Last updated on 2024-12-22 10:50:16 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| MOCHA | 5 | 4 | 4 |
Current CRAN status: ERROR: 5, NOTE: 4, OK: 4
Version: 1.1.0
Check: package dependencies
Result: ERROR
Packages required but not available:
'plyranges', 'ggbio', 'GenomicFeatures', 'ensembldb', 'BSgenome'
Packages suggested but not available for checking:
'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19',
'chromVAR', 'rtracklayer'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-clang
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’ [49s/58s]
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’ [78s/107s]
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’ [47s/55s]
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’ [73s/99s]
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