Julien Gagneur
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/genomeIntervals |
| Branch: RELEASE_3_10 |
| Last Commit: c91c96c |
| Last Changed Date: 2019-10-29 13:08:04 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:18:45 -0400 (Wed, 15 Apr 2020).
| Package 677/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genomeIntervals 1.42.0 Julien Gagneur
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: genomeIntervals |
| Version: 1.42.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genomeIntervals.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings genomeIntervals_1.42.0.tar.gz |
| StartedAt: 2020-04-15 03:26:26 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:29:07 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 160.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genomeIntervals.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genomeIntervals.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings genomeIntervals_1.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/genomeIntervals.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.42.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'genomeIntervals' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpEtwsYW/R.INSTALL1860580743c6/genomeIntervals/man/Genome_intervals-class.Rd:110: file link 'width' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpEtwsYW/R.INSTALL1860580743c6/genomeIntervals/man/Genome_intervals-coercion-methods.Rd:49: file link 'readGff3' in package 'genomeIntervals' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/genomeIntervals.Rcheck/00install.out' for details.
* 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 ... NOTE
interval_complement,Genome_intervals: warning in
factor(rep(as.character(fac.comb[, 2]), times = nrows), level =
levels(seqnames(x))): partial argument match of 'level' to 'levels'
interval_complement,Genome_intervals_stranded: warning in
factor(rep(names(s), times = sapply(gi.list, nrow)), level =
levels(strand(x))): partial argument match of 'level' to 'levels'
coerce,Genome_intervals-RangedData: no visible global function
definition for 'na.omit'
writeGff3,data.frame: no visible global function definition for
'write.table'
Undefined global functions or variables:
na.omit write.table
Consider adding
importFrom("stats", "na.omit")
importFrom("utils", "write.table")
to your NAMESPACE file.
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
distance_to_nearest-methods 0.28 0 6.49
** 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' ...13,38d12
<
< 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
<
Running 'consistency-tests.R'
Running 'fullShow.R'
OK
** running tests for arch 'x64' ...
Running 'benchmarking-tests.R'
Comparing 'benchmarking-tests.Rout' to 'benchmarking-tests.Rout.save' ...13,38d12
<
< 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
<
Running 'consistency-tests.R'
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: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/genomeIntervals.Rcheck/00check.log'
for details.
genomeIntervals.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/genomeIntervals_1.42.0.tar.gz && rm -rf genomeIntervals.buildbin-libdir && mkdir genomeIntervals.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genomeIntervals.buildbin-libdir genomeIntervals_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL genomeIntervals_1.42.0.zip && rm genomeIntervals_1.42.0.tar.gz genomeIntervals_1.42.0.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 38294 100 38294 0 0 673k 0 --:--:-- --:--:-- --:--:-- 719k
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
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpEtwsYW/R.INSTALL1860580743c6/genomeIntervals/man/Genome_intervals-class.Rd:110: file link 'width' in package 'IRanges' does not exist and so has been treated as a topic
Genome_intervals-coercion-methods html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpEtwsYW/R.INSTALL1860580743c6/genomeIntervals/man/Genome_intervals-coercion-methods.Rd:49: file link 'readGff3' in package 'genomeIntervals' does not exist and so has been treated as a topic
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
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_1.42.0.zip
* DONE (genomeIntervals)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'genomeIntervals' successfully unpacked and MD5 sums checked
|
genomeIntervals.Rcheck/tests_i386/benchmarking-tests.Rout.save
R version 2.12.1 (2010-12-16)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (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.
Natural language support but running in an English locale
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
> 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")
>
>
|
genomeIntervals.Rcheck/tests_x64/benchmarking-tests.Rout.save
R version 2.12.1 (2010-12-16)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (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.
Natural language support but running in an English locale
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
> 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")
>
>
|
|
genomeIntervals.Rcheck/tests_i386/consistency-tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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 = paste("chr", sample(k, n, replace=TRUE) ),
+ inter_base = sample( c(FALSE,TRUE), n, replace =TRUE),
+ strand = 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
4.42 0.37 4.81
|
genomeIntervals.Rcheck/tests_x64/consistency-tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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 = paste("chr", sample(k, n, replace=TRUE) ),
+ inter_base = sample( c(FALSE,TRUE), n, replace =TRUE),
+ strand = 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
4.62 0.15 4.76
|
|
genomeIntervals.Rcheck/tests_i386/fullShow.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
0.26 0.01 0.35
|
genomeIntervals.Rcheck/tests_x64/fullShow.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
0.15 0.03 0.17
|
|
genomeIntervals.Rcheck/tests_i386/benchmarking-tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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
5.46 0.34 5.79
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genomeIntervals.Rcheck/tests_x64/benchmarking-tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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
5.84 0.18 6.01
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genomeIntervals.Rcheck/examples_i386/genomeIntervals-Ex.timings
|
genomeIntervals.Rcheck/examples_x64/genomeIntervals-Ex.timings
|