Multiple platform build/check report for BioC 3.20 - CHECK results for genomeIntervals on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4481
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4479
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4359
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for genomeIntervals on lconway

To the developers/maintainers of the genomeIntervals package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genomeIntervals.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: genomeIntervals

Version: 1.62.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomeIntervals.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomeIntervals_1.62.0.tar.gz

StartedAt: 2024-11-19 22:25:45 -0500 (Tue, 19 Nov 2024)

EndedAt: 2024-11-19 22:30:46 -0500 (Tue, 19 Nov 2024)

EllapsedTime: 301.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: genomeIntervals.Rcheck

Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomeIntervals.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomeIntervals_1.62.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/genomeIntervals.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomeIntervals/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomeIntervals’ version ‘1.62.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genomeIntervals’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
checkRd: (-1) Genome_intervals-class.Rd:42: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals-class.Rd:66: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals-class.Rd:67: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals-class.Rd:68: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals-class.Rd:69: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals-class.Rd:70: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals-class.Rd:77: Escaped LaTeX specials: \$
checkRd: (-1) Genome_intervals-class.Rd:78: Escaped LaTeX specials: \$
checkRd: (-1) Genome_intervals-class.Rd:86: Escaped LaTeX specials: \_ \_
checkRd: (-1) Genome_intervals-class.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals-class.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals-class.Rd:89: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals-class.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals-class.Rd:91: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals-class.Rd:92: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals-class.Rd:97: Escaped LaTeX specials: \_
checkRd: (5) Genome_intervals-ordering.Rd:75-82: \item in \describe must have non-empty label
checkRd: (5) Genome_intervals-ordering.Rd:83-87: \item in \describe must have non-empty label
checkRd: (5) Genome_intervals-ordering.Rd:88-92: \item in \describe must have non-empty label
checkRd: (5) Genome_intervals-ordering.Rd:93-98: \item in \describe must have non-empty label
checkRd: (-1) Genome_intervals_stranded-class.Rd:12: Escaped LaTeX specials: \_ \_
checkRd: (-1) Genome_intervals_stranded-class.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals_stranded-class.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals_stranded-class.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals_stranded-class.Rd:29: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals_stranded-class.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals_stranded-class.Rd:31: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals_stranded-class.Rd:36: Escaped LaTeX specials: \_ \_
checkRd: (-1) Genome_intervals_stranded-class.Rd:37: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals_stranded-class.Rd:38: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals_stranded-class.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) Genome_intervals_stranded-class.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) genomeIntervals-package.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) genomeIntervals-package.Rd:33: Escaped LaTeX specials: \_ \_
checkRd: (-1) genomeIntervals-readGff3.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) genomeIntervals-readGff3.Rd:49-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) genomeIntervals-readGff3.Rd:53-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) genomeIntervals-readGff3.Rd:57-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) genomeIntervals-readGff3.Rd:35-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) genomeIntervals-readGff3.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) interval_overlap-methods.Rd:37: Escaped LaTeX specials: \_
checkRd: (-1) parseGffAttributes.Rd:5: Escaped LaTeX specials: \_
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘benchmarking-tests.R’
  Comparing ‘benchmarking-tests.Rout’ to ‘benchmarking-tests.Rout.save’ ...15a16,21
> The following objects are masked from 'package:parallel':
> 
>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>     clusterExport, clusterMap, parApply, parCapply, parLapply,
>     parLapplyLB, parRapply, parSapply, parSapplyLB
> 
26c32
<     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
---
>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
30,31c36,37
<     pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
<     tapply, union, unique, unsplit, which.max, which.min
---
>     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
>     tapply, union, unique, unsplit, which, which.max, which.min
  Running ‘consistency-tests.R’
  Comparing ‘consistency-tests.Rout’ to ‘consistency-tests.Rout.save’ ...12a13,18
> The following objects are masked from 'package:parallel':
> 
>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>     clusterExport, clusterMap, parApply, parCapply, parLapply,
>     parLapplyLB, parRapply, parSapply, parSapplyLB
> 
23c29
<     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
---
>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
27,28c33,34
<     pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
<     tapply, union, unique, unsplit, which.max, which.min
---
>     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
>     tapply, union, unique, unsplit, which, which.max, which.min
  Running ‘fullShow.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/genomeIntervals.Rcheck/00check.log’
for details.

