* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/rescue.Rcheck’ * using R Under development (unstable) (2023-06-09 r84528) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2) GNU Fortran (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2) * running under: Fedora 34 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘rescue/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rescue’ version ‘1.0.3’ * 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 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 ‘rescue’ can be installed ... OK * checking package directory ... 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 R 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 loading without being on the library search path ... 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 ... OK * checking Rd files ... 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 examples ... OK * checking examples with --run-donttest ... ERROR Running examples in ‘rescue-Ex.R’ failed The error most likely occurred in: > ### Name: bootstrapImputation > ### Title: Bootstrap Imputation > ### Aliases: bootstrapImputation > > ### ** Examples > > set.seed(0) > requireNamespace("Matrix") Loading required namespace: Matrix > > ## generate (meaningless) counts > c1 <- stats::rpois(5e3, 1) > c2 <- stats::rpois(5e3, 2) > m <- t( + rbind( + matrix(c1, nrow = 20), + matrix(c2, nrow = 20) + ) + ) > > ## construct an expression matrix m > colnames(m) <- paste0('cell', 1:ncol(m)) > rownames(m) <- paste0('gene', 1:nrow(m)) > m <- log(m/colSums(m)*1e4 + 1) > m <- methods::as(m, 'dgCMatrix') > > ## impute > ## No test: > m_imputed <- rescue::bootstrapImputation( + expression_matrix = m, + proportion_genes = .9, + bootstrap_samples = 2, + k_neighbors = 10 + ) Error in py_run_file_impl(file, local, convert) : ModuleNotFoundError: No module named 'community' Run `reticulate::py_last_error()` for details. Calls: ... clusterLouvain -> -> py_run_file -> py_run_file_impl Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/rescue.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 0:23.95, 19.93 + 9.61