Aaron Lun
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/diffHic |
| git_branch: RELEASE_3_18 |
| git_last_commit: d7d9f66 |
| git_last_commit_date: 2023-10-24 10:43:16 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:35:54 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 563/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| diffHic 1.34.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the diffHic package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diffHic.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: diffHic |
| Version: 1.34.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:diffHic.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings diffHic_1.34.0.tar.gz |
| StartedAt: 2024-03-27 21:56:56 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 22:02:32 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 336.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: diffHic.Rcheck |
| Warnings: 2 |
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### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:diffHic.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings diffHic_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/diffHic.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘diffHic/DESCRIPTION’ ... OK
* this is package ‘diffHic’ version ‘1.34.0’
* 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 ‘diffHic’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 13.0Mb
sub-directories of 1Mb or more:
doc 1.3Mb
libs 10.4Mb
* 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 loading without being on the library search path ... 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: (5) pairParam.Rd:48-51: \item in \describe must have non-empty label
checkRd: (5) pairParam.Rd:58-60: \item in \describe must have non-empty label
checkRd: (5) pairParam.Rd:67-69: \item in \describe must have non-empty label
checkRd: (5) pairParam.Rd:70-73: \item in \describe must have non-empty label
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.18-bioc/R/site-library/diffHic/libs/diffHic.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
normalizeCNV 7.746 0.032 7.779
cutGenome 6.196 0.088 6.284
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-basic.R’
Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ...208,210d207
< Warning message:
< In DGEList.default(group = "a", lib.size = 17L, norm.factors = 2, :
< norm factors don't multiply to 1
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘diffHic.Rnw’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/diffHic.Rcheck/00check.log’
for details.
diffHic.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL diffHic
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘diffHic’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c binner.cpp -o binner.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c check_input.cpp -o check_input.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c cluster_2d.cpp -o cluster_2d.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c count_background.cpp -o count_background.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c count_connect.cpp -o count_connect.o
count_connect.cpp: In function ‘SEXPREC* count_connect(SEXP, SEXP)’:
count_connect.cpp:57:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
57 | for (size_t odex=0; odex < ncombos; ++odex) {
| ~~~~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c count_patch.cpp -o count_patch.o
count_patch.cpp: In function ‘SEXPREC* count_patch(SEXP, SEXP, SEXP, SEXP, SEXP)’:
count_patch.cpp:45:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
45 | for (size_t vecdex=0; vecdex<ncombos; ++vecdex) {
| ~~~~~~^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c directionality.cpp -o directionality.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c iterative_correction.cpp -o iterative_correction.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c neighbors.cpp -o neighbors.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c pair_stats.cpp -o pair_stats.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c quadrant_bg.cpp -o quadrant_bg.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c report_hic_pairs.cpp -o report_hic_pairs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c trended_filter.cpp -o trended_filter.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o diffHic.so binner.o check_input.o cluster_2d.o count_background.o count_connect.o count_patch.o directionality.o init.o iterative_correction.o neighbors.o pair_stats.o quadrant_bg.o report_hic_pairs.o trended_filter.o utils.o /home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-diffHic/00new/diffHic/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (diffHic)
diffHic.Rcheck/tests/test-basic.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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.
> # These are just placeholders for the real things in inst/tests.
>
> suppressWarnings(suppressPackageStartupMessages(require(diffHic)))
>
> hic.file <- system.file("exdata", "hic_sort.bam", package="diffHic")
> cuts <- readRDS(system.file("exdata", "cuts.rds", package="diffHic"))
> param <- pairParam(fragments=cuts)
>
> # Setting up the parameters
> fout <- "output.h5"
> preparePairs(hic.file, param, file=fout)
$pairs
total marked filtered mapped
32 7 3 22
$same.id
dangling self.circle
4 1
$singles
[1] 2
$chimeras
total mapped multi invalid
12 8 7 5
> head(getPairData(fout, param))
length orientation insert
1 40 1 40
2 80 1 80
3 60 2 54
4 40 3 160
5 20 1 66
6 80 0 114
>
> loadChromos(fout)
anchor1 anchor2
1 chrA chrA
2 chrB chrA
3 chrB chrB
> head(loadData(fout, "chrA", "chrA"))
anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len
1 2 1 49 14 -5 10
2 2 1 79 9 -10 10
3 2 1 65 21 10 -10
4 4 1 156 6 -10 -10
5 4 2 141 80 -5 10
6 4 2 154 50 10 10
> head(loadData(fout, "chrA", "chrB"))
anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len
1 5 2 19 44 10 -10
2 5 3 14 105 10 -10
3 6 1 65 19 5 10
4 6 2 24 90 -5 5
5 6 3 24 100 -5 -10
6 6 3 24 95 -5 -10
Warning message:
In value[[3L]](cond) : anchor definitions are reversed
>
> # Loading the counts.
