############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialDecon.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SpatialDecon_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SpatialDecon.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'SpatialDecon/DESCRIPTION' ... OK * this is package 'SpatialDecon' version '1.15.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'SpatialDecon' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE download_profile_matrix: no visible binding for global variable 'profile_matrix' Undefined global functions or variables: profile_matrix * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed runCollapseCellTypes 76.82 2.81 79.79 runReverseDecon 74.42 3.10 77.72 runspatialdecon 62.67 5.03 68.34 runMergeTumorIntoX 14.92 1.79 17.09 runErrorModel 14.32 1.57 16.00 reverseDecon 7.77 0.12 7.89 SpatialDecon-package 5.59 0.03 5.63 spatialdecon 4.88 0.64 5.52 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/SpatialDecon.Rcheck/00check.log' for details.