############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiTC_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/HiTC.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘HiTC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HiTC’ version ‘1.44.0’ * 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 ‘HiTC’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: SIGNIFICANT USER-VISIBLE CHANGES Cannot process chunk/lines: BUG FIXES Cannot process chunk/lines: NEW FEATURES * 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 ... NOTE directionalityIndex: no visible global function definition for ‘subjectHits’ directionalityIndex: no visible global function definition for ‘queryHits’ getBlocsIndex: no visible global function definition for ‘Rle’ getExpectedCountsMean: no visible global function definition for ‘Rle’ normLGF: no visible global function definition for ‘glm.nb’ slidingWindow: no visible binding for global variable ‘consV’ splitCombinedContacts : : no visible global function definition for ‘seqlevels<-’ divide,HTCexp-HTCexp: no visible global function definition for ‘queryHits’ divide,HTCexp-HTCexp: no visible global function definition for ‘subjectHits’ isBinned,HTCexp: no visible global function definition for ‘countMatches’ substract,HTCexp-HTCexp: no visible global function definition for ‘queryHits’ substract,HTCexp-HTCexp: no visible global function definition for ‘subjectHits’ Undefined global functions or variables: Rle consV countMatches glm.nb queryHits seqlevels<- subjectHits * checking Rd files ... WARNING checkRd: (5) HTClist-class.Rd:52-54: \item in \describe must have non-empty label * 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 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 directionalityIndex 16.835 0.536 17.373 CQC 5.147 0.128 5.276 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘HiC_analysis.Rnw’... failed ‘HiTC.Rnw’... OK WARNING Errors in running code in vignettes: when running code in ‘HiC_analysis.Rnw’ ... > resFrag <- getRestrictionFragmentsPerChromosome(resSite = "AAGCTT", + overhangs5 = 1, chromosomes = "chr6", genomePack = "BSgenome.Hsapiens.UCS ..." ... [TRUNCATED] Loading required package: BSgenome.Hsapiens.UCSC.hg18 Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘BSgenome.Hsapiens.UCSC.hg18’ When sourcing ‘HiC_analysis.R’: Error: require(genomePack, character.only = TRUE) is not TRUE Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘HiC_analysis.Rnw’ using Sweave Loading required package: HiTC Loading required package: IRanges Loading required package: BiocGenerics 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 Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: HiCDataHumanIMR90 'as(, "dgTMatrix")' is deprecated. Use 'as(as(., "generalMatrix"), "TsparseMatrix")' instead. See help("Deprecated") and help("Matrix-deprecated"). Warning: file stem ‘./HiTC-plot1’ is not portable Bin size 'xgi' =5e+05 [1x5e+05] Bin size 'ygi' =5e+05 [1x5e+05] Bin size 'xgi' =5e+05 [1x5e+05] Bin size 'ygi' =5e+05 [1x5e+05] Bin size 'xgi' =5e+05 [1x5e+05] Bin size 'ygi' =5e+05 [1x5e+05] Bin size 'xgi' =5e+05 [1x5e+05] Bin size 'ygi' =5e+05 [1x5e+05] Bin size 'xgi' =5e+05 [1x5e+05] Bin size 'ygi' =5e+05 [1x5e+05] Bin size 'xgi' =5e+05 [1x5e+05] Bin size 'ygi' =5e+05 [1x5e+05] Plotting chr5chr5... minrange= 2 - maxrange= 569 Plotting chr5chr6... minrange= 1 - maxrange= 8 Plotting chr5chr7... minrange= 1 - maxrange= 8 Plotting chr6chr6... minrange= 3 - maxrange= 593.02 Plotting chr6chr7... minrange= 1 - maxrange= 8 Plotting chr7chr7... minrange= 2 - maxrange= 571 Warning: file stem ‘./HiTC-plot2’ is not portable Plotting chr5chr5... minrange= 1 - maxrange= 200 Plotting chr5chr6... minrange= 1 - maxrange= 200 Plotting chr5chr7... minrange= 1 - maxrange= 119 Plotting chr6chr5... minrange= 1 - maxrange= 200 Plotting chr6chr6... minrange= 1 - maxrange= 200 Plotting chr6chr7... minrange= 1 - maxrange= 81 Plotting chr7chr5... minrange= 1 - maxrange= 119 Plotting chr7chr6... minrange= 1 - maxrange= 81 Plotting chr7chr7... minrange= 1 - maxrange= 200 Loading required package: BSgenome.Hsapiens.UCSC.hg18 Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘BSgenome.Hsapiens.UCSC.hg18’ Error: processing vignette 'HiC_analysis.Rnw' failed with diagnostics: chunk 6 (label = resFrag) Error in getRestrictionFragmentsPerChromosome(resSite = "AAGCTT", overhangs5 = 1, : require(genomePack, character.only = TRUE) is not TRUE --- failed re-building ‘HiC_analysis.Rnw’ --- re-building ‘HiTC.Rnw’ using Sweave Loading required package: IRanges Loading required package: BiocGenerics 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 Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: Matrix Attaching package: ‘Matrix’ The following object is masked from ‘package:S4Vectors’: expand Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) 'as(, "dgTMatrix")' is deprecated. Use 'as(as(., "generalMatrix"), "TsparseMatrix")' instead. See help("Deprecated") and help("Matrix-deprecated"). Warning: file stem ‘./HiTC-qcc’ is not portable Get data ... Generate quality control plots ... minrange= 1 - maxrange= 741 Warning: file stem ‘./HiTC-bin5C’ is not portable Bin size 'xgi' =102420 [3x34140] Bin size 'ygi' =102420 [3x34140] minrange= 3 - maxrange= 477.2 Lowess fit ... Standard deviation calculation ... Delta=8876.395 Calculating stdev ... Warning: file stem ‘./HiTC-norm5Cznorm’ is not portable Lowess fit ... Standard deviation calculation ... Delta=8876.395 Calculating stdev ... minrange= 0.027 - maxrange= 2.139 Warning: file stem ‘./HiTC-annot5C’ is not portable Bin size 'xgi' =102087 [3x34029] Bin size 'ygi' =102087 [3x34029] Loading required package: rtracklayer minrange= 0.5 - maxrange= 10 Warning: file stem ‘./HiTC-comp5C’ is not portable Bin size 'xgi' =102087 [3x34029] Bin size 'ygi' =102087 [3x34029] minrange= 0.5 - maxrange= 10 minrange= 0.5 - maxrange= 10 Warning: file stem ‘./HiTC-mapClist’ is not portable Plotting chr12chr12... minrange= 1 - maxrange= 100 Plotting chr12chr13... minrange= 1 - maxrange= 20 Plotting chr12chr14... minrange= 1 - maxrange= 39 Plotting chr13chr13... minrange= 1 - maxrange= 100 Plotting chr13chr14... minrange= 1 - maxrange= 18 Plotting chr14chr14... minrange= 1 - maxrange= 100 Warning: file stem ‘./HiTC-mapChic’ is not portable Plotting chr14chr14... minrange= 1 - maxrange= 100 Warning: file stem ‘./HiTC-mapNormhic’ is not portable Lowess fit ... Plotting chr14chr14... minrange= 0.015 - maxrange= 2.519 Warning: file stem ‘./HiTC-mapCorhic’ is not portable Plotting chr14chr14... minrange= 0 - maxrange= 1 Warning: file stem ‘./HiTC-mapPCAhic’ is not portable Lowess fit ... --- finished re-building ‘HiTC.Rnw’ SUMMARY: processing the following file failed: ‘HiC_analysis.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/HiTC.Rcheck/00check.log’ for details.