CRAN Package Check Results for Maintainer ‘Imran McGrath <aifi.compbio.support at alleninstitute.org>’

Last updated on 2024-05-04 17:53:18 CEST.

Package	ERROR	WARN	NOTE
MOCHA	5	1	7

Package MOCHA

Current CRAN status: ERROR: 5, WARN: 1, NOTE: 7

Additional issues

noSuggests

Version: 1.1.0
Check: package dependencies
Result: ERROR Packages required but not available: 'plyranges', 'GenomicRanges', 'RaggedExperiment', 'MultiAssayExperiment', 'SummarizedExperiment', 'ggbio', 'AnnotationDbi', 'GenomicFeatures', 'ensembldb', 'BSgenome' Packages suggested but not available for checking: 'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'org.Hs.eg.db', '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-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1.0
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘ArchR’ Imports includes 31 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. Flavor: r-devel-linux-x86_64-fedora-clang

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

Version: 1.1.0
Check: for unstated dependencies in ‘tests’
Result: WARN Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' Flavor: r-devel-windows-x86_64

Version: 1.1.0
Check: package dependencies
Result: ERROR Package required but not available: ‘ggbio’ Packages suggested but not available for checking: 'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavor: r-release-macos-arm64

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' Flavor: r-release-macos-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [83s/201s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── 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', '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’ [46s/65s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── 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 14 | 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/157s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── 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 14 | SKIP 23 | PASS 21 ] Error: Test failures Execution halted Flavor: r-oldrel-macos-x86_64