############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GenomicFiles.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GenomicFiles_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomicFiles.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘GenomicFiles/DESCRIPTION’ ... OK * this is package ‘GenomicFiles’ version ‘1.45.0’ * checking package namespace information ... OK * checking package dependencies ... INFO Depends: includes the non-default packages: 'BiocGenerics', 'MatrixGenerics', 'GenomicRanges', 'SummarizedExperiment', 'BiocParallel', 'Rsamtools', 'rtracklayer' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘GenomicFiles’ 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 code 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’ See the note in ?`:::` about the use of this operator. * 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 ... WARNING checkRd: (5) GenomicFiles-class.Rd:40-43: \item in \describe must have non-empty label checkRd: (5) VcfStack-class.Rd:61-89: \item in \describe must have non-empty label checkRd: (5) VcfStack-class.Rd:90-105: \item in \describe must have non-empty label checkRd: (5) pack-methods.Rd:57-61: \item in \describe must have non-empty label checkRd: (-1) reduceByFile-methods.Rd:132-139: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) reduceByFile-methods.Rd:140-143: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) reduceByRange-methods.Rd:143-150: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) reduceByRange-methods.Rd:151-154: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) registry-utils.Rd:45-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) registry-utils.Rd:60-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) registry-utils.Rd:64-68: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'VcfStack-class.Rd': ‘[GenomeInfoDb]{seqinfo<-}’ ‘[GenomeInfoDb:Seqinfo-class]{seqnames}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘GenomicFiles-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: VcfStack > ### Title: VcfStack and RangedVcfStack Objects > ### Aliases: class:VcfStack VcfStack-class RangedVcfStack-class VcfStack > ### RangedVcfStack colnames,VcfStack-method rownames,VcfStack-method > ### dimnames,VcfStack-method files,VcfStack-method > ### files<-,VcfStack,character-method files<-,VcfStack,VcfFile-method > ### files<-,VcfStack,VcfFileList-method seqinfo,VcfStack-method > ### seqinfo<-,VcfStack-method seqinfo<-,RangedVcfStack-method > ### seqlevelsStyle<-,VcfStack-method > ### seqlevelsStyle<-,RangedVcfStack-method colData,VcfStack-method > ### colData<-,VcfStack,DataFrame-method rowRanges,RangedVcfStack-method > ### rowRanges<-,RangedVcfStack,GRanges-method vcfFields,VcfStack-method > ### assay,VcfStack,ANY-method assay,RangedVcfStack,ANY-method > ### readVcfStack show,VcfStack-method [,VcfStack,ANY,ANY-method > ### [,VcfStack,ANY,ANY,ANY-method [,RangedVcfStack,ANY,ANY-method > ### [,RangedVcfStack,ANY,ANY,ANY-method paths1kg dim,VcfStack-method > > ### ** Examples > > ## --------------------------------------------------------------------- > ## CONSTRUCTION > ## --------------------------------------------------------------------- > ## point to VCF files and add names corresponding to the sequence > ## present in the file > extdata <- system.file(package="GenomicFiles", "extdata") > files <- dir(extdata, pattern="^CEUtrio.*bgz$", full=TRUE) > names(files) <- sub(".*_([0-9XY]+).