Installation output

genomeIntervals.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL genomeIntervals
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘genomeIntervals’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genomeIntervals)

Tests output

genomeIntervals.Rcheck/tests/benchmarking-tests.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # benchmarking tests
> # 
> # on modifications, regenerate .Rout.save with:
> # R --vanilla <./benchmarking-tests.R >& ./benchmarking-tests.Rout.save
> # and use svn' diff to check for differences
> #
> # Author: julien.gagneur
> ###############################################################################
> 
> library(genomeIntervals)
Loading required package: intervals
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:intervals':

    type, type<-

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

> source("fullShow.R")
> options(warn = -1)
> 
> #---------------
> # make data
> #---------------
> # toy examples
> data("gen_ints")
> 
> # non-stranded versions
> i0 = as(i, "Genome_intervals")
> j0 = as(j, "Genome_intervals")
> k0 = as(k, "Genome_intervals")
> 
> # empty intervals
> e = k[1:3,]
> e[,2] = e[,1]
> closed(e) = FALSE
> 
> #---------------
> # checks
> #---------------
> # distance to nearest
> cat("distance_to_nearest\n")
distance_to_nearest
> print( distance_to_nearest(i,j) )		# x
[1]  0  2  3  0  0  0 NA
> print( distance_to_nearest(j,i) )		# x
[1]  0  2 NA  0  0
> print( distance_to_nearest(i,k) )		# x
[1] 0.0 1.5 2.5 0.5 0.0 0.0  NA
> print( distance_to_nearest(i,e) )		# x
[1] NA NA NA NA NA NA NA
> print( distance_to_nearest(e,i) )		# x
[1] NA NA NA
> 
> print( distance_to_nearest(i0,j0) )		# x
[1]  0  0  1  0  0  0 NA
> print( distance_to_nearest(j0,i0) )		# x
[1] 0 2 0 0 0
> cat("\n")

> 
> # interval overlap
> cat("interval_overlap\n")
interval_overlap
> print( interval_overlap(i,k) )			# x
[[1]]
[1] 1

[[2]]
integer(0)

[[3]]
integer(0)

[[4]]
integer(0)

[[5]]
[1] 5

[[6]]
[1] 4

[[7]]
integer(0)

> print( interval_overlap(i,e) )			# x
[[1]]
integer(0)

[[2]]
integer(0)

[[3]]
integer(0)

[[4]]
integer(0)

[[5]]
integer(0)

[[6]]
integer(0)

[[7]]
integer(0)

> print( interval_overlap(i0,j0) )		# x
[[1]]
[1] 1

[[2]]
[1] 3

[[3]]
integer(0)

[[4]]
[1] 5

[[5]]
[1] 5

[[6]]
[1] 4 5

[[7]]
integer(0)

> cat("\n")

