* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SpaCCI.Rcheck’ * using R Under development (unstable) (2025-05-11 r88197) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3) Debian flang-new version 19.1.7 (3) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘SpaCCI/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpaCCI’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] WARNING Maintainer: ‘Li-Ting Ku ’ Insufficient package version (submitted: 1.0.0, existing: 1.0.3) Found the following (possibly) invalid URLs: URL: https://www.rna-society.org/cellinker/ From: DESCRIPTION Status: 416 Message: Range Not Satisfiable * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SpaCCI’ can be installed ... [21s/21s] OK * used C++ compiler: ‘Debian clang version 19.1.7 (3)’ * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * 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 ... [3s/3s] OK * checking whether the package can be loaded with stated dependencies ... [3s/3s] OK * checking whether the package can be unloaded cleanly ... [3s/3s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK * checking whether the namespace can be unloaded cleanly ... [3s/3s] OK * checking loading without being on the library search path ... [3s/3s] OK * checking use of S3 registration ... 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 ... [16s/16s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [11s/11s] ERROR Running examples in ‘SpaCCI-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: run_SpaCCI > ### Title: Run SpaCCI Analysis > ### Aliases: run_SpaCCI > > ### ** Examples > > library(SpaCCI) > library(nnls) > library(FNN) > library(Matrix) > #Load the example data > data(test_data) > gene_spot_df <- test_data$gene_spot_df > cell_prop_df <- test_data$cell_prop_df > spatial_coords_df <- test_data$spatial_coords_df > > result <- LR_database(species = "Human", + database_name = "CellChat", + gene_spot_expression_dataframe = gene_spot_df) > # global > result_global <- run_SpaCCI(gene_spot_expression_dataframe = gene_spot_df, + spot_cell_proportion_dataframe = cell_prop_df, + spatial_coordinates_dataframe = spatial_coords_df, + LR_database_list = result, + analysis_scale = "global") | | | 0% | |========= | 12% | |================== | 25% | |========================== | 38% | |=================================== | 50% | |============================================ | 62% | |==================================================== | 75% | |============================================================= | 88% | |======================================================================| 100% writing data frame > > # local > result_local <- run_SpaCCI(gene_spot_expression_dataframe = gene_spot_df, + spot_cell_proportion_dataframe = cell_prop_df, + spatial_coordinates_dataframe = spatial_coords_df, + LR_database_list = result, + specific_LR_pair = "EDN2_EDNRA", + analysis_scale = "local", + local_scale_proportion = 0.1, + neighborhood_radius = 2.5) Now analyzing localized detection using 10% of spots in the whole slide, with a radius of 2.5. Now finding the neighborhoods for 10 spots | | | 0% | |========== | 14%Error in matching_L_R_pairs$ligand_vector[[i]] : subscript out of bounds Calls: run_SpaCCI -> SpaCCI_local Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 WARNING