############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GenomicRanges_1.63.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/GenomicRanges.Rcheck’ * using R Under development (unstable) (2025-10-20 r88955) * 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 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘GenomicRanges/DESCRIPTION’ ... OK * this is package ‘GenomicRanges’ version ‘1.63.0’ * 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 ‘GenomicRanges’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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: DEPRECATED AND DEFUNCT * 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 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 cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: GPos-class.Rd: IRanges, IntegerRanges GRanges-class.Rd: strand, Seqinfo, DataFrame, seqlevels, List GRangesList-class.Rd: RleList, CharacterList, CompressedIRangesList, IntegerRangesList, DataFrame, Seqinfo, seqlevels, Rle, AtomicList absoluteRanges.Rd: IntegerRanges, Seqinfo, seqlengths findOverlaps-methods.Rd: Hits strand-utils.Rd: RleList tileGenome.Rd: Seqinfo, seqlengths Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... INFO Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘GenomicRanges-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: makeGRangesFromDataFrame > ### Title: Make a GRanges object from a data.frame or DataFrame > ### Aliases: makeGRangesFromDataFrame coerce,data.frame,GRanges-method > ### coerce,DataFrame,GRanges-method makeGPosFromDataFrame > ### coerce,data.frame,GPos-method coerce,DataFrame,GPos-method > ### Keywords: manip > > ### ** Examples > > ## --------------------------------------------------------------------- > ## BASIC makeGRangesFromDataFrame() EXAMPLES > ## --------------------------------------------------------------------- > > df <- data.frame(chr="chr1", start=11:15, end=12:16, + strand=c("+","-","+","*","."), score=1:5) > df chr start end strand score 1 chr1 11 12 + 1 2 chr1 12 13 - 2 3 chr1 13 14 + 3 4 chr1 14 15 * 4 5 chr1 15 16 . 5 > makeGRangesFromDataFrame(df) # strand value "." is replaced with "*" GRanges object with 5 ranges and 0 metadata columns: seqnames ranges strand [1] chr1 11-12 + [2] chr1 12-13 - [3] chr1 13-14 + [4] chr1 14-15 * [5] chr1 15-16 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths > > ## With NAs in range-defining columns: > df$start[5] <- df$end[2] <- NA > df chr start end strand score 1 chr1 11 12 + 1 2 chr1 12 NA - 2 3 chr1 13 14 + 3 4 chr1 14 15 * 4 5 chr1 NA 16 . 5 > #makeGRangesFromDataFrame(df) # error! > makeGRangesFromDataFrame(df, na.rm=TRUE) # rows with NAs got dropped GRanges object with 3 ranges and 0 metadata columns: seqnames ranges strand [1] chr1 11-12 + [2] chr1 13-14 + [3] chr1 14-15 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths > > ## The strand column is optional: > df <- data.frame(chr="chr1", start=11:15, end=12:16, score=1:5) > makeGRangesFromDataFrame(df) GRanges object with 5 ranges and 0 metadata columns: seqnames ranges strand [1] chr1 11-12 * [2] chr1 12-13 * [3] chr1 13-14 * [4] chr1 14-15 * [5] chr1 15-16 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths > > gr <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE) > gr2 <- as(df, "GRanges") # equivalent to the above > stopifnot(identical(gr, gr2)) > gr2 <- GRanges(df) # equivalent to the above > stopifnot(identical(gr, gr2)) > > makeGRangesFromDataFrame(df, ignore.strand=TRUE) GRanges object with 5 ranges and 0 metadata columns: seqnames ranges strand [1] chr1 11-12 * [2] chr1 12-13 * [3] chr1 13-14 * [4] chr1 14-15 * [5] chr1 15-16 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths > makeGRangesFromDataFrame(df, keep.extra.columns=TRUE, + ignore.strand=TRUE) GRanges object with 5 ranges and 1 metadata column: seqnames ranges strand | score | [1] chr1 11-12 * | 1 [2] chr1 12-13 * | 2 [3] chr1 13-14 * | 3 [4] chr1 14-15 * | 4 [5] chr1 15-16 * | 5 ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths > > makeGRangesFromDataFrame(df, seqinfo=paste0("chr", 4:1)) GRanges object with 5 ranges and 0 metadata columns: seqnames ranges strand [1] chr1 11-12 * [2] chr1 12-13 * [3] chr1 13-14 * [4] chr1 14-15 * [5] chr1 15-16 * ------- seqinfo: 4 sequences from an unspecified genome; no seqlengths > makeGRangesFromDataFrame(df, seqinfo=c(chrM=NA, chr1=500, chrX=100)) GRanges object with 5 ranges and 0 metadata columns: seqnames ranges strand [1] chr1 11-12 * [2] chr1 12-13 * [3] chr1 13-14 * [4] chr1 14-15 * [5] chr1 15-16 * ------- seqinfo: 3 sequences from an unspecified genome > makeGRangesFromDataFrame(df, seqinfo=Seqinfo(paste0("chr", 4:1))) GRanges object with 5 ranges and 0 metadata columns: seqnames ranges strand [1] chr1 11-12 * [2] chr1 12-13 * [3] chr1 13-14 * [4] chr1 14-15 * [5] chr1 15-16 * ------- seqinfo: 4 sequences from an unspecified genome; no seqlengths > > ## --------------------------------------------------------------------- > ## BASIC makeGPosFromDataFrame() EXAMPLES > ## --------------------------------------------------------------------- > > df <- data.frame( + rsids= c("rs7927381", "rs79273813", "rs79273815", + "rs79273819", "rs79273817", "rs79273811", "rs79273814"), + seqnames= c("11", "1", "11", "1", "5", "8", "8"), + positions=c("67579271", "179599437", "70746832", + "5066529", "107006951", "95077418", "43582071"), + alleles= c("T/C", "A/G", "C/G, C/T", "G/A, G/C", "T/C, T/G", + "G/A, G/T", "G/A, G/T"), + genes= c(NA, "TDRD5", "SHANK2", NA, "LOC102467213", "NDUFAF6", NA), + row.names=letters[1:7] + ) > > makeGPosFromDataFrame(df) UnstitchedGPos object with 7 positions and 0 metadata columns: seqnames pos strand a 11 67579271 * b 1 179599437 * c 11 70746832 * d 1 5066529 * e 5 107006951 * f 8 95077418 * g 8 43582071 * ------- seqinfo: 4 sequences from an unspecified genome; no seqlengths > makeGPosFromDataFrame(df, keep.extra.columns=TRUE) UnstitchedGPos object with 7 positions and 3 metadata columns: seqnames pos strand | rsids alleles genes | a 11 67579271 * | rs7927381 T/C b 1 179599437 * | rs79273813 A/G TDRD5 c 11 70746832 * | rs79273815 C/G, C/T SHANK2 d 1 5066529 * | rs79273819 G/A, G/C e 5 107006951 * | rs79273817 T/C, T/G LOC102467213 f 8 95077418 * | rs79273811 G/A, G/T NDUFAF6 g 8 43582071 * | rs79273814 G/A, G/T ------- seqinfo: 4 sequences from an unspecified genome; no seqlengths > as(df, "GPos") # same as above UnstitchedGPos object with 7 positions and 3 metadata columns: seqnames pos strand | rsids alleles genes | a 11 67579271 * | rs7927381 T/C b 1 179599437 * | rs79273813 A/G TDRD5 c 11 70746832 * | rs79273815 C/G, C/T SHANK2 d 1 5066529 * | rs79273819 G/A, G/C e 5 107006951 * | rs79273817 T/C, T/G LOC102467213 f 8 95077418 * | rs79273811 G/A, G/T NDUFAF6 g 8 43582071 * | rs79273814 G/A, G/T ------- seqinfo: 4 sequences from an unspecified genome; no seqlengths > > ## With missing positions: > df$positions[2L] <- NA > df rsids seqnames positions alleles genes a rs7927381 11 67579271 T/C b rs79273813 1 A/G TDRD5 c rs79273815 11 70746832 C/G, C/T SHANK2 d rs79273819 1 5066529 G/A, G/C e rs79273817 5 107006951 T/C, T/G LOC102467213 f rs79273811 