Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1800/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rqubic 1.52.0 (landing page) Jitao David Zhang
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the rqubic package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rqubic.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: rqubic |
Version: 1.52.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rqubic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rqubic_1.52.0.tar.gz |
StartedAt: 2024-12-20 08:50:42 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 08:52:39 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 117.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: rqubic.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rqubic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rqubic_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/rqubic.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rqubic/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rqubic’ version ‘1.52.0’ * 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 ‘rqubic’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.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 whether startup messages can be suppressed ... 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 ... NOTE writeQubicInputFile: no visible global function definition for ‘write.table’ Undefined global functions or variables: write.table Consider adding importFrom("utils", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) discretize.Rd:28-31: Lost braces in \itemize; meant \describe ? checkRd: (-1) discretize.Rd:32-37: Lost braces in \itemize; meant \describe ? * 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 compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘c_output_parser_tests.R’ Running ‘rqubic_implementations.R’ Running ‘test_read.R’ Running ‘test_utilities.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 * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/rqubic.Rcheck/00check.log’ for details.
rqubic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rqubic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘rqubic’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bicluster.c -o bicluster.o bicluster.c:354:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (flag=ss) (*m_cnt)++; ~~~~^~~ bicluster.c:354:15: note: place parentheses around the assignment to silence this warning if (flag=ss) (*m_cnt)++; ^ ( ) bicluster.c:354:15: note: use '==' to turn this assignment into an equality comparison if (flag=ss) (*m_cnt)++; ^ == 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c discretize.c -o discretize.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fib.c -o fib.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c graph.c -o graph.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rqubic.c -o rqubic.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o rqubic.so bicluster.o discretize.o fib.o graph.o rqubic.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-rqubic/00new/rqubic/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 (rqubic)
