* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SCEGHiC.Rcheck’ * using R Under development (unstable) (2026-04-26 r89963) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.8 (3+b1) Debian flang version 21.1.8 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-04-27 06:03:36 UTC * checking for file ‘SCEGHiC/DESCRIPTION’ ... OK * this is package ‘SCEGHiC’ version ‘1.0.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [9s/66s] NOTE Maintainer: ‘Xuan Liang ’ New submission Possibly misspelled words in DESCRIPTION: HiC (9:19) SCEG (9:14) ome (9:85) omics (10:44) scATAC (9:111, 9:130) scRNA (9:97) wlasso (10:124) Package has a VignetteBuilder field but no prebuilt vignette index. Found the following (possibly) invalid URLs: URL: https://www.encodeproject.org/files/ENCFF134PUN/@@download/ENCFF134PUN.bed.gz From: README.md Status: Error Message: Timeout was reached [encode-public.s3.amazonaws.com]: Operation timed out after 60032 milliseconds with 1189411615 out of 58070147883 bytes received The Title field should be in title case. Current version is: ‘Predicting Single-cell Enhancer Gene Interactions by Integrating Prior Hi-C Information’ In title case that is: ‘Predicting Single-Cell Enhancer Gene Interactions by Integrating Prior Hi-C Information’ Size of tarball: 13348414 bytes * 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 serialization versions ... OK * checking whether package ‘SCEGHiC’ can be installed ... [43s/43s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘README.html’ * 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 ... [13s/13s] OK * checking whether the package can be loaded with stated dependencies ... [14s/14s] OK * checking whether the package can be unloaded cleanly ... [14s/14s] OK * checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK * checking whether the namespace can be unloaded cleanly ... [13s/13s] OK * checking loading without being on the library search path ... [13s/13s] 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 ... [55s/55s] NOTE coverPlot: no visible binding for global variable 'pos' Undefined global functions or variables: pos * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'LinksPlot.Rd': \examples lines wider than 100 characters: gene = "CTLA4", peak = c("chr2_203623664_203623982", "chr2_203730093_203731243", "chr2_203992800_203993979"), links <- LinksPlot(links, geneanno, gene = "CTLA4", region, lowcolor = "blue", highcolor = "orange", titlename = "SCEG-HiC") Rd file 'Run_SCEG_HiC.Rd': \examples lines wider than 100 characters: weight <- calculateHiCWeights(SCEGdata, species = "Homo sapiens", genome = "hg38", focus_gene = gene, averHicPath = fpath) Rd file 'calculateHiCWeights.Rd': \examples lines wider than 100 characters: weight <- calculateHiCWeights(SCEGdata, species = "Homo sapiens", genome = "hg38", focus_gene = gene, averHicPath = fpath) Rd file 'connections_Plot.Rd': \examples lines wider than 100 characters: weight <- calculateHiCWeights(SCEGdata, species = "Homo sapiens", genome = "hg38", focus_gene = gene, averHicPath = fpath) connections_Plot(results_SCEGHiC, species = "Homo sapiens", genome = "hg38", focus_gene = "CTLA4", cutoff = 0.01, gene_anno = NULL) Rd file 'coverPlot.Rd': \examples lines wider than 100 characters: weight <- calculateHiCWeights(SCEGdata, species = "Homo sapiens", genome = "hg38", focus_gene = gene, averHicPath = fpath) coverPlot(multiomic_small, focus_gene = "CTLA4", species = "Homo sapiens", genome = "hg38", assay = "peaks", SCEG_HiC_Result = results_ ... [TRUNCATED] Rd file 'liftOverPeaks.Rd': \examples lines wider than 100 characters: "chr2-973888-974755", "chr2-3195868-3196264", "chr2-3242398-3243508", "chr2-6863856-6866834", "chr2-6913141-6914394", "chr2-6924663-6924972", "chr2-6999095-6999554", "chr2-7007713-7008819", "chr2-7083945-7084032", "chr2-7097148-7098029" Rd file 'normalizeHiCWeights.Rd': \examples lines wider than 100 characters: "chr2_174901074_174901475", "chr2_174901074_174901475", "chr2_174990102_174990619", "chr2_174990102_174990619", "chr2_174990102_174990619", "chr2_175048293_175048704", "chr2_175048293_175048704", "chr2_175167038_175169195" "chr2_174901074_174901475", "chr2_174990102_174990619", "chr2_175048293_175048704", "chr2_175167038_175169195", "chr2_175187467_175187717", "chr2_174990102_174990619", "chr2_175048293_175048704", "chr2_175167038_175169195", "chr2_175187467_175187717", "chr2_175048293_175048704", "chr2_175167038_175169195", "chr2_175187467_175187717", 0.0016062358, 0.0076253167, 0.0031021570, 0.0012148262, 0.0010788392, 0.0019968580, 0.0012957845, 0.0009198567, 0.0011448870, 0.0023991885, 0.0010785481, 0.0009664508, 0.0012865316, 0.0012122647, 0.0057781939 These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'LinksPlot.Rd' ‘geneanno’ Documented arguments not in \usage in Rd file 'LinksPlot.Rd': ‘gene_anno’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [5s/5s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘PBMC_multiomic_CD4T.Rmd’ ‘PBMC_multiomic_CD4T.html’ ‘PBMC_multiomic_aggregation.Rmd’ ‘PBMC_multiomic_aggregation.html’ ‘human_covid_19_scATAC_seq_monocytes.Rmd’ ‘human_covid_19_scATAC_seq_monocytes.html’ ‘mouse_skin_multiomic_aggregation.Rmd’ ‘mouse_skin_multiomic_aggregation.html’ Files named as vignettes but with no recognized vignette engine: ‘vignettes/PBMC_multiomic_CD4T.Rmd’ ‘vignettes/PBMC_multiomic_aggregation.Rmd’ ‘vignettes/human_covid_19_scATAC_seq_monocytes.Rmd’ ‘vignettes/mouse_skin_multiomic_aggregation.Rmd’ (Is a VignetteBuilder field missing?) * checking examples ... [43s/43s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed coverPlot 5.195 0.04 5.238 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [53s/53s] OK Running ‘testthat.R’ [52s/52s] * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... [4s/4s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character ≤ (U+2264) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character ≤ (U+2264) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘SCEGHiC-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 3 WARNINGs, 7 NOTEs