> data <- squareCounts(fout, param, width=50, filter=1)
> data
class: InteractionSet
dim: 10 1
metadata(2): param width
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 6
>
> margins <- marginCounts(fout, param, width=50)
> margins
class: RangedSummarizedExperiment
dim: 6 1
metadata(1): param
assays(1): counts
rownames: NULL
rowData names(1): nfrags
colnames: NULL
colData names(1): totals
> totalCounts(fout, param)
[1] 17
>
> regions <- GRanges("chrA", IRanges(c(1, 100, 150), c(20, 140, 160)))
> connectCounts(fout, param, regions=regions, filter=1L)
class: InteractionSet
dim: 2 1
metadata(1): param
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 3
>
> # Checking some values.
> head(getArea(data))
[1] 2208 2304 2208 2208 3312 3174
> head(pairdist(data))
[1] 47 140 93 47 NA NA
>
> anchors(data, type="first")
GRanges object with 10 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA 49-94 * | 1
[2] chrA 141-188 * | 1
[3] chrA 141-188 * | 1
[4] chrA 141-188 * | 1
[5] chrB 1-69 * | 2
[6] chrB 1-69 * | 2
[7] chrB 1-69 * | 2
[8] chrB 1-69 * | 2
[9] chrB 70-92 * | 1
[10] chrB 70-92 * | 1
-------
seqinfo: 2 sequences from an unspecified genome
> anchors(data, type="second")
GRanges object with 10 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA 1-48 * | 1
[2] chrA 1-48 * | 1
[3] chrA 49-94 * | 1
[4] chrA 95-140 * | 1
[5] chrA 1-48 * | 1
[6] chrA 49-94 * | 1
[7] chrA 95-140 * | 1
[8] chrB 1-69 * | 2
[9] chrB 1-69 * | 2
[10] chrB 70-92 * | 1
-------
seqinfo: 2 sequences from an unspecified genome
> assay(data)
[,1]
[1,] 3
[2,] 1
[3,] 2
[4,] 1
[5,] 1
[6,] 2
[7,] 3
[8,] 1
[9,] 2
[10,] 1
> regions(data)
GRanges object with 6 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA 1-48 * | 1
[2] chrA 49-94 * | 1
[3] chrA 95-140 * | 1
[4] chrA 141-188 * | 1
[5] chrB 1-69 * | 2
[6] chrB 70-92 * | 1
-------
seqinfo: 2 sequences from an unspecified genome
>
> data$totals
[1] 17
> colData(data)
DataFrame with 1 row and 1 column
totals
<integer>
1 17
> metadata(data)
$param
Genome contains 7 restriction fragments across 2 chromosomes
No discard regions are specified
No limits on chromosomes for read extraction
No cap on the read pairs per pair of restriction fragments
$width
[1] 50
>
> asDGEList(data)
An object of class "DGEList"
$counts
Sample1
1 3
2 1
3 2
4 1
5 1
6 2
7 3
8 1
9 2
10 1
$samples
group lib.size norm.factors
Sample1 1 17 1
> asDGEList(data, lib.size=20)$samples
group lib.size norm.factors
Sample1 1 20 1
> asDGEList(data, norm.factors=2, group="a")$samples
group lib.size norm.factors
Sample1 a 17 2
Warning message:
In DGEList.default(group = "a", lib.size = 17L, norm.factors = 2, :
norm factors don't multiply to 1
>
> # Playing around with some bin counts.
> stuff <- correctedContact(data)
> head(stuff$truth)
[1] 1.517032e+04 6.123523e-01 6.123523e-01 8.162749e-01 2.041633e-01
[6] 2.041633e-01
>
> data.large <- squareCounts(fout, param, width=100, filter=1)
> boxed <- boxPairs(larger=data.large, smaller=data)
> head(boxed$indices$larger)
[1] 1 2 3 4 5 6
> head(boxed$indices$smaller)
[1] 1 2 2 3 4 4
>
> head(enrichedPairs(data))
class: InteractionSet
dim: 6 1
metadata(2): param width
assays(5): counts quadrant vertical horizontal surrounding
rownames: NULL
rowData names(4): N.quadrant N.vertical N.horizontal N.surrounding
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 6
> head(clusterPairs(data, tol=10)$indices[[1]])
[1] 1 2 2 2 3 3
>
> # End.
