Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 801/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
genomeIntervals 1.61.0 (landing page) Julien Gagneur
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
To the developers/maintainers of the genomeIntervals package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genomeIntervals.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: genomeIntervals |
Version: 1.61.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomeIntervals.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomeIntervals_1.61.0.tar.gz |
StartedAt: 2024-06-10 20:32:17 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 20:34:08 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 111.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: genomeIntervals.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomeIntervals.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomeIntervals_1.61.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/genomeIntervals.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘genomeIntervals/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘genomeIntervals’ version ‘1.61.0’ * 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 ‘genomeIntervals’ 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 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 ... WARNING checkRd: (-1) Genome_intervals-class.Rd:42: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:66: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:67: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:68: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:69: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:70: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:77: Escaped LaTeX specials: \$ checkRd: (-1) Genome_intervals-class.Rd:78: Escaped LaTeX specials: \$ checkRd: (-1) Genome_intervals-class.Rd:86: Escaped LaTeX specials: \_ \_ checkRd: (-1) Genome_intervals-class.Rd:87: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:88: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:89: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:90: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:91: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:92: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:97: Escaped LaTeX specials: \_ checkRd: (5) Genome_intervals-ordering.Rd:75-82: \item in \describe must have non-empty label checkRd: (5) Genome_intervals-ordering.Rd:83-87: \item in \describe must have non-empty label checkRd: (5) Genome_intervals-ordering.Rd:88-92: \item in \describe must have non-empty label checkRd: (5) Genome_intervals-ordering.Rd:93-98: \item in \describe must have non-empty label checkRd: (-1) Genome_intervals_stranded-class.Rd:12: Escaped LaTeX specials: \_ \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:26: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:27: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:28: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:29: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:30: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:31: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:36: Escaped LaTeX specials: \_ \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:37: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:38: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:39: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:40: Escaped LaTeX specials: \_ checkRd: (-1) genomeIntervals-package.Rd:32: Escaped LaTeX specials: \_ checkRd: (-1) genomeIntervals-package.Rd:33: Escaped LaTeX specials: \_ \_ checkRd: (-1) genomeIntervals-readGff3.Rd:47-48: Lost braces in \itemize; meant \describe ? checkRd: (-1) genomeIntervals-readGff3.Rd:49-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) genomeIntervals-readGff3.Rd:53-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) genomeIntervals-readGff3.Rd:57-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) genomeIntervals-readGff3.Rd:35-38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) genomeIntervals-readGff3.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) interval_overlap-methods.Rd:37: Escaped LaTeX specials: \_ checkRd: (-1) parseGffAttributes.Rd:5: Escaped LaTeX specials: \_ * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘benchmarking-tests.R’ Comparing ‘benchmarking-tests.Rout’ to ‘benchmarking-tests.Rout.save’ ...15a16,21 > The following objects are masked from 'package:parallel': > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > 26c32 < Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, --- > Filter, Find, Map, Position, Reduce, anyDuplicated, append, 30,31c36,37 < pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, < union, unique, unsplit, which.max, which.min --- > pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, > tapply, union, unique, unsplit, which, which.max, which.min Running ‘consistency-tests.R’ Comparing ‘consistency-tests.Rout’ to ‘consistency-tests.Rout.save’ ...12a13,18 > The following objects are masked from 'package:parallel': > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > 23c29 < Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, --- > Filter, Find, Map, Position, Reduce, anyDuplicated, append, 27,28c33,34 < pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, < union, unique, unsplit, which.max, which.min --- > pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, > tapply, union, unique, unsplit, which, which.max, which.min Running ‘fullShow.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING See ‘/Users/biocbuild/bbs-3.20-bioc/meat/genomeIntervals.Rcheck/00check.log’ for details.