8 95077418 G/A, G/T NDUFAF6 g rs79273814 8 43582071 G/A, G/T > #makeGPosFromDataFrame(df) # error! > makeGPosFromDataFrame(df, na.rm=TRUE) # rows with NAs got dropped UnstitchedGPos object with 6 positions and 0 metadata columns: seqnames pos strand a 11 67579271 * c 11 70746832 * d 1 5066529 * e 5 107006951 * f 8 95077418 * g 8 43582071 * ------- seqinfo: 4 sequences from an unspecified genome; no seqlengths > > ## --------------------------------------------------------------------- > ## ABOUT AUTOMATIC DETECTION OF THE seqnames/start/end/strand COLUMNS > ## --------------------------------------------------------------------- > > ## Automatic detection of the seqnames/start/end/strand columns is > ## case insensitive: > df <- data.frame(ChRoM="chr1", StarT=11:15, stoP=12:16, + STRAND=c("+","-","+","*","."), score=1:5) > makeGRangesFromDataFrame(df) GRanges object with 5 ranges and 0 metadata columns: seqnames ranges strand [1] chr1 11-12 + [2] chr1 12-13 - [3] chr1 13-14 + [4] chr1 14-15 * [5] chr1 15-16 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths > > ## It also ignores a common prefix between the start and end columns: > df <- data.frame(seqnames="chr1", tx_start=11:15, tx_end=12:16, + strand=c("+","-","+","*","."), score=1:5) > makeGRangesFromDataFrame(df) GRanges object with 5 ranges and 0 metadata columns: seqnames ranges strand [1] chr1 11-12 + [2] chr1 12-13 - [3] chr1 13-14 + [4] chr1 14-15 * [5] chr1 15-16 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths > > ## The common prefix between the start and end columns is used to > ## disambiguate between more than one seqnames column: > df <- data.frame(chrom="chr1", tx_start=11:15, tx_end=12:16, + tx_chr="chr2", score=1:5) > makeGRangesFromDataFrame(df) GRanges object with 5 ranges and 0 metadata columns: seqnames ranges strand [1] chr2 11-12 * [2] chr2 12-13 * [3] chr2 13-14 * [4] chr2 14-15 * [5] chr2 15-16 * ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths > > ## --------------------------------------------------------------------- > ## 0-BASED VS 1-BASED START POSITIONS > ## --------------------------------------------------------------------- > > if (require(rtracklayer)) { + session <- browserSession() + genome(session) <- "sacCer2" + query <- ucscTableQuery(session, "Assembly") + df <- getTable(query) + head(df) + + ## A common pitfall is to forget that the UCSC Table Browser uses the + ## "0-based start" convention: + gr0 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE, + start.field="chromStart", + end.field="chromEnd") + head(gr0) + + ## The start positions need to be converted into 1-based positions, + ## to adhere to the convention used in Bioconductor: + gr1 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE, + start.field="chromStart", + end.field="chromEnd", + starts.in.df.are.0based=TRUE) + head(gr1) + } Loading required package: rtracklayer Warning in .local(x, ...) : 'track' parameter is deprecated now you go by the 'table' instead Use ucscTables(genome, track) to retrieve the list of tables for a track Error in if (file == "" || length(file) == 0) stop("empty or no content specified") : missing value where TRUE/FALSE needed Calls: ucscTableQuery ... .local -> ucscTables -> rtracklayerGET -> htmlParse Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed genomicvars 43.636 5.098 48.744 GPos-class 36.973 5.666 42.650 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.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 NOTEs See ‘/home/biocbuild/bbs-3.23-bioc/meat/GenomicRanges.Rcheck/00check.log’ for details.