> 
> 
> # set operations
> cat("interval_union\n")
interval_union
> fullShow( close_intervals( interval_union(i) ) )		# x
Object of class Genome_intervals_stranded
4 base intervals and 0 inter-base intervals(*):
chr01 + [1, 4] 
chr02 + [4, 12] 
chr03 + [2, 5] 
chr02 - [5, 11] 
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr02      FALSE      +
3    chr03      FALSE      +
4    chr02      FALSE      -
> fullShow( close_intervals( interval_union(i,k) ) )		# x
Object of class Genome_intervals_stranded
6 base intervals and 2 inter-base intervals(*):
chr01 + [1, 4] 
chr01 + [6, 10] 
chr01 + [1, 1] *
chr02 + [4, 15] 
chr03 + [2, 5] 
chr01 - [4, 5] 
chr02 - [5, 11] 
chr02 - [8, 8] *
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr01      FALSE      +
3    chr01       TRUE      +
4    chr02      FALSE      +
5    chr03      FALSE      +
6    chr01      FALSE      -
7    chr02      FALSE      -
8    chr02       TRUE      -
> fullShow( close_intervals( interval_union(i0,k0) ) )	# x
Object of class Genome_intervals
3 base intervals and 2 inter-base intervals(*):
chr01 [1, 10] 
chr01 [1, 1] *
chr02 [4, 15] 
chr02 [8, 8] *
chr03 [2, 5] 
annotation:
  inter_base seq_name
1      FALSE    chr01
2       TRUE    chr01
3      FALSE    chr02
4       TRUE    chr02
5      FALSE    chr03
> fullShow( close_intervals( interval_union(e) ) )		# x
Object of class Genome_intervals_stranded
0 base intervals and 0 inter-base intervals(*):

annotation:
[1] seq_name   inter_base strand    
<0 rows> (or 0-length row.names)
> cat("\n")

> 
> cat("interval_intersection\n")
interval_intersection
> fullShow( close_intervals( interval_intersection(i,j) ) ) # x
Object of class Genome_intervals_stranded
3 base intervals and 0 inter-base intervals(*):
chr01 + [1, 1] 
chr02 - [8, 8] 
chr02 + [12, 12] 
annotation:
  inter_base seq_name strand
1      FALSE    chr01      +
2      FALSE    chr02      -
3      FALSE    chr02      +
> fullShow( close_intervals( interval_intersection(i,k) ) ) # x
Object of class Genome_intervals_stranded
1 base interval and 0 inter-base intervals(*):
chr02 + [12, 12] 
annotation:
  inter_base seq_name strand
1      FALSE    chr02      +
> fullShow( close_intervals( interval_intersection(i,e) ) ) # x
Object of class Genome_intervals_stranded
0 base intervals and 0 inter-base intervals(*):

annotation:
[1] inter_base seq_name   strand    
<0 rows> (or 0-length row.names)
> cat("\n")

> 
> cat("interval_complement\n")
interval_complement
> fullShow( close_intervals( interval_complement(j) ) )	# x
Object of class Genome_intervals_stranded
9 base intervals and 0 inter-base intervals(*):
chr01 + [-Inf, 0] 
chr01 + [2, 5] 
chr01 + [11, Inf] 
chr02 + [-Inf, 11] 
chr02 + [16, Inf] 
chr01 - [-Inf, 3] 
chr01 - [6, Inf] 
chr02 - [-Inf, 7] 
chr02 - [9, Inf] 
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr01      FALSE      +
3    chr01      FALSE      +
4    chr02      FALSE      +
5    chr02      FALSE      +
6    chr01      FALSE      -
7    chr01      FALSE      -
8    chr02      FALSE      -
9    chr02      FALSE      -
> fullShow( close_intervals( interval_complement(j0) ) )	# x
Object of class Genome_intervals
6 base intervals and 0 inter-base intervals(*):
chr01 [-Inf, 0] 
chr01 [2, 3] 
chr01 [11, Inf] 
chr02 [-Inf, 7] 
chr02 [9, 11] 
chr02 [16, Inf] 
annotation:
  inter_base seq_name
1      FALSE    chr01
2      FALSE    chr01
3      FALSE    chr01
4      FALSE    chr02
5      FALSE    chr02
6      FALSE    chr02
> fullShow( close_intervals( interval_complement(k) ) ) # x
Object of class Genome_intervals_stranded
7 base intervals and 6 inter-base intervals(*):
chr01 + [-Inf, 5] 
chr01 + [11, Inf] 
chr01 + [-Inf, 0] *
chr01 + [2, Inf] *
chr02 + [-Inf, 11] 
chr02 + [16, Inf] 
chr02 + [-Inf, Inf] *
chr01 - [-Inf, 3] 
chr01 - [6, Inf] 
chr01 - [-Inf, Inf] *
chr02 - [-Inf, Inf] 
chr02 - [-Inf, 7] *
chr02 - [9, Inf] *
annotation:
   seq_name inter_base strand
1     chr01      FALSE      +
2     chr01      FALSE      +
3     chr01       TRUE      +
4     chr01       TRUE      +
5     chr02      FALSE      +
6     chr02      FALSE      +
7     chr02       TRUE      +
8     chr01      FALSE      -
9     chr01      FALSE      -
10    chr01       TRUE      -
11    chr02      FALSE      -
12    chr02       TRUE      -
13    chr02       TRUE      -
> fullShow( close_intervals( interval_complement(e) ) ) # x
Object of class Genome_intervals_stranded
4 base intervals and 2 inter-base intervals(*):
chr01 + [-Inf, Inf] 
chr01 + [-Inf, Inf] *
chr02 + [-Inf, Inf] 
chr02 + [-Inf, Inf] *
chr01 - [-Inf, Inf] 
chr02 - [-Inf, Inf] 
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr01       TRUE      +
3    chr02      FALSE      +
4    chr02       TRUE      +
5    chr01      FALSE      -
6    chr02      FALSE      -
> cat("\n")

