* using log directory ‘/srv/hornik/tmp/CRAN/SCdeconR.Rcheck’ * using R Under development (unstable) (2024-02-19 r85946) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘SCdeconR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SCdeconR’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] NOTE Maintainer: ‘Yuanhang Liu ’ New submission Possibly misspelled words in DESCRIPTION: Deconvolution (3:8) deconvolution (7:40) Suggests or Enhances not in mainstream repositories: MuSiC, SCDC, spacexr, xbioc Found the following (possibly) invalid URLs: URL: http://www.gsea-msigdb.org/gsea/downloads.jsp (moved to https://www.gsea-msigdb.org:443/gsea/downloads.jsp) From: inst/doc/Cell_type_deconvolution_and_differential_analysis.html Status: 301 Message: Moved Permanently URL: https://cran.r-project.org/web/packages/FARDEEP/index.html From: man/scdecon.Rd Status: 200 Message: OK CRAN URL not in canonical form URL: https://cran.r-project.org/web/packages/MASS/index.html From: man/scdecon.Rd Status: 200 Message: OK CRAN URL not in canonical form URL: https://cran.r-project.org/web/packages/nnls/index.html From: man/scdecon.Rd Status: 200 Message: OK CRAN URL not in canonical form URL: https://mojaveazure.github.io/seurat-object/reference/AssayData.html From: inst/doc/Deconvolution_with_scaden_for_spatial_transcriptomics_data.html Status: 404 Message: Not Found URL: https://mojaveazure.github.io/seurat-object/reference/CreateAssayObject.html From: inst/doc/Deconvolution_with_scaden_for_spatial_transcriptomics_data.html Status: 404 Message: Not Found URL: https://mojaveazure.github.io/seurat-object/reference/DefaultAssay.html From: inst/doc/Deconvolution_with_scaden_for_spatial_transcriptomics_data.html Status: 404 Message: Not Found URL: https://satijalab.org/seurat/reference/InstallData.html From: inst/doc/Deconvolution_with_scaden_for_spatial_transcriptomics_data.html Status: 404 Message: Not Found URL: https://satijalab.org/seurat/reference/LoadData.html From: inst/doc/Deconvolution_with_scaden_for_spatial_transcriptomics_data.html Status: 404 Message: Not Found The canonical URL of the CRAN page for a package is https://CRAN.R-project.org/package=pkgname For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. The Title field should be in title case. Current version is: ‘Deconvolution of bulk RNA-seq data using single-cell RNA-seq data as reference’ In title case that is: ‘Deconvolution of Bulk RNA-Seq Data using Single-Cell RNA-Seq Data as Reference’ Size of tarball: 33854303 bytes * checking package namespace information ... OK * checking package dependencies ... ERROR Packages suggested but not available for checking: 'MuSiC', 'SCDC', 'spacexr', 'xbioc' Namespace dependency missing from DESCRIPTION Imports/Depends entries: ‘reshape2’ Depends: includes the non-default packages: 'dplyr', 'edgeR', 'foreach', 'ggplot2', 'glmGamPoi', 'Seurat' Adding so many packages to the search path is excessive and importing selectively is preferable. See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. * DONE Status: 1 ERROR, 1 NOTE