1:1', 'test_MotifSetEnrichmentAnalysis.R:1:1', 'test_addMotifSet.R:1:1', 'test_callOpenTiles.R:3:1', 'test_exportCoverage.R:1:1', 'test_extractRegion.R:1:1', 'test_getCoAccessibleLinks.R:22:3', 'test_getCoAccessibleLinks.R:53:3', 'test_getCoverage.R:1:1', 'test_getDifferentialAccessibleTiles.R:1:1', 'test_getPopFrags.R:13:1', 'test_getSampleTileMatrix.R:18:3', 'test_packMOCHA.R:1:1', 'test_plotRegion.R:1:1', 'test_subsetMOCHAObject.R:13:3', 'test_subsetMOCHAObject.R:25:3', 'test_subsetMOCHAObject.R:67:3', 'test_subsetMOCHAObject.R:97:3', 'test_subsetMOCHAObject.R:127:3' • {BSgenome.Hsapiens.UCSC.hg19} is not installed (3): 'test_combineSampleTileMatrix.R:2:1', 'test_dimensionalityReduction.R:1:1', 'test_testCoAccessibility.R:2:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_exportDifferentials.R:28:3'): exportDifferentials works on a 3 sample test dataset ── Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed. You first need to install it, which you can do with: library(BiocManager) install("BSgenome.Hsapiens.UCSC.hg19") Backtrace: ▆ 1. └─MOCHA::exportDifferentials(...) at test_exportDifferentials.R:28:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome) 3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked) 4. └─BSgenome:::.stopOnAvailablePkg(genome) ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials works on a 3 sample test dataset ── Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed. You first need to install it, which you can do with: library(BiocManager) install("BSgenome.Hsapiens.UCSC.hg19") Backtrace: ▆ 1. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome) 3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked) 4. └─BSgenome:::.stopOnAvailablePkg(genome) [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ] Error: Test failures Execution halted Flavor: r-release-macos-arm64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [79s/113s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(MOCHA) > > test_check("MOCHA") Loading required package: chromVARmotifs harmonizing input: removing 1 sampleMap rows not in names(experiments) harmonizing input: removing 3 sampleMap rows not in names(experiments) [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ] ══ Skipped tests (23) ══════════════════════════════════════════════════════════ • On CRAN (20): 'test_COVID_data_pipeline.R:1:1', 'test_MotifEnrichment.R:1:1', 'test_MotifSetEnrichmentAnalysis.R:1:1', 'test_addMotifSet.R:1:1', 'test_callOpenTiles.R:3:1', 'test_exportCoverage.R:1:1', 'test_extractRegion.R:1:1', 'test_getCoAccessibleLinks.R:22:3', 'test_getCoAccessibleLinks.R:53:3', 'test_getCoverage.R:1:1', 'test_getDifferentialAccessibleTiles.R:1:1', 'test_getPopFrags.R:13:1', 'test_getSampleTileMatrix.R:18:3', 'test_packMOCHA.R:1:1', 'test_plotRegion.R:1:1', 'test_subsetMOCHAObject.R:13:3', 'test_subsetMOCHAObject.R:25:3', 'test_subsetMOCHAObject.R:67:3', 'test_subsetMOCHAObject.R:97:3', 'test_subsetMOCHAObject.R:127:3' • {BSgenome.Hsapiens.UCSC.hg19} is not installed (3): 'test_combineSampleTileMatrix.R:2:1', 'test_dimensionalityReduction.R:1:1', 'test_testCoAccessibility.R:2:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_exportDifferentials.R:28:3'): exportDifferentials works on a 3 sample test dataset ── Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed. You first need to install it, which you can do with: library(BiocManager) install("BSgenome.Hsapiens.UCSC.hg19") Backtrace: ▆ 1. └─MOCHA::exportDifferentials(...) at test_exportDifferentials.R:28:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome) 3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked) 4. └─BSgenome:::.stopOnAvailablePkg(genome) ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials works on a 3 sample test dataset ── Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed. You first need to install it, which you can do with: library(BiocManager) install("BSgenome.Hsapiens.UCSC.hg19") Backtrace: ▆ 1. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome) 3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked) 4. └─BSgenome:::.stopOnAvailablePkg(genome) [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ] Error: Test failures Execution halted Flavor: r-release-macos-x86_64

Version: 1.1.0
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene' Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 1.1.0
