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CHECK report for diffHic on malbec2

This page was generated on 2020-10-17 11:54:40 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE diffHic PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 473/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffHic 1.20.0
Aaron Lun
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/diffHic
Branch: RELEASE_3_11
Last Commit: ca6d240
Last Changed Date: 2020-04-27 14:48:43 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: diffHic
Version: 1.20.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:diffHic.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings diffHic_1.20.0.tar.gz
StartedAt: 2020-10-17 00:44:35 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:52:38 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 483.1 seconds
RetCode: 0
Status:  OK 
CheckDir: diffHic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:diffHic.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings diffHic_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/diffHic.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffHic/DESCRIPTION’ ... OK
* this is package ‘diffHic’ version ‘1.20.0’
* 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
* checking installed package size ... NOTE
  installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   9.0Mb
* 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 ‘/home/biocbuild/bbs-3.11-bioc/R/library/diffHic/libs/diffHic.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘srand48’, possibly from ‘srand48’ (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. 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 12.979  0.012  13.042
cutGenome     8.635  0.107   9.345
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/diffHic.Rcheck/00check.log’
for details.



Installation output

diffHic.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL diffHic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘diffHic’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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 between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t odex=0; odex < ncombos; ++odex) {
                         ~~~~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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 between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t vecdex=0; vecdex<ncombos; ++vecdex) {
                           ~~~~~~^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.11-bioc/R/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-3.11-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-3.11-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 (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 
 17.426   0.540  20.672 

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.

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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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: InteractionSet
Loading required package: SummarizedExperiment
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> 
> test_check("diffHic")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 427 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 67.181   0.894  71.108 

Example timings

diffHic.Rcheck/diffHic-Ex.timings

nameusersystemelapsed
DNaseHiC0.2580.0000.258
annotatePairs1.2230.0001.224
boxPairs1.0210.0481.069
clusterPairs0.9150.0000.950
compartmentalize0.6840.0040.688
connectCounts1.7890.0131.825
consolidatePairs0.6280.0000.628
correctedContact0.4090.0000.412
cutGenome8.6350.1079.345
diClusters2.8000.0003.061
diffHicUsersGuide0.0010.0000.001
domainDirections0.2040.0000.204
enrichedPairs0.7350.0000.837
extractPatch0.8130.0040.818
filterDiag0.1910.0040.229
filterPeaks0.3690.0000.373
filters0.3710.0040.378
getArea0.1630.0000.201
getPairData0.0510.0000.051
loadData0.0660.0000.066
marginCounts0.7850.0000.842
mergeCMs0.8300.0001.133
mergePairs0.1640.0080.172
neighborCounts0.1680.0000.167
normalizeCNV12.979 0.01213.042
pairParam0.160.000.16
plotDI0.7540.0000.753
plotPlaid2.3150.0082.323
preparePairs0.2310.0000.231
prunePairs0.2750.0080.283
readMTX2IntSet0.3220.0000.321
savePairs0.0490.0000.049
squareCounts0.7190.0040.724
totalCounts0.4240.0040.428