*", "\\1", basename(files)) > > ## input data.frame describing the length of each sequence, coerce to > ## 'Seqinfo' object > seqinfo <- as(readRDS(file.path(extdata, "seqinfo.rds")), "Seqinfo") > > stack <- VcfStack(files, seqinfo) > stack VcfStack object with 7 files and 3 samples Seqinfo object with 25 sequences from hg19 genome use 'readVcfStack()' to extract VariantAnnotation VCF. > > ## Use seqinfo from VCF files instead of explict value > stack2 <- VcfStack(files) > > rstack <- RangedVcfStack(stack) > gr <- GRanges(c("7:1-159138000", "X:1-155270560")) > rstack2 <- RangedVcfStack(stack, gr) > rstack2 VcfStack object with 7 files and 3 samples GRanges object with 2 ranges and 0 metadata columns Seqinfo object with 25 sequences from hg19 genome use 'readVcfStack()' to extract VariantAnnotation VCF. > > ## --------------------------------------------------------------------- > ## ACCESSORS > ## --------------------------------------------------------------------- > dim(stack) [1] 7 3 > colnames(stack) [1] "NA12878" "NA12891" "NA12892" > rownames(stack) [1] "11" "20" "21" "22" "7" "X" "Y" > dimnames(stack) [[1]] [1] "11" "20" "21" "22" "7" "X" "Y" [[2]] [1] "NA12878" "NA12891" "NA12892" > head(files(stack)) VcfFileList of length 6 names(6): 11 20 21 22 7 X > seqinfo(stack) Seqinfo object with 25 sequences from hg19 genome: seqnames seqlengths isCircular genome 1 249250621 hg19 2 243199373 hg19 3 198022430 hg19 4 191154276 hg19 5 180915260 hg19 ... ... ... ... 21 48129895 hg19 22 51304566 hg19 X 155270560 hg19 Y 59373566 hg19 MT 16569 hg19 > colData(stack) DataFrame with 3 rows and 0 columns > > ## --------------------------------------------------------------------- > ## METHODS > ## --------------------------------------------------------------------- > readVcfStack(stack, i=GRanges("20:862167-62858306")) class: CollapsedVCF dim: 317 3 rowRanges(vcf): GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER info(vcf): DataFrame with 26 columns: AC, AF, AN, BaseQRankSum, CCC, ClippingRankSum,... info(header(vcf)): Number Type Description AC A Integer Allele count in genotypes, for each ALT al... AF A Float Allele Frequency, for each ALT allele, in ... AN 1 Integer Total number of alleles in called genotypes BaseQRankSum 1 Float Z-score from Wilcoxon rank sum test of Alt... CCC 1 Integer Number of called chromosomes ClippingRankSum 1 Float Z-score From Wilcoxon rank sum test of Alt... DB 0 Flag dbSNP Membership DP 1 Integer Approximate read depth; some reads may hav... DS 0 Flag Were any of the samples downsampled? END 1 Integer Stop position of the interval FS 1 Float Phred-scaled p-value using Fisher's exact ... GQ_MEAN 1 Float Mean of all GQ values GQ_STDDEV 1 Float Standard deviation of all GQ values HWP 1 Float P value from test of Hardy Weinberg Equili... HaplotypeScore 1 Float Consistency of the site with at most two s... InbreedingCoeff 1 Float Inbreeding coefficient as estimated from t... MLEAC A Integer Maximum likelihood expectation (MLE) for t... MLEAF A Float Maximum likelihood expectation (MLE) for t... MQ 1 Float RMS Mapping Quality MQ0 1 Integer Total Mapping Quality Zero Reads MQRankSum 1 Float Z-score From Wilcoxon rank sum test of Alt... NCC 1 Integer Number of no-called samples QD 1 Float Variant Confidence/Quality by Depth ReadPosRankSum 1 Float Z-score from Wilcoxon rank sum test of Alt... SOR 1 Float Symmetric Odds Ratio of 2x2 contingency ta... set 1 String Source VCF for the merged record in Combin... geno(vcf): List of length 9: GT, AD, DP, GQ, MIN_DP, PGT, PID, PL, SB geno(header(vcf)): Number Type Description GT 1 String Genotype AD . Integer Allelic depths for the ref and alt alleles in the o... DP 1 Integer Approximate read depth (reads with MQ=255 or with b... GQ 1 Integer Genotype Quality MIN_DP 1 Integer Minimum DP observed within the GVCF block PGT 1 String Physical phasing haplotype information, describing ... PID 1 String Physical phasing ID information, where each unique ... PL G Integer Normalized, Phred-scaled likelihoods for genotypes ... SB 4 Integer Per-sample component statistics which comprise the ... > i <- GRanges(c("20:862167-62858306", "7:1-159138000")) > readVcfStack(stack, i=i, j="NA12891") class: CollapsedVCF dim: 318 1 rowRanges(vcf): GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER info(vcf): DataFrame with 26 columns: