############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:cicero.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings cicero_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/cicero.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cicero/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cicero’ version ‘1.20.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘cicero’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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 ... WARNING Loading required package: monocle Loading required package: methods Loading required package: Matrix Loading required package: Biobase Loading required package: BiocGenerics Loading required package: utils Attaching package: ‘utils’ The following objects are masked from ‘package:Matrix’: head, tail Loading required package: graphics Attaching package: ‘graphics’ The following object is masked from ‘package:Matrix’: image Loading required package: stats Attaching package: ‘stats’ The following objects are masked from ‘package:Matrix’: cov2cor, toeplitz, update Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: ggplot2 Loading required package: VGAM Loading required package: stats4 Loading required package: splines Loading required package: DDRTree Loading required package: irlba Loading required package: Gviz Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:Matrix’: expand, unname The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: grid It looks like this package (or one of its dependent packages) has an unstated dependence on a standard package. All dependencies must be declared in DESCRIPTION. See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. * 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 ... NOTE aggregate_nearby_peaks: no visible binding for global variable 'val' annotate_cds_by_site: no visible binding for global variable 'row_name' assemble_connections : : no visible global function definition for 'patterns' assemble_connections: no visible binding for global variable 'value' estimateDispersionsForCellDataSet: no visible global function definition for 'cooks.distance' estimateSizeFactorsSimp: no visible global function definition for 'sizeFactors<-' find_overlapping_ccans: no visible binding for global variable 'CCAN' generate_windows: no visible binding for global variable 'V1' parametricDispersionFit: no visible global function definition for 'glm' parametricDispersionFit: no visible global function definition for 'Gamma' plot_accessibility_in_pseudotime: no visible binding for global variable 'f_id' plot_accessibility_in_pseudotime: no visible binding for global variable 'Var1' Undefined global functions or variables: CCAN Gamma V1 Var1 cooks.distance f_id glm patterns row_name sizeFactors<- val value Consider adding importFrom("stats", "Gamma", "cooks.distance", "glm") to your NAMESPACE file. * 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 ... ERROR Running examples in ‘cicero-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: build_gene_activity_matrix > ### Title: Calculate initial Cicero gene activity matrix > ### Aliases: build_gene_activity_matrix > > ### ** Examples > > data("cicero_data") > data("human.hg19.genome") > sample_genome <- subset(human.hg19.genome, V1 == "chr18") > sample_genome$V2[1] <- 100000 > input_cds <- make_atac_cds(cicero_data, binarize = TRUE) > input_cds <- detectGenes(input_cds) > input_cds <- reduceDimension(input_cds, max_components = 2, num_dim=6, + reduction_method = 'tSNE', + norm_method = "none") * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 635393 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: grid > > test_check("cicero") * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/cicero.Rcheck/00check.log’ for details.