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene', 'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR' Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [42s/51s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(MOCHA) > > test_check("MOCHA") Loading required package: chromVARmotifs harmonizing input: removing 1 sampleMap rows not in names(experiments) harmonizing input: removing 3 sampleMap rows not in names(experiments) [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ] ══ Skipped tests (23) ══════════════════════════════════════════════════════════ • On CRAN (20): 'test_COVID_data_pipeline.R:1:1', 'test_MotifEnrichment.R:1:1', 'test_MotifSetEnrichmentAnalysis.R:1:1', 'test_addMotifSet.R:1:1', 'test_callOpenTiles.R:3:1', 'test_exportCoverage.R:1:1', 'test_extractRegion.R:1:1', 'test_getCoAccessibleLinks.R:22:3', 'test_getCoAccessibleLinks.R:53:3', 'test_getCoverage.R:1:1', 'test_getDifferentialAccessibleTiles.R:1:1', 'test_getPopFrags.R:13:1', 'test_getSampleTileMatrix.R:18:3', 'test_packMOCHA.R:1:1', 'test_plotRegion.R:1:1', 'test_subsetMOCHAObject.R:13:3', 'test_subsetMOCHAObject.R:25:3', 'test_subsetMOCHAObject.R:67:3', 'test_subsetMOCHAObject.R:97:3', 'test_subsetMOCHAObject.R:127:3' • {BSgenome.Hsapiens.UCSC.hg19} is not installed (1): 'test_dimensionalityReduction.R:1:1' • {chromVAR} is not installed (2): 'test_combineSampleTileMatrix.R:1:1', 'test_testCoAccessibility.R:1:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_exportDifferentials.R:28:3'): exportDifferentials works on a 3 sample test dataset ── Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed. You first need to install it, which you can do with: library(BiocManager) install("BSgenome.Hsapiens.UCSC.hg19") Backtrace: ▆ 1. └─MOCHA::exportDifferentials(...) at test_exportDifferentials.R:28:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome) 3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked) 4. └─BSgenome:::.stopOnAvailablePkg(genome) ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials works on a 3 sample test dataset ── Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed. You first need to install it, which you can do with: library(BiocManager) install("BSgenome.Hsapiens.UCSC.hg19") Backtrace: ▆ 1. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome) 3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked) 4. └─BSgenome:::.stopOnAvailablePkg(genome) [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ] Error: Test failures Execution halted Flavor: r-oldrel-macos-arm64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [74s/100s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(MOCHA) > > test_check("MOCHA") Loading required package: chromVARmotifs harmonizing input: removing 1 sampleMap rows not in names(experiments) harmonizing input: removing 3 sampleMap rows not in names(experiments) [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ] ══ Skipped tests (23) ══════════════════════════════════════════════════════════ • On CRAN (20): 'test_COVID_data_pipeline.R:1:1', 'test_MotifEnrichment.R:1:1', 'test_MotifSetEnrichmentAnalysis.R:1:1', 'test_addMotifSet.R:1:1', 'test_callOpenTiles.R:3:1', 'test_exportCoverage.R:1:1', 'test_extractRegion.R:1:1', 'test_getCoAccessibleLinks.R:22:3', 'test_getCoAccessibleLinks.R:53:3', 'test_getCoverage.R:1:1', 'test_getDifferentialAccessibleTiles.R:1:1', 'test_getPopFrags.R:13:1', 'test_getSampleTileMatrix.R:18:3', 'test_packMOCHA.R:1:1', 'test_plotRegion.R:1:1', 'test_subsetMOCHAObject.R:13:3', 'test_subsetMOCHAObject.R:25:3', 'test_subsetMOCHAObject.R:67:3', 'test_subsetMOCHAObject.R:97:3', 'test_subsetMOCHAObject.R:127:3' • {BSgenome.Hsapiens.UCSC.hg19} is not installed (1): 'test_dimensionalityReduction.R:1:1' • {chromVAR} is not installed (2): 'test_combineSampleTileMatrix.R:1:1', 'test_testCoAccessibility.R:1:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_exportDifferentials.R:28:3'): exportDifferentials works on a 3 sample test dataset ── Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed. You first need to install it, which you can do with: library(BiocManager) install("BSgenome.Hsapiens.UCSC.hg19") Backtrace: ▆ 1. └─MOCHA::exportDifferentials(...) at test_exportDifferentials.R:28:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome) 3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked) 4. └─BSgenome:::.stopOnAvailablePkg(genome) ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials works on a 3 sample test dataset ── Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed. You first need to install it, which you can do with: library(BiocManager) install("BSgenome.Hsapiens.UCSC.hg19") Backtrace: ▆ 1. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome) 3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked) 4. └─BSgenome:::.stopOnAvailablePkg(genome) [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ] Error: Test failures Execution halted Flavor: r-oldrel-macos-x86_64