rqubic.Rcheck/tests/c_output_parser_tests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(rqubic) > source("test_utilities.R") > > ## parse QUBIC rules > rule.file <- getTestFile("sampleExpressionSet.rules") > rule.data <- parseQubicRules(rule.file) > > ## parse QUBIC chars > chars.file <- getTestFile("sampleExpressionSet.chars") > chars.data <- parseQubicChars(chars.file) > > ## parse QUBIC blocks > block.file <- getTestFile("sampleExpressionSet.blocks") > block.data <- parseQubicBlocks(block.file) > > ## QUBICBiclusterSet methods > length(block.data) [1] 86 > dim(block.data) [1] 469 20 > block.data.rxn <- RowxNumber(block.data) > block.data.nxc <- NumberxCol(block.data) > Svalue(block.data) [1] 222 168 147 140 123 118 118 93 92 92 92 90 90 88 88 88 86 75 74 [20] 72 72 68 68 66 64 62 62 62 61 61 61 60 59 58 57 54 54 53 [39] 53 52 51 51 49 49 49 49 47 47 47 46 45 44 43 42 42 41 39 [58] 36 35 33 31 31 30 29 29 29 29 29 27 27 27 25 24 24 24 24 [77] 22 22 21 18 15 15 13 13 13 9 > Svalue(block.data, 1:5) [1] 222 168 147 140 123 > Svalue(block.data, TRUE) [1] 222 168 147 140 123 118 118 93 92 92 92 90 90 88 88 88 86 75 74 [20] 72 72 68 68 66 64 62 62 62 61 61 61 60 59 58 57 54 54 53 [39] 53 52 51 51 49 49 49 49 47 47 47 46 45 44 43 42 42 41 39 [58] 36 35 33 31 31 30 29 29 29 29 29 27 27 27 25 24 24 24 24 [77] 22 22 21 18 15 15 13 13 13 9 > > block.features <- features(block.data) > featureCount(block.data) [1] 469 > block.bcFeatures <- BCfeatures(block.data) > BCfeatures(block.data, 3:5) [[1]] [1] 1 7 14 24 55 84 87 95 108 113 114 117 128 137 139 142 169 181 219 [20] 234 235 238 243 251 280 289 290 293 303 309 317 326 350 377 392 407 408 414 [39] 417 419 421 422 424 447 455 458 461 467 468 [[2]] [1] 1 4 7 24 40 55 63 68 75 77 84 87 102 113 114 117 128 129 136 [20] 137 138 139 140 142 169 179 181 191 201 219 234 235 238 243 263 273 280 281 [39] 289 290 293 295 301 303 309 317 326 348 350 355 369 377 386 392 407 408 409 [58] 415 417 419 421 422 424 438 447 455 458 461 467 468 [[3]] [1] 1 4 6 7 24 35 37 38 46 50 52 53 55 57 58 63 65 68 [19] 75 77 82 84 87 93 102 113 114 116 117 119 128 129 136 137 139 140 [37] 142 169 179 181 185 191 195 200 201 204 209 211 219 224 226 227 234 235 [55] 238 243 251 258 260 261 262 263 269 273 275 280 281 289 290 293 295 299 [73] 301 302 303 306 309 317 323 324 325 326 334 342 346 348 350 355 366 369 [91] 377 379 380 382 390 391 392 398 402 407 408 409 415 416 417 419 421 422 [109] 424 426 438 447 450 455 456 458 460 461 463 464 466 467 468 > BCfeatureCount(block.data) [1] 74 42 49 70 123 59 59 93 46 92 92 18 30 22 44 44 43 75 74 [20] 18 18 17 68 66 32 62 62 62 61 61 61 60 59 58 19 54 27 53 [39] 53 52 17 17 49 49 49 49 47 47 47 46 45 44 43 21 21 41 39 [58] 36 35 11 31 31 30 29 29 29 29 29 27 9 27 5 12 24 24 24 [77] 22 22 21 18 15 15 13 13 13 9 > BCfeatureCount(block.data, 3:5) [1] 49 70 123 > > block.conds <- conditions(block.data) > conditionCount(block.data) [1] 20 > block.bcConditions <- BCconditions(block.data) > BCfeatures(block.data, 3:5) [[1]] [1] 1 7 14 24 55 84 87 95 108 113 114 117 128 137 139 142 169 181 219 [20] 234 235 238 243 251 280 289 290 293 303 309 317 326 350 377 392 407 408 414 [39] 417 419 421 422 424 447 455 458 461 467 468 [[2]] [1] 1 4 7 24 40 55 63 68 75 