> 
> 
> proc.time()
   user  system elapsed 
  3.445   0.194   3.647

genomeIntervals.Rcheck/tests/benchmarking-tests.Rout.save


R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # benchmarking tests
> # 
> # on modifications, regenerate .Rout.save with:
> # R --vanilla <./benchmarking-tests.R >& ./benchmarking-tests.Rout.save
> # and use svn' diff to check for differences
> #
> # Author: julien.gagneur
> ###############################################################################
> 
> library(genomeIntervals)
Loading required package: intervals
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:intervals':

    type, type<-

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

> source("fullShow.R")
> options(warn = -1)
> 
> #---------------
> # make data
> #---------------
> # toy examples
> data("gen_ints")
> 
> # non-stranded versions
> i0 = as(i, "Genome_intervals")
> j0 = as(j, "Genome_intervals")
> k0 = as(k, "Genome_intervals")
> 
> # empty intervals
> e = k[1:3,]
> e[,2] = e[,1]
> closed(e) = FALSE
> 
> #---------------
> # checks
> #---------------
> # distance to nearest
> cat("distance_to_nearest\n")
distance_to_nearest
> print( distance_to_nearest(i,j) )		# x
[1]  0  2  3  0  0  0 NA
> print( distance_to_nearest(j,i) )		# x
[1]  0  2 NA  0  0
> print( distance_to_nearest(i,k) )		# x
[1] 0.0 1.5 2.5 0.5 0.0 0.0  NA
> print( distance_to_nearest(i,e) )		# x
[1] NA NA NA NA NA NA NA
> print( distance_to_nearest(e,i) )		# x
[1] NA NA NA
> 
> print( distance_to_nearest(i0,j0) )		# x
[1]  0  0  1  0  0  0 NA
> print( distance_to_nearest(j0,i0) )		# x
[1] 0 2 0 0 0
> cat("\n")

> 
> # interval overlap
> cat("interval_overlap\n")
interval_overlap
> print( interval_overlap(i,k) )			# x
[[1]]
[1] 1

[[2]]
integer(0)

[[3]]
integer(0)

[[4]]
integer(0)

[[5]]
[1] 5

[[6]]
[1] 4

[[7]]
integer(0)

> print( interval_overlap(i,e) )			# x
[[1]]
integer(0)

[[2]]
integer(0)

[[3]]
integer(0)

[[4]]
integer(0)

[[5]]
integer(0)

[[6]]
integer(0)

[[7]]
integer(0)

> print( interval_overlap(i0,j0) )		# x
[[1]]
[1] 1

[[2]]
[1] 3

[[3]]
integer(0)

