Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD check --install=check:diffHic.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings diffHic_1.42.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/diffHic.Rcheck’* using R version 4.5.0 (2025-04-11)* using platform: aarch64-unknown-linux-gnu* R was compiled by    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0    GNU Fortran (GCC) 14.2.0* running under: openEuler 24.03 (LTS)* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘diffHic/DESCRIPTION’ ... OK* this is package ‘diffHic’ version ‘1.42.0’* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’* checking installed package size ... INFO  installed size is 13.5Mb  sub-directories of 1Mb or more:    doc    1.3Mb    libs  11.0Mb* 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 code files for non-ASCII characters ... OK* checking R files for syntax errors ... OK* checking whether the package can be loaded ... OK* checking whether the package can be loaded with stated dependencies ... OK* checking whether the package can be unloaded cleanly ... OK* checking whether the namespace can be loaded with stated dependencies ... OK* checking whether the namespace can be unloaded cleanly ... OK* checking 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 ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  annotatePairs.Rd: findOverlaps  connectCounts.Rd: findOverlaps, linkOverlaps  consolidatePairs.Rd: combineTests  correctedContact.Rd: mglmOneGroup  cutGenome.Rd: BSgenome-class, GRanges-class, matchPattern  diClusters.Rd: controlClusterFDR  filterDiag.Rd: pairdist  filterPeaks.Rd: aveLogCPM  filters.Rd: loessFit, scaledAverage  normalizeCNV.Rd: locfit, lp  readMTX2IntSet.Rd: InteractionSet-class, GInteractionsPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* 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 ... INFOGNU 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 ... NOTENote: information on .o files is not availableFile ‘/home/biocbuild/R/R-4.5.0/site-library/diffHic/libs/diffHic.so’:  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 norwrite to stdout/stderr instead of to the console, nor use Fortran I/Onor system RNGs nor [v]sprintf. The detected symbols are linked intothe 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 ... OKExamples with CPU (user + system) or elapsed time > 5s               user system elapsednormalizeCNV 10.136  0.004  10.160cutGenome     6.594  0.051   6.689* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘test-basic.R’  Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ... OK  Running ‘testthat.R’ OK* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking running R code from vignettes ... SKIPPED* checking re-building of vignette outputs ... SKIPPED* checking PDF version of manual ... OK* DONEStatus: 2 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/diffHic.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD INSTALL diffHic###############################################################################################################################################################* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’* installing *source* package ‘diffHic’ ...** this is package ‘diffHic’ version ‘1.42.0’** using staged installation** libsusing C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c binner.cpp -o binner.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c check_input.cpp -o check_input.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c cluster_2d.cpp -o cluster_2d.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c count_background.cpp -o count_background.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c count_connect.cpp -o count_connect.ocount_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) {      |                         ~~~~~^~~~~~~~~/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c count_patch.cpp -o count_patch.ocount_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) {      |                           ~~~~~~^~~~~~~~/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c directionality.cpp -o directionality.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c init.cpp -o init.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c iterative_correction.cpp -o iterative_correction.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c neighbors.cpp -o neighbors.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c pair_stats.cpp -o pair_stats.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c quadrant_bg.cpp -o quadrant_bg.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c report_hic_pairs.cpp -o report_hic_pairs.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c trended_filter.cpp -o trended_filter.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.5.0/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c utils.cpp -o utils.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R-4.5.0/lib -lRinstalling to /home/biocbuild/R/R-4.5.0/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)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-unknown-linux-gnuR 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 insert1     40           1     402     80           1     803     60           2     544     40           3    1605     20           1     666     80           0    114> > loadChromos(fout)  anchor1 anchor21    chrA    chrA2    chrB    chrA3    chrB    chrB> head(loadData(fout, "chrA", "chrA"))  anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len1          2          1          49          14          -5          102          2          1          79           9         -10          103          2          1          65          21          10         -104          4          1         156           6         -10         -105          4          2         141          80          -5          106          4          2         154          50          10          10> head(loadData(fout, "chrA", "chrB"))  anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len1          5          2          19          44          10         -102          5          3          14         105          10         -103          6          1          65          19           5          104          6          2          24          90          -5           55          6          3          24         100          -5         -106          6          3          24          95          -5         -10Warning message:In value[[3L]](cond) : anchor definitions are reversed> > # Loading the counts.