77 84 87 102 113 114 117 128 129 136 [20] 137 138 139 140 142 169 179 181 191 201 219 234 235 238 243 263 273 280 281 [39] 289 290 293 295 301 303 309 317 326 348 350 355 369 377 386 392 407 408 409 [58] 415 417 419 421 422 424 438 447 455 458 461 467 468 [[3]] [1] 1 4 6 7 24 35 37 38 46 50 52 53 55 57 58 63 65 68 [19] 75 77 82 84 87 93 102 113 114 116 117 119 128 129 136 137 139 140 [37] 142 169 179 181 185 191 195 200 201 204 209 211 219 224 226 227 234 235 [55] 238 243 251 258 260 261 262 263 269 273 275 280 281 289 290 293 295 299 [73] 301 302 303 306 309 317 323 324 325 326 334 342 346 348 350 355 366 369 [91] 377 379 380 382 390 391 392 398 402 407 408 409 415 416 417 419 421 422 [109] 424 426 438 447 450 455 456 458 460 461 463 464 466 467 468 > BCconditionCount(block.data) [1] 3 4 3 2 1 2 2 1 2 1 1 5 3 4 2 2 2 1 1 4 4 4 1 1 2 1 1 1 1 1 1 1 1 1 3 1 2 1 [39] 1 1 3 3 1 1 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 3 1 1 1 1 1 1 1 1 1 3 1 5 2 1 1 1 [77] 1 1 1 1 1 1 1 1 1 1 > BCconditionCount(block.data, 3:5) [1] 3 2 1 > > block.features <- featureNames(block.data) > block.conds <- sampleNames(block.data) > > show(block.data) An object of class QUBICBiclusterSet Used features: 469 Used conditions: 20 Parameters: k=2, f=1, c=0.95, o=100, q=0.06, r=1 Call: parseQubicBlocks(filename = block.file) Number of Biclusters found: 86 First 5 Cluster sizes: BC 1 BC 2 BC 3 BC 4 BC 5 Number of Rows: 74 42 49 70 123 Number of Columns: 3 4 3 2 1 > > ## subset > block.data.sub <- block.data[1:3] > > > proc.time() user system elapsed 3.507 0.343 4.090
rqubic.Rcheck/tests/rqubic_implementations.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(rqubic) > library(Biobase) Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > source("test_utilities.R") > > ## quantileDiscretize > data(sample.ExpressionSet, package="Biobase") > exp.eset <- sample.ExpressionSet > fData(exp.eset) <- data.frame(label=rownames(exprs(exp.eset)), + row.names=rownames(exprs(exp.eset))) > > ## test for C code > ## note that to let QUBIC use all the samples, the first cell of the rectangular table must be a "o"! > dis.rank <- 1L > exp.discret <- quantileDiscretize(exp.eset, rank=dis.rank) > stopifnot(identical(exprs(exp.discret), quantileDiscretize(exprs(exp.eset), rank=dis.rank))) > > ## Note that the return value of quantileDiscretize is not exactly the same as the version implemented in the C tool of QUBIC > ## The reason is that in this implementation we use data type "double" to represent expression value, which has higher precision > ## than the "float" type used in the QUBIC tool > > ## The following codes visualizes the differences. They mostly appear where there are many tied values. > if(FALSE) { + chars.mat <- as.matrix(chars.data[,-1]) + diff.max <- chars.mat - exprs(exp.discret) + diff.max.rowMan <- apply(diff.max, 1, function(x) sum(x!