[[4]]
[1] 5

[[5]]
[1] 5

[[6]]
[1] 4 5

[[7]]
integer(0)

> cat("\n")

> 
> 
> # set operations
> cat("interval_union\n")
interval_union
> fullShow( close_intervals( interval_union(i) ) )		# x
Object of class Genome_intervals_stranded
4 base intervals and 0 inter-base intervals(*):
chr01 + [1, 4] 
chr02 + [4, 12] 
chr03 + [2, 5] 
chr02 - [5, 11] 
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr02      FALSE      +
3    chr03      FALSE      +
4    chr02      FALSE      -
> fullShow( close_intervals( interval_union(i,k) ) )		# x
Object of class Genome_intervals_stranded
6 base intervals and 2 inter-base intervals(*):
chr01 + [1, 4] 
chr01 + [6, 10] 
chr01 + [1, 1] *
chr02 + [4, 15] 
chr03 + [2, 5] 
chr01 - [4, 5] 
chr02 - [5, 11] 
chr02 - [8, 8] *
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr01      FALSE      +
3    chr01       TRUE      +
4    chr02      FALSE      +
5    chr03      FALSE      +
6    chr01      FALSE      -
7    chr02      FALSE      -
8    chr02       TRUE      -
> fullShow( close_intervals( interval_union(i0,k0) ) )	# x
Object of class Genome_intervals
3 base intervals and 2 inter-base intervals(*):
chr01 [1, 10] 
chr01 [1, 1] *
chr02 [4, 15] 
chr02 [8, 8] *
chr03 [2, 5] 
annotation:
  inter_base seq_name
1      FALSE    chr01
2       TRUE    chr01
3      FALSE    chr02
4       TRUE    chr02
5      FALSE    chr03
> fullShow( close_intervals( interval_union(e) ) )		# x
Object of class Genome_intervals_stranded
0 base intervals and 0 inter-base intervals(*):

annotation:
[1] seq_name   inter_base strand    
<0 rows> (or 0-length row.names)
> cat("\n")

> 
> cat("interval_intersection\n")
interval_intersection
> fullShow( close_intervals( interval_intersection(i,j) ) ) # x
Object of class Genome_intervals_stranded
3 base intervals and 0 inter-base intervals(*):
chr01 + [1, 1] 
chr02 - [8, 8] 
chr02 + [12, 12] 
annotation:
  inter_base seq_name strand
1      FALSE    chr01      +
2      FALSE    chr02      -
3      FALSE    chr02      +
> fullShow( close_intervals( interval_intersection(i,k) ) ) # x
Object of class Genome_intervals_stranded
1 base interval and 0 inter-base intervals(*):
chr02 + [12, 12] 
annotation:
  inter_base seq_name strand
1      FALSE    chr02      +
> fullShow( close_intervals( interval_intersection(i,e) ) ) # x
Object of class Genome_intervals_stranded
0 base intervals and 0 inter-base intervals(*):

annotation:
[1] inter_base seq_name   strand    
<0 rows> (or 0-length row.names)
> cat("\n")