AC, AF, AN, BaseQRankSum, CCC, ClippingRankSum,... info(header(vcf)): Number Type Description AC A Integer Allele count in genotypes, for each ALT al... AF A Float Allele Frequency, for each ALT allele, in ... AN 1 Integer Total number of alleles in called genotypes BaseQRankSum 1 Float Z-score from Wilcoxon rank sum test of Alt... CCC 1 Integer Number of called chromosomes ClippingRankSum 1 Float Z-score From Wilcoxon rank sum test of Alt... DB 0 Flag dbSNP Membership DP 1 Integer Approximate read depth; some reads may hav... DS 0 Flag Were any of the samples downsampled? END 1 Integer Stop position of the interval FS 1 Float Phred-scaled p-value using Fisher's exact ... GQ_MEAN 1 Float Mean of all GQ values GQ_STDDEV 1 Float Standard deviation of all GQ values HWP 1 Float P value from test of Hardy Weinberg Equili... HaplotypeScore 1 Float Consistency of the site with at most two s... InbreedingCoeff 1 Float Inbreeding coefficient as estimated from t... MLEAC A Integer Maximum likelihood expectation (MLE) for t... MLEAF A Float Maximum likelihood expectation (MLE) for t... MQ 1 Float RMS Mapping Quality MQ0 1 Integer Total Mapping Quality Zero Reads MQRankSum 1 Float Z-score From Wilcoxon rank sum test of Alt... NCC 1 Integer Number of no-called samples QD 1 Float Variant Confidence/Quality by Depth ReadPosRankSum 1 Float Z-score from Wilcoxon rank sum test of Alt... SOR 1 Float Symmetric Odds Ratio of 2x2 contingency ta... set 1 String Source VCF for the merged record in Combin... geno(vcf): List of length 9: GT, AD, DP, GQ, MIN_DP, PGT, PID, PL, SB geno(header(vcf)): Number Type Description GT 1 String Genotype AD . Integer Allelic depths for the ref and alt alleles in the o... DP 1 Integer Approximate read depth (reads with MQ=255 or with b... GQ 1 Integer Genotype Quality MIN_DP 1 Integer Minimum DP observed within the GVCF block PGT 1 String Physical phasing haplotype information, describing ... PID 1 String Physical phasing ID information, where each unique ... PL G Integer Normalized, Phred-scaled likelihoods for genotypes ... SB 4 Integer Per-sample component statistics which comprise the ... > > head(assay(stack, gr)) Attaching package: ‘Matrix’ The following objects are masked from ‘package:GenomicFiles’: pack, unpack The following object is masked from ‘package:S4Vectors’: expand Attaching package: ‘Matrix’ The following objects are masked from ‘package:GenomicFiles’: pack, unpack The following object is masked from ‘package:S4Vectors’: expand non-single nucleotide variations are set to NA Warning in .local(x, ...) : non-diploid variants are set to NA NA12878 NA12891 NA12892 rs760352870 1 0 0 X:193438_G/C 2 2 NA X:386831_A/G 2 NA NA X:672818_T/C NA 2 NA X:1784428_C/G 0 0 2 X:1861132_C/T 2 NA 0 > head(assay(rstack2)) Attaching package: ‘Matrix’ The following objects are masked from ‘package:GenomicFiles’: pack, unpack The following object is masked from ‘package:S4Vectors’: expand Attaching package: ‘Matrix’ The following objects are masked from ‘package:GenomicFiles’: pack, unpack The following object is masked from ‘package:S4Vectors’: expand non-single nucleotide variations are set to NA Warning in .local(x, ...) : non-diploid variants are set to NA NA12878 NA12891 NA12892 rs760352870 1 0 0 X:193438_G/C 2 2 NA X:386831_A/G 2 NA NA X:672818_T/C NA 2 NA X:1784428_C/G 0 0 2 X:1861132_C/T 2 NA 0 > > seqlevels(stack2) [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" [16] "16" "17" "18" "19" "20" "21" "22" "X" "Y" "MT" > rownames(stack2) [1] "11" "20" "21" "22" "7" "X" "Y" > seqlevelsStyle(stack2) Error in seqlevelsStyle(stack2) : could not find function "seqlevelsStyle" Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed GenomicFiles-class 6.506 1.212 5.307 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘GenomicFiles_unit_tests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomicFiles.Rcheck/00check.log’ for details.