>
> unlink(fout)
>
> proc.time()
user system elapsed
12.585 0.463 13.036
diffHic.Rcheck/tests/test-basic.Rout.save
R version 3.5.0 Patched (2018-04-30 r74679) -- "Joy in Playing"
Copyright (C) 2018 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.
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.
> # These are just placeholders for the real things in inst/tests.
>
> suppressWarnings(suppressPackageStartupMessages(require(diffHic)))
>
> hic.file <- system.file("exdata", "hic_sort.bam", package="diffHic")
> cuts <- readRDS(system.file("exdata", "cuts.rds", package="diffHic"))
> param <- pairParam(fragments=cuts)
>
> # Setting up the parameters
> fout <- "output.h5"
> preparePairs(hic.file, param, file=fout)
$pairs
total marked filtered mapped
32 7 3 22
$same.id
dangling self.circle
4 1
$singles
[1] 2
$chimeras
total mapped multi invalid
12 8 7 5
> head(getPairData(fout, param))
length orientation insert
1 40 1 40
2 80 1 80
3 60 2 54
4 40 3 160
5 20 1 66
6 80 0 114
>
> loadChromos(fout)
anchor1 anchor2
1 chrA chrA
2 chrB chrA
3 chrB chrB
> head(loadData(fout, "chrA", "chrA"))
anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len
1 2 1 49 14 -5 10
2 2 1 79 9 -10 10
3 2 1 65 21 10 -10
4 4 1 156 6 -10 -10
5 4 2 141 80 -5 10
6 4 2 154 50 10 10
> head(loadData(fout, "chrA", "chrB"))
anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len
1 5 2 19 44 10 -10
2 5 3 14 105 10 -10
3 6 1 65 19 5 10
4 6 2 24 90 -5 5
5 6 3 24 100 -5 -10
6 6 3 24 95 -5 -10
Warning message:
In value[[3L]](cond) : anchor definitions are reversed
>
> # Loading the counts.
> data <- squareCounts(fout, param, width=50, filter=1)
> data
class: InteractionSet
dim: 10 1
metadata(2): param width
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 6
>
> margins <- marginCounts(fout, param, width=50)
> margins
class: RangedSummarizedExperiment
dim: 6 1
metadata(1): param
assays(1): counts
rownames: NULL
rowData names(1): nfrags
colnames: NULL
colData names(1): totals
> totalCounts(fout, param)
[1] 17
>
> regions <- GRanges("chrA", IRanges(c(1, 100, 150), c(20, 140, 160)))
> connectCounts(fout, param, regions=regions, filter=1L)
class: InteractionSet
dim: 2 1
metadata(1): param
assays(1): counts
rownames: NULL
rowData names(0):
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 3
>
> # Checking some values.
> head(getArea(data))
[1] 2208 2304 2208 2208 3312 3174
> head(pairdist(data))
[1] 47 140 93 47 NA NA
>
> anchors(data, type="first")
GRanges object with 10 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA 49-94 * | 1
[2] chrA 141-188 * | 1
[3] chrA 141-188 * | 1
[4] chrA 141-188 * | 1
[5] chrB 1-69 * | 2
[6] chrB 1-69 * | 2
[7] chrB 1-69 * | 2
[8] chrB 1-69 * | 2
[9] chrB 70-92 * | 1
[10] chrB 70-92 * | 1
-------
seqinfo: 2 sequences from an unspecified genome
> anchors(data, type="second")
GRanges object with 10 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA 1-48 * | 1
[2] chrA 1-48 * | 1
[3] chrA 49-94 * | 1
[4] chrA 95-140 * | 1
[5] chrA 1-48 * | 1
[6] chrA 49-94 * | 1
[7] chrA 95-140 * | 1
[8] chrB 1-69 * | 2
[9] chrB 1-69 * | 2
[10] chrB 70-92 * | 1
-------
seqinfo: 2 sequences from an unspecified genome
> assay(data)
[,1]
[1,] 3
[2,] 1
[3,] 2
[4,] 1
[5,] 1
[6,] 2
[7,] 3
[8,] 1
[9,] 2
[10,] 1
> regions(data)
GRanges object with 6 ranges and 1 metadata column:
seqnames ranges strand | nfrags
<Rle> <IRanges> <Rle> | <integer>
[1] chrA 1-48 * | 1
[2] chrA 49-94 * | 1
[3] chrA 95-140 * | 1
[4] chrA 141-188 * | 1
[5] chrB 1-69 * | 2
[6] chrB 70-92 * | 1
-------
seqinfo: 2 sequences from an unspecified genome
>
> data$totals
[1] 17
> colData(data)
DataFrame with 1 row and 1 column
totals
<integer>
1 17
> metadata(data)
$param
Genome contains 7 restriction fragments across 2 chromosomes
No discard regions are specified
No limits on chromosomes for read extraction
No cap on the read pairs per pair of restriction fragments
$width
[1] 50
>
> asDGEList(data)
An object of class "DGEList"
$counts
Sample1
1 3
2 1
3 2
4 1
5 1
6 2
7 3
8 1
9 2
10 1
$samples
group lib.size norm.factors
Sample1 1 17 1
> asDGEList(data, lib.size=20)$samples
group lib.size norm.factors
Sample1 1 20 1
> asDGEList(data, norm.factors=2, group="a")$samples
group lib.size norm.factors
Sample1 a 17 2
>
> # Playing around with some bin counts.