> 
> cat("interval_complement\n")
interval_complement
> fullShow( close_intervals( interval_complement(j) ) )	# x
Object of class Genome_intervals_stranded
9 base intervals and 0 inter-base intervals(*):
chr01 + [-Inf, 0] 
chr01 + [2, 5] 
chr01 + [11, Inf] 
chr02 + [-Inf, 11] 
chr02 + [16, Inf] 
chr01 - [-Inf, 3] 
chr01 - [6, Inf] 
chr02 - [-Inf, 7] 
chr02 - [9, Inf] 
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr01      FALSE      +
3    chr01      FALSE      +
4    chr02      FALSE      +
5    chr02      FALSE      +
6    chr01      FALSE      -
7    chr01      FALSE      -
8    chr02      FALSE      -
9    chr02      FALSE      -
> fullShow( close_intervals( interval_complement(j0) ) )	# x
Object of class Genome_intervals
6 base intervals and 0 inter-base intervals(*):
chr01 [-Inf, 0] 
chr01 [2, 3] 
chr01 [11, Inf] 
chr02 [-Inf, 7] 
chr02 [9, 11] 
chr02 [16, Inf] 
annotation:
  inter_base seq_name
1      FALSE    chr01
2      FALSE    chr01
3      FALSE    chr01
4      FALSE    chr02
5      FALSE    chr02
6      FALSE    chr02
> fullShow( close_intervals( interval_complement(k) ) ) # x
Object of class Genome_intervals_stranded
7 base intervals and 6 inter-base intervals(*):
chr01 + [-Inf, 5] 
chr01 + [11, Inf] 
chr01 + [-Inf, 0] *
chr01 + [2, Inf] *
chr02 + [-Inf, 11] 
chr02 + [16, Inf] 
chr02 + [-Inf, Inf] *
chr01 - [-Inf, 3] 
chr01 - [6, Inf] 
chr01 - [-Inf, Inf] *
chr02 - [-Inf, Inf] 
chr02 - [-Inf, 7] *
chr02 - [9, Inf] *
annotation:
   seq_name inter_base strand
1     chr01      FALSE      +
2     chr01      FALSE      +
3     chr01       TRUE      +
4     chr01       TRUE      +
5     chr02      FALSE      +
6     chr02      FALSE      +
7     chr02       TRUE      +
8     chr01      FALSE      -
9     chr01      FALSE      -
10    chr01       TRUE      -
11    chr02      FALSE      -
12    chr02       TRUE      -
13    chr02       TRUE      -
> fullShow( close_intervals( interval_complement(e) ) ) # x
Object of class Genome_intervals_stranded
4 base intervals and 2 inter-base intervals(*):
chr01 + [-Inf, Inf] 
chr01 + [-Inf, Inf] *
chr02 + [-Inf, Inf] 
chr02 + [-Inf, Inf] *
chr01 - [-Inf, Inf] 
chr02 - [-Inf, Inf] 
annotation:
  seq_name inter_base strand
1    chr01      FALSE      +
2    chr01       TRUE      +
3    chr02      FALSE      +
4    chr02       TRUE      +
5    chr01      FALSE      -
6    chr02      FALSE      -
> cat("\n")

> 
> 
> proc.time()
   user  system elapsed 
  3.697   0.178   3.876

genomeIntervals.Rcheck/tests/consistency-tests.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # consistency test
> #
> # Author: julien.gagneur
> ###############################################################################
> 
> 
> library( genomeIntervals )
Loading required package: intervals
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:intervals':