=0)) + cbind(qubic=chars.mat[134,], rqubic=exprs(exp.discret)[134,]) + if(require(RColorBrewer)) + image(t(diff.max), col=brewer.pal(5, "RdBu")) + } > > ## Generate seeds > exp.sel <- 1:nrow(exp.discret) > exp.sel.mincol <- 2L > exp.discret.sel <- exp.discret[exp.sel,] > exp.sel.seeds <- generateSeeds(exp.discret.sel, minColWidth=exp.sel.mincol) > exp.sel.seeds rqubic sorted seeds (associating C pointer): Number of seeds: 37161 Minimum sample number: 2 > > ## writeQubicInputFile(exp.discret.sel, file="testCase.csv", sampleNames=1:ncol(exp.discret.sel)) > > ## TODO > ## quBicluster: a list of > exp.blocks <- quBicluster(exp.sel.seeds,exp.discret.sel, + report.no=100L, + filter.proportion=0.1) > exp.blocks An object of class QUBICBiclusterSet Used features: 500 Used conditions: 26 Parameters: k=2, f=0.1, c=0.95, o=100, q=0.06, r=1 Call: blocksByIndex(seeds = seeds, eset = eset, index = rcIndex, report.no = report.no, tolerance = tolerance, filter.proportion = filter.proportion) Number of Biclusters found: 17 First 5 Cluster sizes: BC 1 BC 2 BC 3 BC 4 BC 5 Number of Rows: 74 92 44 75 62 Number of Columns: 3 1 2 1 1 > exp.blocks[1] An object of class QUBICBiclusterSet Used features: 500 Used conditions: 26 Parameters: k=2, f=0.1, c=0.95, o=100, q=0.06, r=1 Call: blocksByIndex(seeds = seeds, eset = eset, index = rcIndex, report.no = report.no, tolerance = tolerance, filter.proportion = filter.proportion) There was one cluster found with 74 Rows and 3 columns > parameter(exp.blocks) $Call blocksByIndex(seeds = seeds, eset = eset, index = rcIndex, report.no = report.no, tolerance = tolerance, filter.proportion = filter.proportion) $Method [1] "rqubic" $qubicVersion [1] "rqubic 1.52.0" $inputDataFile [1] NA $k [1] 2 $f [1] 0.1 $c [1] 0.95 $o [1] 100 $q [1] 0.06 $r [1] 1 > features(exp.blocks) [1] "AFFX-MurIL2_at" "AFFX-MurIL10_at" [3] "AFFX-MurIL4_at" "AFFX-MurFAS_at" [5] "AFFX-BioB-5_at" "AFFX-BioB-M_at" [7] "AFFX-BioB-3_at" "AFFX-BioC-5_at" [9] "AFFX-BioC-3_at" "AFFX-BioDn-5_at" [11] "AFFX-BioDn-3_at" "AFFX-CreX-5_at" [13] "AFFX-CreX-3_at" "AFFX-BioB-5_st" [15] "AFFX-BioB-M_st" "AFFX-BioB-3_st" [17] "AFFX-BioC-5_st" "AFFX-BioC-3_st" [19] "AFFX-BioDn-5_st" "AFFX-BioDn-3_st" [21] "AFFX-CreX-5_st" "AFFX-CreX-3_st" [23] "AFFX-hum_alu_at" "AFFX-DapX-5_at" [25] "AFFX-DapX-M_at" "AFFX-DapX-3_at" [27] "AFFX-LysX-5_at" "AFFX-LysX-M_at" [29] "AFFX-LysX-3_at" "AFFX-PheX-5_at" [31] "AFFX-PheX-M_at" "AFFX-PheX-3_at" [33] "AFFX-ThrX-5_at" "AFFX-ThrX-M_at" [35] "AFFX-ThrX-3_at" "AFFX-TrpnX-5_at" [37] "AFFX-TrpnX-M_at" "AFFX-TrpnX-3_at" [39] "AFFX-HUMISGF3A/M97935_5_at" "AFFX-HUMISGF3A/M97935_MA_at" [41] "AFFX-HUMISGF3A/M97935_MB_at" "AFFX-HUMISGF3A/M97935_3_at" [43] "AFFX-HUMRGE/M10098_5_at" "AFFX-HUMRGE/M10098_M_at" [45] "AFFX-HUMRGE/M10098_3_at" "AFFX-HUMGAPDH/M33197_5_at" [47] "AFFX-HUMGAPDH/M33197_M_at" "AFFX-HUMGAPDH/M33197_3_at" [49] "AFFX-HSAC07/X00351_5_at" "AFFX-HSAC07/X00351_M_at" [51] "AFFX-HSAC07/X00351_3_at" "AFFX-HUMTFRR/M11507_5_at" [53] "AFFX-HUMTFRR/M11507_M_at" "AFFX-HUMTFRR/M11507_3_at" [55] "AFFX-M27830_5_at" "AFFX-M27830_M_at" [57] "AFFX-M27830_3_at" "AFFX-HSAC07/X00351_3_st" [59] "AFFX-HUMGAPDH/M33197_5_st" "AFFX-HUMGAPDH/M33197_M_st" [61] "AFFX-HUMGAPDH/M33197_3_st" "AFFX-HSAC07/X00351_5_st" [63] "AFFX-HSAC07/X00351_M_st" "AFFX-YEL002c/WBP1_at" [65] "AFFX-YEL018w/_at" "AFFX-YEL024w/RIP1_at" [67] "AFFX-YEL021w/URA3_at" "31307_at" [69] "31308_at" "31309_r_at" [71] "31310_at" "31311_at" [73] "31312_at" "31313_at" [75] "31314_at" "31315_at" [77] "31316_at" "31317_r_at