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

Last updated on 2024-07-14 00:55:45 CEST.

Package ERROR NOTE
MOCHA 4 9

Package MOCHA

Current CRAN status: ERROR: 4, NOTE: 9

Additional issues

noSuggests

Version: 1.1.0
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘ArchR’ Flavors: r-devel-linux-x86_64-debian-clang, 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: 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’ [78s/171s] 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’ [41s/54s] 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-oldrel-macos-arm64

Version: 1.1.0
Check: running R code from vignettes
Result: WARN Errors in running code in vignettes: when running code in ‘COVID-walkthrough.Rmd’ ... > knitr::opts_chunk$set(collapse = TRUE, comment = "#>", + eval = FALSE) > library(MOCHA) > library(ArchR) When sourcing ‘COVID-walkthrough.R’: Error: there is no package called ‘ArchR’ Execution halted when running code in ‘ImportingFromOtherSources.Rmd’ ... The following objects are masked from ‘package:base’: intersect, t > library(SeuratDisk) When sourcing ‘ImportingFromOtherSources.R’: Error: there is no package called ‘SeuratDisk’ Execution halted ‘COVID-walkthrough.Rmd’ using ‘UTF-8’... failed ‘ImportingFromOtherSources.Rmd’ using ‘UTF-8’... failed Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [73s/120s] 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-oldrel-macos-x86_64