    type, type<-

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

> 
> options(warn = -1)
> 
> #---------
> # settings
> #---------
> # size of random objects
> n = 1e+3
> # chrom length
> l = 1e+3
> # nb of chroms
> k = 3
> 
> #---------
> # data generation
> #---------
> 
> randGenint = function(n,l,k){
+     m = matrix( sample(l, 2*n, replace=TRUE), nc = 2 )
+     m = cbind( apply( m, 1, min), apply( m, 1, max ) )
+ 
+     cl = matrix( sample( c(FALSE,TRUE), 2*n, replace =TRUE), nc=2 )
+     new(
+         "Genome_intervals_stranded",
+         m,
+         closed = cl,
+         annotation = data.frame(
+                 seq_name = factor(paste("chr", sample(k, n, replace=TRUE) )),
+                 inter_base = sample( c(FALSE,TRUE), n, replace =TRUE),
+                 strand = factor(sample(c("-", "+"), n, replace =TRUE))
+         )
+     )
+ }
> 
> i = randGenint(n,l,k)
> j = randGenint(n,l,k)
> i0 = as(i, "Genome_intervals")
> j0 = as(j, "Genome_intervals")
> 
> #---------
> # checks
> #---------
> 
> # distances from i to j
> dn = distance_to_nearest(i,j)
> 
> # distance is NA or >=0
> if( any( !is.na(dn) & dn < 0) ) stop("negative distance.")
> 
> # distance == 0 if and only if the interval overlaps another one:
> io = interval_overlap(i,j)
> if( any( ( sapply(io, length) >0 )  != (!is.na(dn) & dn ==0) ) )
+     stop("The property 'distance == 0 if and only if the interval overlaps another one' is not followed for at least one instance.")
> 
> # same test for not stranded objects
> dn0 = distance_to_nearest(i0,j0)
> if( any( !is.na(dn0) & dn0 < 0) ) stop("negative distance.")
> 
> io = interval_overlap(i0,j0)
> if( any( ( sapply(io, length) >0 )  != (!is.na(dn0) & dn0 ==0) ) )
+     stop("The property 'distance == 0 if and only if the interval overlaps another one' is not followed for at least one instance.")
> 
> # unstranded distance <= stranded distance
> delta = dn - dn0
> if( any(!is.na(delta)  & delta < 0) ) stop("some unstranded distance larger than a stranded one.")
> 
> # intersection with complement is empty
> stopifnot( nrow( interval_intersection(i, interval_complement(i) ) ) == 0 )
> 
> # distance of union with complement is 1
> # test must be done for not inter-base (or inter-base) independently
> a = interval_union(i[!inter_base(i),] )
> b = interval_complement(i[!inter_base(i),])
> 
> if(!(all.equal( distance_to_nearest( a, b ), rep(1, nrow(a) )  ) ) )
+     stop("distance of union with complement is not 1.")
> 
> # width is reported consistently
> # they should all be 4 in length (we alternate the open/closed state of the intervals
> # pairwise)
> gi <- GenomeIntervals(start=c(6,6,5,5),
+                       end=c(10,9,10,9),
+                       chromosome=rep("chr1",4),
+                       leftOpen = c(FALSE,FALSE,TRUE,TRUE),
+                       rightOpen=c(TRUE,FALSE,TRUE,FALSE))
> 
> stopifnot(all(width(gi)==4))
> 
> proc.time()
   user  system elapsed 
  3.582   0.212   3.801

genomeIntervals.Rcheck/tests/consistency-tests.Rout.save


R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # consistency test
> #
> # Author: julien.gagneur
> ###############################################################################
> 
> 
> library( genomeIntervals )
Loading required package: intervals
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:intervals':