> stuff <- correctedContact(data)
> head(stuff$truth)
[1] 1.517032e+04 6.123523e-01 6.123523e-01 8.162749e-01 2.041633e-01
[6] 2.041633e-01
>
> data.large <- squareCounts(fout, param, width=100, filter=1)
> boxed <- boxPairs(larger=data.large, smaller=data)
> head(boxed$indices$larger)
[1] 1 2 3 4 5 6
> head(boxed$indices$smaller)
[1] 1 2 2 3 4 4
>
> head(enrichedPairs(data))
class: InteractionSet
dim: 6 1
metadata(2): param width
assays(5): counts quadrant vertical horizontal surrounding
rownames: NULL
rowData names(4): N.quadrant N.vertical N.horizontal N.surrounding
colnames: NULL
colData names(1): totals
type: ReverseStrictGInteractions
regions: 6
> head(clusterPairs(data, tol=10)$indices[[1]])
[1] 1 2 2 2 3 3
>
> # End.
>
> unlink(fout)
>
> proc.time()
user system elapsed
5.571 0.168 5.757
diffHic.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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.
> library(testthat)
> library(diffHic)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: InteractionSet
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
>
> test_check("diffHic")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 427 ]
>
> proc.time()
user system elapsed
51.725 2.303 54.018
diffHic.Rcheck/diffHic-Ex.timings
| name | user | system | elapsed | |
| DNaseHiC | 0.135 | 0.000 | 0.135 | |
| annotatePairs | 0.344 | 0.003 | 0.348 | |
| boxPairs | 0.612 | 0.068 | 0.680 | |
| clusterPairs | 0.757 | 0.005 | 0.762 | |
| compartmentalize | 0.605 | 0.011 | 0.617 | |
| connectCounts | 1.351 | 0.112 | 1.464 | |
| consolidatePairs | 1.403 | 0.264 | 1.667 | |
| correctedContact | 0.375 | 0.000 | 0.375 | |
| cutGenome | 6.196 | 0.088 | 6.284 | |
| diClusters | 1.391 | 0.004 | 1.395 | |
| diffHicUsersGuide | 0.001 | 0.000 | 0.001 | |
| domainDirections | 0.102 | 0.000 | 0.103 | |
| enrichedPairs | 0.367 | 0.000 | 0.368 | |
| extractPatch | 0.359 | 0.000 | 0.359 | |
| filterDiag | 0.096 | 0.000 | 0.095 | |
| filterPeaks | 0.168 | 0.000 | 0.167 | |
| filters | 0.197 | 0.000 | 0.197 | |
| getArea | 0.112 | 0.004 | 0.116 | |
| getPairData | 0.041 | 0.004 | 0.045 | |
| loadData | 0.044 | 0.003 | 0.047 | |
| marginCounts | 0.447 | 0.000 | 0.446 | |
| mergeCMs | 0.383 | 0.000 | 0.384 | |
| mergePairs | 0.151 | 0.008 | 0.159 | |
| neighborCounts | 0.111 | 0.000 | 0.111 | |
| normalizeCNV | 7.746 | 0.032 | 7.779 | |
| pairParam | 0.082 | 0.000 | 0.082 | |
| plotDI | 0.377 | 0.000 | 0.377 | |
| plotPlaid | 1.156 | 0.012 | 1.169 | |
| preparePairs | 0.142 | 0.004 | 0.146 | |
| prunePairs | 0.165 | 0.012 | 0.176 | |
| readMTX2IntSet | 0.268 | 0.004 | 0.273 | |
| savePairs | 0.042 | 0.004 | 0.046 | |
| squareCounts | 0.547 | 0.000 | 0.548 | |
| totalCounts | 0.363 | 0.000 | 0.363 | |