genomeIntervals.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL genomeIntervals ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘genomeIntervals’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (genomeIntervals)
genomeIntervals.Rcheck/tests/benchmarking-tests.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # benchmarking tests > # > # on modifications, regenerate .Rout.save with: > # R --vanilla <./benchmarking-tests.R >& ./benchmarking-tests.Rout.save > # and use svn' diff to check for differences > # > # Author: julien.gagneur > ############################################################################### > > library(genomeIntervals) Loading required package: intervals Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:intervals': type, type<- 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, table, tapply, union, unique, unsplit, which.max, which.min > source("fullShow.R") > options(warn = -1) > > #--------------- > # make data > #--------------- > # toy examples > data("gen_ints") > > # non-stranded versions > i0 = as(i, "Genome_intervals") > j0 = as(j, "Genome_intervals") > k0 = as(k, "Genome_intervals") > > # empty intervals > e = k[1:3,] > e[,2] = e[,1] > closed(e) = FALSE > > #--------------- > # checks > #--------------- > # distance to nearest > cat("distance_to_nearest\n") distance_to_nearest > print( distance_to_nearest(i,j) ) # x [1] 0 2 3 0 0 0 NA > print( distance_to_nearest(j,i) ) # x [1] 0 2 NA 0 0 > print( distance_to_nearest(i,k) ) # x [1] 0.0 1.5 2.5 0.5 0.0 0.0 NA > print( distance_to_nearest(i,e) ) # x [1] NA NA NA NA NA NA NA > print( distance_to_nearest(e,i) ) # x [1] NA NA NA > > print( distance_to_nearest(i0,j0) ) # x [1] 0 0 1 0 0 0 NA > print( distance_to_nearest(j0,i0) ) # x [1] 0 2 0 0 0 > cat("\n") > > # interval overlap > cat("interval_overlap\n") interval_overlap > print( interval_overlap(i,k) ) # x [[1]] [1] 1 [[2]] integer(0) [[3]] integer(0) [[4]] integer(0) [[5]] [1] 5 [[6]] [1] 4 [[7]] integer(0) > print( interval_overlap(i,e) ) # x [[1]] integer(0) [[2]] integer(0) [[3]] integer(0) [[4]] integer(0) [[5]] integer(0) [[6]] integer(0) [[7]] integer(0) > print( interval_overlap(i0,j0) ) # x [[1]] [1] 1 [[2]] [1] 3 [[3]] integer(0) [[4]] [1] 5 [[5]] [1] 5 [[6]] [1] 4 5 [[7]] integer(0) > cat("\n") > > > # set operations > cat("interval_union\n") interval_union > fullShow( close_intervals( interval_union(i) ) ) # x Object of class Genome_intervals_stranded 4 base intervals and 0 inter-base intervals(*): chr01 + [1, 4] chr02 + [4, 12] chr03 + [2, 5] chr02 - [5, 11] annotation: seq_name inter_base strand 1 chr01 FALSE + 2 chr02 FALSE + 3 chr03 FALSE + 4 chr02 FALSE - > fullShow( close_intervals( interval_union(i,k) ) ) # x Object of class Genome_intervals_stranded 6 base intervals and 2 inter-base intervals(*): chr01 + [1, 4] chr01 + [6, 10] chr01 + [1, 1] * chr02 + [4, 15] chr03 + [2, 5] chr01 - [4, 5] chr02 - [5, 11] chr02 - [8, 8] * annotation: seq_name inter_base strand 1 chr01 FALSE + 2 chr01 FALSE + 3 chr01 TRUE + 4 chr02 FALSE + 5 chr03 FALSE + 6 chr01 FALSE - 7 chr02 FALSE - 8 chr02 TRUE - > fullShow( close_intervals( interval_union(i0,k0) ) ) # x Object of class Genome_intervals 3 base intervals and 2 inter-base intervals(*): chr01 [1, 10] chr01 [1, 1] * chr02 [4, 15] chr02 [8, 8] * chr03 [2, 5] annotation: inter_base seq_name 1 FALSE chr01 2 TRUE chr01 3 FALSE chr02 4 TRUE chr02 5 FALSE chr03 > fullShow( close_intervals( interval_union(e) ) ) # x Object of class