Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:diffHic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings diffHic_1.42.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/diffHic.Rcheck’* using R version 4.5.2 Patched (2025-11-04 r88984)* using platform: aarch64-apple-darwin20* R was compiled by    Apple clang version 16.0.0 (clang-1600.0.26.6)    GNU Fortran (GCC) 14.2.0* running under: macOS Ventura 13.7.8* 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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’* used SDK: ‘MacOSX11.3.1.sdk’* checking installed package size ... OK* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... OK* checking top-level files ... OK* checking for left-over files ... OK* checking index information ... OK* checking package subdirectories ... OK* checking code files for non-ASCII characters ... OK* checking R files for syntax errors ... OK* checking whether the package can be loaded ... OK* checking whether the package can be loaded with stated dependencies ... OK* checking whether the package can be unloaded cleanly ... OK* checking whether the namespace can be loaded with stated dependencies ... OK* checking whether the namespace can be unloaded cleanly ... OK* checking dependencies in R code ... OK* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... OK* checking Rd files ... 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 ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/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)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 sizes of PDF files under ‘inst/doc’ ... OK* 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 12.824  0.141  18.230cutGenome     7.831  0.167  12.165* 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  ‘/Users/biocbuild/bbs-3.22-bioc/meat/diffHic.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL diffHic###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’* installing *source* package ‘diffHic’ ...** this is package ‘diffHic’ version ‘1.42.0’** using staged installation** libsusing C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’using SDK: ‘MacOSX11.3.1.sdk’clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c binner.cpp -o binner.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c check_input.cpp -o check_input.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cluster_2d.cpp -o cluster_2d.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c count_background.cpp -o count_background.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c count_connect.cpp -o count_connect.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c count_patch.cpp -o count_patch.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c directionality.cpp -o directionality.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c init.cpp -o init.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c iterative_correction.cpp -o iterative_correction.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c neighbors.cpp -o neighbors.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pair_stats.cpp -o pair_stats.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c quadrant_bg.cpp -o quadrant_bg.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c report_hic_pairs.cpp -o report_hic_pairs.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c trended_filter.cpp -o trended_filter.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.oclang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.5-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Library/Frameworks/R.framework/Versions/4.5-arm64/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** 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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-apple-darwin20R 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  16.054   0.674  23.880

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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-apple-darwin20R 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  62.443   1.765  88.606