Julien Gagneur
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/genomeIntervals |
| Branch: RELEASE_3_8 |
| Last Commit: 1acbdc9 |
| Last Changed Date: 2018-10-30 11:41:45 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:48:42 -0400 (Tue, 16 Apr 2019).
| Package 621/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genomeIntervals 1.38.0 Julien Gagneur
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: genomeIntervals |
| Version: 1.38.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:genomeIntervals.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings genomeIntervals_1.38.0.tar.gz |
| StartedAt: 2019-04-16 00:11:00 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:12:36 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 96.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: genomeIntervals.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:genomeIntervals.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings genomeIntervals_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/genomeIntervals.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomeIntervals/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomeIntervals’ version ‘1.38.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘genomeIntervals’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘benchmarking-tests.R’
Comparing ‘benchmarking-tests.Rout’ to ‘benchmarking-tests.Rout.save’ ...13,35d12
<
< 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: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, colMeans, colSums, colnames,
< dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
< intersect, is.unsorted, lapply, lengths, mapply, match, mget,
< order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
< rowMeans, rowSums, 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 NOTE
See
‘/home/biocbuild/bbs-3.8-bioc/meat/genomeIntervals.Rcheck/00check.log’
for details.
genomeIntervals.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL genomeIntervals ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘genomeIntervals’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (genomeIntervals)
genomeIntervals.Rcheck/tests/benchmarking-tests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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
5.468 0.172 5.643
genomeIntervals.Rcheck/tests/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/consistency-tests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
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> # 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: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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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
4.868 0.160 5.026
genomeIntervals.Rcheck/tests/fullShow.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
0.236 0.016 0.246
genomeIntervals.Rcheck/genomeIntervals-Ex.timings
| name | user | system | elapsed | |
| GenomeIntervals-constructor | 0.080 | 0.008 | 0.086 | |
| Genome_intervals-class | 0.04 | 0.00 | 0.04 | |
| Genome_intervals-coercion-methods | 0 | 0 | 0 | |
| Genome_intervals-ordering | 0.052 | 0.004 | 0.054 | |
| Genome_intervals_stranded-class | 0.040 | 0.008 | 0.049 | |
| c.Genome_intervals | 0.076 | 0.024 | 0.100 | |
| core_annotated | 0.088 | 0.000 | 0.086 | |
| distance_to_nearest-methods | 0.352 | 0.000 | 0.355 | |
| genomeIntervals-readGff3 | 1.208 | 0.072 | 1.289 | |
| getGffAttribute | 0.068 | 0.000 | 0.068 | |
| interval_overlap-methods | 0.132 | 0.000 | 0.133 | |
| interval_set_operations-methods | 0.808 | 0.004 | 0.815 | |
| parseGffAttributes | 0.068 | 0.000 | 0.064 | |