Genome_intervals_stranded 0 base intervals and 0 inter-base intervals(*): annotation: [1] seq_name inter_base strand <0 rows> (or 0-length row.names) > cat("\n") > > cat("interval_intersection\n") interval_intersection > fullShow( close_intervals( interval_intersection(i,j) ) ) # x Object of class Genome_intervals_stranded 3 base intervals and 0 inter-base intervals(*): chr01 + [1, 1] chr02 - [8, 8] chr02 + [12, 12] annotation: inter_base seq_name strand 1 FALSE chr01 + 2 FALSE chr02 - 3 FALSE chr02 + > fullShow( close_intervals( interval_intersection(i,k) ) ) # x Object of class Genome_intervals_stranded 1 base interval and 0 inter-base intervals(*): chr02 + [12, 12] annotation: inter_base seq_name strand 1 FALSE chr02 + > fullShow( close_intervals( interval_intersection(i,e) ) ) # x Object of class Genome_intervals_stranded 0 base intervals and 0 inter-base intervals(*): annotation: [1] inter_base seq_name strand <0 rows> (or 0-length row.names) > cat("\n") > > cat("interval_complement\n") interval_complement > fullShow( close_intervals( interval_complement(j) ) ) # x Object of class Genome_intervals_stranded 9 base intervals and 0 inter-base intervals(*): chr01 + [-Inf, 0] chr01 + [2, 5] chr01 + [11, Inf] chr02 + [-Inf, 11] chr02 + [16, Inf] chr01 - [-Inf, 3] chr01 - [6, Inf] chr02 - [-Inf, 7] chr02 - [9, Inf] annotation: seq_name inter_base strand 1 chr01 FALSE + 2 chr01 FALSE + 3 chr01 FALSE + 4 chr02 FALSE + 5 chr02 FALSE + 6 chr01 FALSE - 7 chr01 FALSE - 8 chr02 FALSE - 9 chr02 FALSE - > fullShow( close_intervals( interval_complement(j0) ) ) # x Object of class Genome_intervals 6 base intervals and 0 inter-base intervals(*): chr01 [-Inf, 0] chr01 [2, 3] chr01 [11, Inf] chr02 [-Inf, 7] chr02 [9, 11] chr02 [16, Inf] annotation: inter_base seq_name 1 FALSE chr01 2 FALSE chr01 3 FALSE chr01 4 FALSE chr02 5 FALSE chr02 6 FALSE chr02 > fullShow( close_intervals( interval_complement(k) ) ) # x Object of class Genome_intervals_stranded 7 base intervals and 6 inter-base intervals(*): chr01 + [-Inf, 5] chr01 + [11, Inf] chr01 + [-Inf, 0] * chr01 + [2, Inf] * chr02 + [-Inf, 11] chr02 + [16, Inf] chr02 + [-Inf, Inf] * chr01 - [-Inf, 3] chr01 - [6, Inf] chr01 - [-Inf, Inf] * chr02 - [-Inf, Inf] chr02 - [-Inf, 7] * chr02 - [9, Inf] * annotation: seq_name inter_base strand 1 chr01 FALSE + 2 chr01 FALSE + 3 chr01 TRUE + 4 chr01 TRUE + 5 chr02 FALSE + 6 chr02 FALSE + 7 chr02 TRUE + 8 chr01 FALSE - 9 chr01 FALSE - 10 chr01 TRUE - 11 chr02 FALSE - 12 chr02 TRUE - 13 chr02 TRUE - > fullShow( close_intervals( interval_complement(e) ) ) # x Object of class Genome_intervals_stranded 4 base intervals and 2 inter-base intervals(*): chr01 + [-Inf, Inf] chr01 + [-Inf, Inf] * chr02 + [-Inf, Inf] chr02 + [-Inf, Inf] * chr01 - [-Inf, Inf] chr02 - [-Inf, Inf] annotation: seq_name inter_base strand 1 chr01 FALSE + 2 chr01 TRUE + 3 chr02 FALSE + 4 chr02 TRUE + 5 chr01 FALSE - 6 chr02 FALSE - > cat("\n") > > > proc.time() user system elapsed 5.187 0.220 5.439
genomeIntervals.Rcheck/tests/benchmarking-tests.Rout.save
