Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:34 -0400 (Fri, 15 Oct 2021).

CHECK results for diffHic on machv2

To the developers/maintainers of the diffHic package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 499/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffHic 1.24.1  (landing page)
Aaron Lun
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/diffHic
git_branch: RELEASE_3_13
git_last_commit: a505f6d
git_last_commit_date: 2021-07-15 04:46:22 -0400 (Thu, 15 Jul 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: diffHic
Version: 1.24.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffHic.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffHic_1.24.1.tar.gz
StartedAt: 2021-10-14 18:24:07 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 18:31:36 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 449.5 seconds
RetCode: 0
Status:   OK  
CheckDir: diffHic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffHic.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffHic_1.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/diffHic.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffHic/DESCRIPTION’ ... OK
* this is package ‘diffHic’ version ‘1.24.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘diffHic’ 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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 ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/diffHic/libs/diffHic.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘_srand48’, possibly from ‘srand48’ (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. 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 sizes of PDF files under ‘inst/doc’ ... OK
* 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 10.309  0.058  10.381
cutGenome     7.773  0.162   7.951
* 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 (function (counts = matrix(0, 0, 0), lib.size = colSums(counts),  :
<   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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/diffHic.Rcheck/00check.log’
for details.



Installation output

diffHic.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL diffHic
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘diffHic’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c binner.cpp -o binner.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c check_input.cpp -o check_input.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cluster_2d.cpp -o cluster_2d.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_background.cpp -o count_background.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_connect.cpp -o count_connect.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_patch.cpp -o count_patch.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c directionality.cpp -o directionality.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c iterative_correction.cpp -o iterative_correction.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c neighbors.cpp -o neighbors.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pair_stats.cpp -o pair_stats.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c quadrant_bg.cpp -o quadrant_bg.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c report_hic_pairs.cpp -o report_hic_pairs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c trended_filter.cpp -o trended_filter.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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
   ‘diffHic.Rnw’ 
** 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)

Tests output

diffHic.Rcheck/tests/test-basic.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> # 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 (function (counts = matrix(0, 0, 0), lib.size = colSums(counts),  :
  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 
 16.005   0.750  16.740 

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)

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> # 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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> library(testthat)
> library(diffHic)
Loading required package: GenomicRanges
Loading required package: stats4
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, 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 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 
 77.682   1.777  88.943 

Example timings

diffHic.Rcheck/diffHic-Ex.timings

nameusersystemelapsed
DNaseHiC0.2920.0140.307
annotatePairs0.6960.0070.703
boxPairs1.3920.1321.526
clusterPairs1.6870.0121.701
compartmentalize1.8430.0361.880
connectCounts3.0750.0753.190
consolidatePairs0.7730.0090.815
correctedContact0.7890.0090.800
cutGenome7.7730.1627.951
diClusters3.4040.0533.459
diffHicUsersGuide0.0010.0010.002
domainDirections0.3120.0080.320
enrichedPairs0.9590.0030.963
extractPatch0.8800.0090.891
filterDiag0.1660.0050.171
filterPeaks0.3870.0010.389
filters0.4850.0030.488
getArea0.2430.0050.249
getPairData0.0660.0060.072
loadData0.0900.0080.098
marginCounts0.9390.0130.954
mergeCMs0.8540.0040.859
mergePairs0.2130.0210.234
neighborCounts0.2620.0060.270
normalizeCNV10.309 0.05810.381
pairParam0.2230.0030.225
plotDI0.8190.0080.897
plotPlaid3.0120.0183.036
preparePairs0.2590.0430.302
prunePairs0.2910.0260.317
readMTX2IntSet0.4880.0210.508
savePairs0.0810.0070.089
squareCounts1.3440.0331.378
totalCounts0.9360.0140.951