    type, type<-

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

> 
> options(warn = -1)
> 
> #---------
> # settings
> #---------
> # size of random objects
> n = 1e+3
> # chrom length
> l = 1e+3
> # nb of chroms
> k = 3
> 
> #---------
> # data generation
> #---------
> 
> randGenint = function(n,l,k){
+     m = matrix( sample(l, 2*n, replace=TRUE), nc = 2 )
+     m = cbind( apply( m, 1, min), apply( m, 1, max ) )
+ 
+     cl = matrix( sample( c(FALSE,TRUE), 2*n, replace =TRUE), nc=2 )
+     new(
+         "Genome_intervals_stranded",
+         m,
+         closed = cl,
+         annotation = data.frame(
+                 seq_name = factor(paste("chr", sample(k, n, replace=TRUE) )),
+                 inter_base = sample( c(FALSE,TRUE), n, replace =TRUE),
+                 strand = factor(sample(c("-", "+"), n, replace =TRUE))
+         )
+     )
+ }
> 
> i = randGenint(n,l,k)
> j = randGenint(n,l,k)
> i0 = as(i, "Genome_intervals")
> j0 = as(j, "Genome_intervals")
> 
> #---------
> # checks
> #---------
> 
> # distances from i to j
> dn = distance_to_nearest(i,j)
> 
> # distance is NA or >=0
> if( any( !is.na(dn) & dn < 0) ) stop("negative distance.")
> 
> # distance == 0 if and only if the interval overlaps another one:
> io = interval_overlap(i,j)
> if( any( ( sapply(io, length) >0 )  != (!is.na(dn) & dn ==0) ) )
+     stop("The property 'distance == 0 if and only if the interval overlaps another one' is not followed for at least one instance.")
> 
> # same test for not stranded objects
> dn0 = distance_to_nearest(i0,j0)
> if( any( !is.na(dn0) & dn0 < 0) ) stop("negative distance.")
> 
> io = interval_overlap(i0,j0)
> if( any( ( sapply(io, length) >0 )  != (!is.na(dn0) & dn0 ==0) ) )
+     stop("The property 'distance == 0 if and only if the interval overlaps another one' is not followed for at least one instance.")
> 
> # unstranded distance <= stranded distance
> delta = dn - dn0
> if( any(!is.na(delta)  & delta < 0) ) stop("some unstranded distance larger than a stranded one.")
> 
> # intersection with complement is empty
> stopifnot( nrow( interval_intersection(i, interval_complement(i) ) ) == 0 )
> 
> # distance of union with complement is 1
> # test must be done for not inter-base (or inter-base) independently
> a = interval_union(i[!inter_base(i),] )
> b = interval_complement(i[!inter_base(i),])
> 
> if(!(all.equal( distance_to_nearest( a, b ), rep(1, nrow(a) )  ) ) )
+     stop("distance of union with complement is not 1.")
> 
> # width is reported consistently
> # they should all be 4 in length (we alternate the open/closed state of the intervals
> # pairwise)
> gi <- GenomeIntervals(start=c(6,6,5,5),
+                       end=c(10,9,10,9),
+                       chromosome=rep("chr1",4),
+                       leftOpen = c(FALSE,FALSE,TRUE,TRUE),
+                       rightOpen=c(TRUE,FALSE,TRUE,FALSE))
> 
> stopifnot(all(width(gi)==4))
> 
> proc.time()
   user  system elapsed 
  3.868   0.188   4.048

genomeIntervals.Rcheck/tests/fullShow.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # the fullShow methods is a show method for Genome_intervals objects.
> # It is called by test scripts so that the full output of the tests can be checked.  
> # 
> # Author: gagneur
> ###############################################################################
> 
> fullShow <- function(object ) {
+ 	cat(
+ 			"Object of class ",
+ 			class( object ),
+ 			"\n",
+ 			sum( !inter_base(object) ),
+ 			" base interval",
+ 			ifelse( sum( !inter_base(object) ) == 1, "", "s" ),
+ 			" and ",
+ 			sum( inter_base(object) ),
+ 			" inter-base interval",
+ 			ifelse( sum( inter_base(object) ) == 1, "", "s" ),
+ 			"(*)",
+ 			":\n",
+ 			sep = ""
+ 	)
+ 	ints <- as( object, "character")
+ 	if ( !is.null( rownames( object ) ) ) {
+ 		fmt <- sprintf( "%%%is", max( nchar( rownames( object ) ) ) )
+ 		ints <- paste( sprintf( fmt, rownames( object ) ), ints )
+ 	}
+ 	cat( ints, sep = "\n" )
+ 	cat( "annotation:\n")
+ 	show( annotation(object) )
+ }
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  0.145   0.055   0.202

Example timings

genomeIntervals.Rcheck/genomeIntervals-Ex.timings

name	user	system	elapsed
GenomeIntervals-constructor	0.069	0.008	0.076
Genome_intervals-class	0.023	0.004	0.027
Genome_intervals-coercion-methods	0	0	0
Genome_intervals-ordering	0.038	0.005	0.043
Genome_intervals_stranded-class	0.036	0.006	0.042
c.Genome_intervals	0.048	0.007	0.055
core_annotated	0.035	0.006	0.041
distance_to_nearest-methods	0.155	0.005	0.159
genomeIntervals-readGff3	1.068	0.589	1.672
getGffAttribute	0.040	0.002	0.042
interval_overlap-methods	0.060	0.003	0.063
interval_set_operations-methods	0.356	0.004	0.360
parseGffAttributes	0.038	0.002	0.040