R version 4.0.0 (2020-04-24) -- "Arbor Day" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # benchmarking tests > # > # on modifications, regenerate .Rout.save with: > # R --vanilla <./benchmarking-tests.R >& ./benchmarking-tests.Rout.save > # and use svn' diff to check for differences > # > # Author: julien.gagneur > ############################################################################### > > library(genomeIntervals) Loading required package: intervals Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:intervals': type, type<- 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, 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, which.max, which.min > source("fullShow.R") > options(warn = -1) > > #--------------- > # make data > #--------------- > # toy examples > data("gen_ints") > > # non-stranded versions > i0 = as(i, "Genome_intervals") > j0 = as(j, "Genome_intervals") > k0 = as(k, "Genome_intervals") > > # empty intervals > e = k[1:3,] > e[,2] = e[,1] > closed(e) = FALSE > > #--------------- > # checks > #--------------- > # distance to nearest > cat("distance_to_nearest\n") distance_to_nearest > print( distance_to_nearest(i,j) ) # x [1] 0 2 3 0 0 0 NA > print( distance_to_nearest(j,i) ) # x [1] 0 2 NA 0 0 > print( distance_to_nearest(i,k) ) # x [1] 0.0 1.5 2.5 0.5 0.0 0.0 NA > print( distance_to_nearest(i,e) ) # x [1] NA NA NA NA NA NA NA > print( distance_to_nearest(e,i) ) # x [1] NA NA NA > > print( distance_to_nearest(i0,j0) ) # x [1] 0 0 1 0 0 0 NA > print( distance_to_nearest(j0,i0) ) # x [1] 0 2 0 0 0 > cat("\n") > > # interval overlap > cat("interval_overlap\n") interval_overlap > print( interval_overlap(i,k) ) # x [[1]] [1] 1 [[2]] integer(0) [[3]] integer(0) [[4]] integer(0) [[5]] [1] 5 [[6]] [1] 4 [[7]] integer(0) > print( interval_overlap(i,e) ) # x [[1]] integer(0) [[2]] integer(0) [[3]] integer(0) [[4]] integer(0) [[5]] integer(0) [[6]] integer(0) [[7]] integer(0) > print( interval_overlap(i0,j0) ) # x [[1]] [1] 1 [[2]] [1] 3 [[3]] integer(0) [[4]] [1] 5 [[5]] [1] 5 [[6]] [1] 4 5 [[7]] integer(0) > cat("\n") > > > # set operations > cat("interval_union\n") interval_union > fullShow( close_intervals( interval_union(i) ) ) # x Object of class Genome_intervals_stranded 4 base intervals and 0 inter-base intervals(*): chr01 + [1, 4] chr02 + [4, 12] chr03 + [2, 5] chr02 - [5, 11] annotation: seq_name inter_base strand 1 chr01 FALSE + 2 chr02 FALSE + 3 chr03 FALSE + 4 chr02 FALSE - > fullShow( close_intervals( interval_union(i,k) ) ) # x Object of class Genome_intervals_stranded 6 base intervals and 2 inter-base intervals(*): chr01 + [1, 4] chr01 + [6, 10] chr01 + [1, 1] * chr02 + [4, 15] chr03 + [2, 5] chr01 - [4, 5] chr02 - [5, 11] chr02 - [8, 8] * annotation: seq_name inter_base strand 1 chr01 FALSE + 2 chr01 FALSE + 3 chr01 TRUE + 4 chr02 FALSE + 5 chr03 FALSE + 6 chr01 FALSE - 7 chr02 FALSE - 8 chr02 TRUE - > fullShow( close_intervals( interval_union(i0,k0) ) ) # x Object of class Genome_intervals 3 base intervals and 2 inter-base intervals(*): chr01 [1, 10] chr01 [1, 1] * chr02 [4, 15] chr02 [8, 8] * chr03 [2, 5] annotation: inter_base seq_name 1 FALSE chr01 2 TRUE chr01 3 FALSE chr02 4 TRUE chr02 5 FALSE chr03 > fullShow( close_intervals( interval_union(e) ) ) # x Object of class Genome_intervals_stranded 0 base intervals and 0 inter-base intervals(*): annotation: [1] seq_name inter_base strand <0 rows> (or 0-length row.names) > cat("\n") > > cat("interval_intersection\n") interval_intersection > fullShow( close_intervals( interval_intersection(i,j) ) ) # x Object of class Genome_intervals_stranded 3 base intervals and 0 inter-base intervals(*): chr01 + [1, 1] chr02 - [8, 8] chr02 + [12, 12] annotation: inter_base seq_name strand 1 FALSE chr01 + 2 FALSE chr02 - 3 FALSE chr02 + > fullShow( close_intervals( interval_intersection(i,k) ) ) # x Object of class Genome_intervals_stranded 1 base interval and 0 inter-base intervals(*): chr02 + [12, 12] annotation: inter_base seq_name strand 1 FALSE chr02 + > fullShow( close_intervals( interval_intersection(i,e) ) ) # x Object of class Genome_intervals_stranded 0 base intervals and 0 inter-base intervals(*): annotation: [1] inter_base seq_name strand <0 rows> (or 0-length row.names) > cat("\n") > > cat("interval_complement\n") interval_complement > fullShow( close_intervals( interval_complement(j) ) ) # x Object of class Genome_intervals_stranded 9 base intervals and 0 inter-base intervals(*): chr01 + [-Inf, 0] chr01 + [2, 5] chr01 + [11, Inf] chr02 + [-Inf, 11] chr02 + [16, Inf] chr01 - [-Inf, 3] chr01 - [6, Inf] chr02 - [-Inf, 7] chr02 - [9, Inf] annotation: seq_name inter_base strand 1 chr01 FALSE + 2 chr01 FALSE + 3 chr01 FALSE + 4 chr02 FALSE + 5 chr02 FALSE + 6 chr01 FALSE - 7 chr01 FALSE - 8 chr02 FALSE - 9 chr02 FALSE - > fullShow( close_intervals( interval_complement(j0) ) ) # x Object of class Genome_intervals 6 base intervals and 0 inter-base intervals(*): chr01 [-Inf, 0] chr01 [2, 3] chr01 [11, Inf] chr02 [-Inf, 7] chr02 [9, 11] chr02 [16, Inf] annotation: inter_base seq_name 1 FALSE chr01 2 FALSE chr01 3 FALSE chr01 4 FALSE chr02 5 FALSE chr02 6 FALSE chr02 > fullShow( close_intervals( interval_complement(k) ) ) # x Object of class Genome_intervals_stranded 7 base intervals and 6 inter-base intervals(*): chr01 + [-Inf, 5] chr01 + [11, Inf] chr01 + [-Inf, 0] * chr01 + [2, Inf] * chr02 + [-Inf, 11] chr02 + [16, Inf] chr02 + [-Inf, Inf] * chr01 - [-Inf, 3] chr01 - [6, Inf] chr01 - [-Inf, Inf] * chr02 - [-Inf, Inf] chr02 - [-Inf, 7] * chr02 - [9, Inf] * annotation: seq_name inter_base strand 1 chr01 FALSE + 2 chr01 FALSE + 3 chr01 TRUE + 4 chr01 TRUE + 5 chr02 FALSE + 6 chr02 FALSE + 7 chr02 TRUE + 8 chr01 FALSE - 9 chr01 FALSE - 10 chr01 TRUE - 11 chr02 FALSE - 12 chr02 TRUE - 13 chr02 TRUE - > fullShow( close_intervals( interval_complement(e) ) ) # x Object of class Genome_intervals_stranded 4 base intervals and 2 inter-base intervals(*): chr01 + [-Inf, Inf] chr01 + [-Inf, Inf] * chr02 + [-Inf, Inf] chr02 + [-Inf, Inf] * chr01 - [-Inf, Inf] chr02 - [-Inf, Inf] annotation: seq_name inter_base strand 1 chr01 FALSE + 2 chr01 TRUE + 3 chr02 FALSE + 4 chr02 TRUE + 5 chr01 FALSE - 6 chr02 FALSE - > cat("\n") > > > proc.time() user system elapsed 3.697 0.178 3.876
genomeIntervals.Rcheck/tests/consistency-tests.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # consistency test > # > # Author: julien.gagneur > ############################################################################### > > > library( genomeIntervals ) Loading required package: intervals Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:intervals': type, type<- 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, table, tapply, union, unique, unsplit, which.max, which.min > > options(warn = -1) > > #--------- > # settings > #--------- > # size of random objects > n = 1e+3 > # chrom length > l = 1e+3 > # nb of chroms > k = 3 > > #--------- > # data generation > #--------- > > randGenint = function(n,l,k){ + m = matrix( sample(l, 2*n, replace=TRUE), nc = 2 ) + m = cbind( apply( m, 1, min), apply( m, 1, max ) ) + + cl = matrix( sample( c(FALSE,TRUE), 2*n, replace =TRUE), nc=2 ) + new( + "Genome_intervals_stranded", + m, + closed = cl, + annotation = data.frame( + seq_name = factor(paste("chr", sample(k, n, replace=TRUE) )), + inter_base = sample( c(FALSE,TRUE), n, replace =TRUE), + strand = factor(sample(c("-", "+"), n, replace =TRUE)) + ) + ) + } > > i = randGenint(n,l,k) > j = randGenint(n,l,k) > i0 = as(i, "Genome_intervals") > j0 = as(j, "Genome_intervals") > > #--------- > # checks > #--------- > > # distances from i to j > dn = distance_to_nearest(i,j) > > # distance is NA or >=0 > if( any( !is.na(dn) & dn < 0) ) stop("negative distance.") > > # distance == 0 if and only if the interval overlaps another one: > io = interval_overlap(i,j) > if( any( ( sapply(io, length) >0 ) != (!is.na(dn) & dn ==0) ) ) + stop("The property 'distance == 0 if and only if the interval overlaps another one' is not followed for at least one instance.") > > # same test for not stranded objects > dn0 = distance_to_nearest(i0,j0) > if( any( !is.na(dn0) & dn0 < 0) ) stop("negative distance.") > > io = interval_overlap(i0,j0) > if( any( ( sapply(io, length) >0 ) != (!is.na(dn0) & dn0 ==0) ) ) + stop("The property 'distance == 0 if and only if the interval overlaps another one' is not followed for at least one instance.") > > # unstranded distance <= stranded distance > delta = dn - dn0 > if( any(!is.na(delta) & delta < 0) ) stop("some unstranded distance larger than a stranded one.") > > # intersection with complement is empty > stopifnot( nrow( interval_intersection(i, interval_complement(i) ) ) == 0 ) > > # distance of union with complement is 1 > # test must be done for not inter-base (or inter-base) independently > a = interval_union(i[!inter_base(i),] ) > b = interval_complement(i[!inter_base(i),]) > > if(!(all.equal( distance_to_nearest( a, b ), rep(1, nrow(a) ) ) ) ) + stop("distance of union with complement is not 1.") > > # width is reported consistently > # they should all be 4 in length (we alternate the open/closed state of the intervals > # pairwise) > gi <- GenomeIntervals(start=c(6,6,5,5), + end=c(10,9,10,9), + chromosome=rep("chr1",4), + leftOpen = c(FALSE,FALSE,TRUE,TRUE), + rightOpen=c(TRUE,FALSE,TRUE,FALSE)) > > stopifnot(all(width(gi)==4)) > > proc.time() user system elapsed 5.244 0.238 5.525
genomeIntervals.Rcheck/tests/consistency-tests.Rout.save
R version 4.0.0 (2020-04-24) -- "Arbor Day" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # consistency test > # > # Author: julien.gagneur > ############################################################################### > > > library( genomeIntervals ) Loading required package: intervals Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:intervals': type, type<- 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, 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, which.max, which.min > > options(warn = -1) > > #--------- > # settings > #--------- > # size of random objects > n = 1e+3 > # chrom length > l = 1e+3 > # nb of chroms > k = 3 > > #--------- > # data generation > #--------- > > randGenint = function(n,l,k){ + m = matrix( sample(l, 2*n, replace=TRUE), nc = 2 ) + m = cbind( apply( m, 1, min), apply( m, 1, max ) ) + + cl = matrix( sample( c(FALSE,TRUE), 2*n, replace =TRUE), nc=2 ) + new( + "Genome_intervals_stranded", + m, + closed = cl, + annotation = data.frame( + seq_name = factor(paste("chr", sample(k, n, replace=TRUE) )), + inter_base = sample( c(FALSE,TRUE), n, replace =TRUE), + strand = factor(sample(c("-", "+"), n, replace =TRUE)) + ) + ) + } > > i = randGenint(n,l,k) > j = randGenint(n,l,k) > i0 = as(i, "Genome_intervals") > j0 = as(j, "Genome_intervals") > > #--------- > # checks > #--------- > > # distances from i to j > dn = distance_to_nearest(i,j) > > # distance is NA or >=0 > if( any( !is.na(dn) & dn < 0) ) stop("negative