> data <- squareCounts(fout, param, width=50, filter=1)> dataclass: InteractionSet dim: 10 1 metadata(2): param widthassays(1): countsrownames: NULLrowData names(0):colnames: NULLcolData names(1): totalstype: ReverseStrictGInteractionsregions: 6> > margins <- marginCounts(fout, param, width=50)> marginsclass: RangedSummarizedExperiment dim: 6 1 metadata(1): paramassays(1): countsrownames: NULLrowData names(1): nfragscolnames: NULLcolData 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): paramassays(1): countsrownames: NULLrowData names(0):colnames: NULLcolData names(1): totalstype: ReverseStrictGInteractionsregions: 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$totals[1] 17> colData(data)DataFrame with 1 row and 1 column     totals  <integer>1        17> metadata(data)$paramGenome contains 7 restriction fragments across 2 chromosomesNo discard regions are specifiedNo limits on chromosomes for read extractionNo cap on the read pairs per pair of restriction fragments$width[1] 50> > asDGEList(data)An object of class "DGEList"$counts   Sample11        32        13        24        15        16        27        38        19        210       1$samples        group lib.size norm.factorsSample1     1       17            1> asDGEList(data, lib.size=20)$samples        group lib.size norm.factorsSample1     1       20            1> asDGEList(data, norm.factors=2, group="a")$samples        group lib.size norm.factorsSample1     a       17            2Warning message:In DGEList.default(group = "a", lib.size = 17L, norm.factors = 2,  :  norm factors don't multiply to 1> > # Playing around with some bin counts.> stuff <- correctedContact(data)> head(stuff$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 widthassays(5): counts quadrant vertical horizontal surroundingrownames: NULLrowData names(4): N.quadrant N.vertical N.horizontal N.surroundingcolnames: NULLcolData names(1): totalstype: ReverseStrictGInteractionsregions: 6> head(clusterPairs(data, tol=10)$indices[[1]])[1] 1 2 2 2 3 3> > # End.> > unlink(fout)> > proc.time()   user  system elapsed  16.367   0.563  17.571

R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"Copyright (C) 2024 The R Foundation for Statistical ComputingPlatform: x86_64-w64-mingw32/x64R 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 insert1     40           1     402     80           1     803     60           2     544     40           3    1605     20           1     666     80           0    114> > loadChromos(fout)  anchor1 anchor21    chrA    chrA2    chrB    chrA3    chrB    chrB> head(loadData(fout, "chrA", "chrA"))  anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len1          2          1          49          14          -5          102          2          1          79           9         -10          103          2          1          65          21          10         -104          4          1         156           6         -10         -105          4          2         141          80          -5          106          4          2         154          50          10          10> head(loadData(fout, "chrA", "chrB"))  anchor1.id anchor2.id anchor1.pos anchor2.pos anchor1.len anchor2.len1          5          2          19          44          10         -102          5          3          14         105          10         -103          6          1          65          19           5          104          6          2          24          90          -5           55          6          3          24         100          -5         -106          6          3          24          95          -5         -10Warning message:In value[[3L]](cond) : anchor definitions are reversed> > # Loading the counts.> data <- squareCounts(fout, param, width=50, filter=1)> dataclass: InteractionSet dim: 10 1 metadata(2): param widthassays(1): countsrownames: NULLrowData names(0):colnames: NULLcolData names(1): totalstype: ReverseStrictGInteractionsregions: 6> > margins <- marginCounts(fout, param, width=50)> marginsclass: RangedSummarizedExperiment dim: 6 1 metadata(1): paramassays(1): countsrownames: NULLrowData names(1): nfragscolnames: NULLcolData 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): paramassays(1): countsrownames: NULLrowData names(0):colnames: NULLcolData names(1): totalstype: ReverseStrictGInteractionsregions: 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$totals[1] 17> colData(data)DataFrame with 1 row and 1 column     totals  <integer>1        17> metadata(data)$paramGenome contains 7 restriction fragments across 2 chromosomesNo discard regions are specifiedNo limits on chromosomes for read extractionNo cap on the read pairs per pair of restriction fragments$width[1] 50> > asDGEList(data)An object of class "DGEList"$counts   Sample11        32        13        24        15        16        27        38        19        210       1$samples        group lib.size norm.factorsSample1     1       17            1> asDGEList(data, lib.size=20)$samples        group lib.size norm.factorsSample1     1       20            1> asDGEList(data, norm.factors=2, group="a")$samples        group lib.size norm.factorsSample1     a       17            2Warning message:In DGEList.default(group = "a", lib.size = 17L, norm.factors = 2,  :  norm factors don't multiply to 1> > # Playing around with some bin counts.> stuff <- correctedContact(data)> head(stuff$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 widthassays(5): counts quadrant vertical horizontal surroundingrownames: NULLrowData names(4): N.quadrant N.vertical N.horizontal N.surroundingcolnames: NULLcolData names(1): totalstype: ReverseStrictGInteractionsregions: 6> head(clusterPairs(data, tol=10)$indices[[1]])[1] 1 2 2 2 3 3> > # End.> > unlink(fout)> > proc.time()   user  system elapsed    4.00    0.42    6.53

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-unknown-linux-gnuR 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: GenomicRangesLoading required package: stats4Loading required package: BiocGenericsLoading required package: genericsAttaching package: 'generics'The following objects are masked from 'package:base':    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,    setequal, unionAttaching package: 'BiocGenerics'The following objects are masked from 'package:stats':    IQR, mad, sd, var, xtabsThe 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, is.unsorted, lapply,    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,    unsplit, which.max, which.minLoading required package: S4VectorsAttaching package: 'S4Vectors'The following object is masked from 'package:utils':    findMatchesThe following objects are masked from 'package:base':    I, expand.grid, unnameLoading required package: IRangesLoading required package: SeqinfoLoading required package: InteractionSetLoading required package: SummarizedExperimentLoading required package: MatrixGenericsLoading required package: matrixStatsAttaching 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, rowWeightedVarsLoading required package: BiobaseWelcome 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':    rowMediansThe 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  57.971   1.100  60.823