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This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the genomeIntervals package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 737/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| genomeIntervals 1.48.0 (landing page) Julien Gagneur
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: genomeIntervals |
| Version: 1.48.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genomeIntervals.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings genomeIntervals_1.48.0.tar.gz |
| StartedAt: 2021-10-14 23:35:28 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:37:57 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 149.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: genomeIntervals.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genomeIntervals.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings genomeIntervals_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/genomeIntervals.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'genomeIntervals/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'genomeIntervals' version '1.48.0' * 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 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... OK * 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'benchmarking-tests.R' Comparing 'benchmarking-tests.Rout' to 'benchmarking-tests.Rout.save' ...37c37 < tapply, union, unique, unsplit, which.max, which.min --- > tapply, union, unique, unsplit, which, which.max, which.min Running 'consistency-tests.R' Comparing 'consistency-tests.Rout' to 'consistency-tests.Rout.save' ...34c34 < tapply, union, unique, unsplit, which.max, which.min --- > tapply, union, unique, unsplit, which, which.max, which.min Running 'fullShow.R' OK ** running tests for arch 'x64' ... Running 'benchmarking-tests.R' Comparing 'benchmarking-tests.Rout' to 'benchmarking-tests.Rout.save' ...37c37 < tapply, union, unique, unsplit, which.max, which.min --- > tapply, union, unique, unsplit, which, which.max, which.min Running 'consistency-tests.R' Comparing 'consistency-tests.Rout' to 'consistency-tests.Rout.save' ...34c34 < tapply, union, unique, unsplit, which.max, which.min --- > tapply, union, unique, unsplit, which, which.max, which.min Running 'fullShow.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
genomeIntervals.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/genomeIntervals_1.48.0.tar.gz && rm -rf genomeIntervals.buildbin-libdir && mkdir genomeIntervals.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genomeIntervals.buildbin-libdir genomeIntervals_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL genomeIntervals_1.48.0.zip && rm genomeIntervals_1.48.0.tar.gz genomeIntervals_1.48.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 38898 100 38898 0 0 290k 0 --:--:-- --:--:-- --:--:-- 292k
install for i386
* installing *source* package 'genomeIntervals' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'genomeIntervals'
finding HTML links ... done
GenomeIntervals-constructor html
Genome_intervals-class html
finding level-2 HTML links ... done
Genome_intervals-coercion-methods html
Genome_intervals-deprecated html
Genome_intervals-ordering html
Genome_intervals_stranded-class html
c.Genome_intervals html
core_annotated html
distance_to_nearest-methods html
gen_ints html
genomeIntervals-package html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/genomeIntervals.buildbin-libdir/00LOCK-genomeIntervals/00new/genomeIntervals/help/genomeIntervals.html
genomeIntervals-readGff3 html
getGffAttribute html
interval_overlap-methods html
interval_set_operations-methods html
parseGffAttributes html
** 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
install for x64
* installing *source* package 'genomeIntervals' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genomeIntervals' as genomeIntervals_1.48.0.zip
* DONE (genomeIntervals)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'genomeIntervals' successfully unpacked and MD5 sums checked
|
genomeIntervals.Rcheck/tests_i386/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_x64/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_i386/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_x64/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_i386/fullShow.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> # 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
0.28 0.04 0.31
|
genomeIntervals.Rcheck/tests_x64/fullShow.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> # 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
0.23 0.04 0.26
|
|
genomeIntervals.Rcheck/tests_i386/benchmarking-tests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.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
4.70 0.42 5.11
|
|
|
genomeIntervals.Rcheck/tests_i386/consistency-tests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.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
5.00 0.37 5.35
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genomeIntervals.Rcheck/tests_x64/benchmarking-tests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.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
5.23 0.21 5.43
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genomeIntervals.Rcheck/tests_x64/consistency-tests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.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
4.85 0.29 5.14
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genomeIntervals.Rcheck/examples_i386/genomeIntervals-Ex.timings
|
genomeIntervals.Rcheck/examples_x64/genomeIntervals-Ex.timings
|