distance.") > > # distance == 0 if and only if the interval overlaps another one: > io = interval_overlap(i,j) > if( any( ( sapply(io, length) >0 ) != (!is.na(dn) & dn ==0) ) ) + stop("The property 'distance == 0 if and only if the interval overlaps another one' is not followed for at least one instance.") > > # same test for not stranded objects > dn0 = distance_to_nearest(i0,j0) > if( any( !is.na(dn0) & dn0 < 0) ) stop("negative distance.") > > io = interval_overlap(i0,j0) > if( any( ( sapply(io, length) >0 ) != (!is.na(dn0) & dn0 ==0) ) ) + stop("The property 'distance == 0 if and only if the interval overlaps another one' is not followed for at least one instance.") > > # unstranded distance <= stranded distance > delta = dn - dn0 > if( any(!is.na(delta) & delta < 0) ) stop("some unstranded distance larger than a stranded one.") > > # intersection with complement is empty > stopifnot( nrow( interval_intersection(i, interval_complement(i) ) ) == 0 ) > > # distance of union with complement is 1 > # test must be done for not inter-base (or inter-base) independently > a = interval_union(i[!inter_base(i),] ) > b = interval_complement(i[!inter_base(i),]) > > if(!(all.equal( distance_to_nearest( a, b ), rep(1, nrow(a) ) ) ) ) + stop("distance of union with complement is not 1.") > > # width is reported consistently > # they should all be 4 in length (we alternate the open/closed state of the intervals > # pairwise) > gi <- GenomeIntervals(start=c(6,6,5,5), + end=c(10,9,10,9), + chromosome=rep("chr1",4), + leftOpen = c(FALSE,FALSE,TRUE,TRUE), + rightOpen=c(TRUE,FALSE,TRUE,FALSE)) > > stopifnot(all(width(gi)==4)) > > proc.time() user system elapsed 3.868 0.188 4.048
genomeIntervals.Rcheck/tests/fullShow.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # the fullShow methods is a show method for Genome_intervals objects. > # It is called by test scripts so that the full output of the tests can be checked. > # > # Author: gagneur > ############################################################################### > > fullShow <- function(object ) { + cat( + "Object of class ", + class( object ), + "\n", + sum( !inter_base(object) ), + " base interval", + ifelse( sum( !inter_base(object) ) == 1, "", "s" ), + " and ", + sum( inter_base(object) ), + " inter-base interval", + ifelse( sum( inter_base(object) ) == 1, "", "s" ), + "(*)", + ":\n", + sep = "" + ) + ints <- as( object, "character") + if ( !is.null( rownames( object ) ) ) { + fmt <- sprintf( "%%%is", max( nchar( rownames( object ) ) ) ) + ints <- paste( sprintf( fmt, rownames( object ) ), ints ) + } + cat( ints, sep = "\n" ) + cat( "annotation:\n") + show( annotation(object) ) + } > > > > > proc.time() user system elapsed 0.228 0.068 0.279
genomeIntervals.Rcheck/genomeIntervals-Ex.timings
name | user | system | elapsed | |
GenomeIntervals-constructor | 0.093 | 0.008 | 0.101 | |
Genome_intervals-class | 0.018 | 0.001 | 0.020 | |
Genome_intervals-coercion-methods | 0 | 0 | 0 | |
Genome_intervals-ordering | 0.020 | 0.001 | 0.021 | |
Genome_intervals_stranded-class | 0.038 | 0.001 | 0.039 | |
c.Genome_intervals | 0.057 | 0.002 | 0.060 | |
core_annotated | 0.040 | 0.003 | 0.044 | |
distance_to_nearest-methods | 0.194 | 0.005 | 0.200 | |
genomeIntervals-readGff3 | 1.112 | 0.439 | 1.565 | |
getGffAttribute | 0.073 | 0.003 | 0.076 | |
interval_overlap-methods | 0.094 | 0.004 | 0.099 | |
interval_set_operations-methods | 0.491 | 0.007 | 0.500 | |
parseGffAttributes | 0.068 | 0.002 | 0.071 | |