" [79] "31318_at" "31319_at" [81] "31320_at" "31321_at" [83] "31322_at" "31323_r_at" [85] "31324_at" "31325_at" [87] "31326_at" "31327_at" [89] "31328_at" "31329_at" [91] "31330_at" "31331_at" [93] "31332_at" "31333_at" [95] "31334_at" "31335_at" [97] "31336_at" "31337_at" [99] "31338_at" "31339_at" [101] "31340_at" "31341_at" [103] "31342_at" "31343_at" [105] "31344_at" "31345_at" [107] "31346_at" "31347_at" [109] "31348_at" "31349_at" [111] "31350_at" "31351_at" [113] "31352_at" "31353_f_at" [115] "31354_r_at" "31355_at" [117] "31356_at" "31357_at" [119] "31358_at" "31359_at" [121] "31360_at" "31361_at" [123] "31362_at" "31363_at" [125] "31364_i_at" "31365_f_at" [127] "31366_at" "31367_at" [129] "31368_at" "31369_at" [131] "31370_at" "31371_at" [133] "31372_at" "31373_at" [135] "31374_at" "31375_at" [137] "31376_at" "31377_r_at" [139] "31378_at" "31379_at" [141] "31380_at" "31381_at" [143] "31382_f_at" "31383_at" [145] "31384_at" "31385_at" [147] "31386_at" "31387_at" [149] "31388_at" "31389_at" [151] "31390_at" "31391_at" [153] "31392_r_at" "31393_r_at" [155] "31394_at" "31395_i_at" [157] "31396_r_at" "31397_at" [159] "31398_at" "31399_at" [161] "31400_at" "31401_r_at" [163] "31402_at" "31403_at" [165] "31404_at" "31405_at" [167] "31406_at" "31407_at" [169] "31408_at" "31409_at" [171] "31410_at" "31411_at" [173] "31412_at" "31413_at" [175] "31414_at" "31415_at" [177] "31416_at" "31417_at" [179] "31418_at" "31419_r_at" [181] "31420_at" "31421_at" [183] "31422_at" "31423_at" [185] "31424_at" "31425_g_at" [187] "31426_at" "31427_at" [189] "31428_at" "31429_at" [191] "31430_at" "31431_at" [193] "31432_g_at" "31433_at" [195] "31434_at" "31435_at" [197] "31436_s_at" "31437_r_at" [199] "31438_s_at" "31439_f_at" [201] "31440_at" "31441_at" [203] "31442_at" "31443_at" [205] "31444_s_at" "31445_at" [207] "31446_s_at" "31447_at" [209] "31448_s_at" "31449_at" [211] "31450_s_at" "31451_at" [213] "31452_at" "31453_s_at" [215] "31454_f_at" "31455_r_at" [217] "31456_at" "31457_at" [219] "31458_at" "31459_i_at" [221] "31460_f_at" "31461_at" [223] "31462_f_at" "31463_s_at" [225] "31464_at" "31465_g_at" [227] "31466_at" "31467_at" [229] "31468_f_at" "31469_s_at" [231] "31470_at" "31471_at" [233] "31472_s_at" "31473_s_at" [235] "31474_r_at" "31475_at" [237] "31476_g_at" "31477_at" [239] "31478_at" "31479_f_at" [241] "31480_f_at" "31481_s_at" [243] "31482_at" "31483_g_at" [245] "31484_at" "31485_at" [247] "31486_s_at" "31487_at" [249] "31488_s_at" "31489_at" [251] "31490_at" "31491_s_at" [253] "31492_at" "31493_s_at" [255] "31494_at" "31495_at" [257] "31496_g_at" "31497_at" [259] "31498_f_at" "31499_s_at" [261] "31500_at" "31501_at" [263] "31502_at" "31503_at" [265] "31504_at" "31505_at" [267] "31506_s_at" "31507_at" [269] "31508_at" "31509_at" [271] "31510_s_at" "31511_at" [273] "31512_at" "31513_at" [275] "31514_at" "31515_at" [277] "31516_f_at" "31517_f_at" [279] "31518_i_at" "31519_f_at" [281] "31520_at" "31521_f_at" [283] "31522_f_at" "31523_f_at" [285] "31524_f_at" "31525_s_at" [287] "31526_f_at" "31527_at" [289] "31528_f_at" "31529_at" [291] "31530_at" "31531_g_at" [293] "31532_at" "31533_s_at" [295] "31534_at" "31535_i_at" [297] "31536_at" "31537_at" [299] "31538_at" "31539_r_at" [301] "31540_at" "31541_at" [303] "31542_at" "31543_at" [305] "31544_at" "31545_at" [307] "31546_at" "31547_at" [309] "31548_at" "31549_at" [311] "31550_at" "31551_at" [313] "31552_at" "31553_at" [315] "31554_at" "31555_at" [317] "31556_at" "31557_at" [319] "31558_at" "31559_at" [321] "31560_at" "31561_at" [323] "31562_at" "31563_at" [325] "31564_at" "31565_at" [327] "31566_at" "31567_at" [329] "31568_at" "31569_at" [331] "31570_at" "31571_at" [333] "31572_at" "31573_at" [335] "31574_i_at" "31575_f_at" [337] "31576_at" "31577_at" [339] "31578_at" "31579_at" [341] "31580_at" "31581_at" [343] "31582_at" "31583_at" [345] "31584_at" "31585_at" [347] "31586_f_at" "31587_at" [349] "31588_at" "31589_at" [351] "31590_g_at" "31591_s_at" [353] "31592_at" "31593_at" [355] "31594_at" "31595_at" [357] "31596_f_at" "31597_r_at" [359] "31598_s_at" "31599_f_at" [361] "31600_s_at" "31601_s_at" [363] "31602_at" "31603_at" [365] "31604_at" "31605_at" [367] "31606_at" "31607_at" [369] "31608_g_at" "31609_s_at" [371] "31610_at" "31611_s_at" [373] "31612_at" "31613_at" [375] "31614_at" "31615_i_at" [377] "31616_r_at" "31617_at" [379] "31618_at" "31619_at" [381] "31620_at" "31621_s_at" [383] "31622_f_at" "31623_f_at" [385] "31624_at" "31625_at" [387] "31626_i_at" "31627_f_at" [389] "31628_at" "31629_at" [391] "31630_at" "31631_f_at" [393] "31632_at" "31633_g_at" [395] "31634_at" "31635_g_at" [397] "31636_s_at" "31637_s_at" [399] "31638_at" "31639_f_at" [401] "31640_r_at" "31641_s_at" [403] "31642_at" "31643_at" [405] "31644_at" "31645_at" [407] "31646_at" "31647_at" [409] "31648_at" "31649_at" [411] "31650_g_at" "31651_at" [413] "31652_at" "31653_at" [415] "31654_at" "31655_at" [417] "31656_at" "31657_at" [419] "31658_at" "31659_at" [421] "31660_at" "31661_at" [423] "31662_at" "31663_at" [425] "31664_at" "31665_s_at" [427] "31666_f_at" "31667_r_at" [429] "31668_f_at" "31669_s_at" [431] "31670_s_at" "31671_at" [433] "31672_g_at" "31673_s_at" [435] "31674_s_at" "31675_s_at" [437] "31676_at" "31677_at" [439] "31678_at" "31679_at" [441] "31680_at" "31681_at" [443] "31682_s_at" "31683_at" [445] "31684_at" "31685_at" [447] "31686_at" "31687_f_at" [449] "31688_at" "31689_at" [451] "31690_at" "31691_g_at" [453] "31692_at" "31693_f_at" [455] "31694_at" "31695_g_at" [457] "31696_at" "31697_s_at" [459] "31698_at" "31699_at" [461] "31700_at" "31701_r_at" [463] "31702_at" "31703_at" [465] "31704_at" "31705_at" [467] "31706_at" "31707_at" [469] "31708_at" "31709_at" [471] "31710_at" "31711_at" [473] "31712_at" "31713_s_at" [475] "31714_at" "31715_at" [477] "31716_at" "31717_at" [479] "31718_at" "31719_at" [481] "31720_s_at" "31721_at" [483] "31722_at" "31723_at" [485] "31724_at" "31725_s_at" [487] "31726_at" "31727_at" [489] "31728_at" "31729_at" [491] "31730_at" "31731_at" [493] "31732_at" "31733_at" [495] "31734_at" "31735_at" [497] "31736_at" "31737_at" [499] "31738_at" "31739_at" > BCfeatures(exp.blocks) [[1]] [1] 1 3 5 6 7 13 14 16 17 20 21 25 26 29 31 34 36 65 66 [20] 67 68 75 92 108 118 124 126 145 147 155 157 158 185 186 190 202 211 213 [39] 214 216 246 256 258 297 298 304 315 316 319 325 334 341 352 358 361 374 375 [58] 379 385 387 389 392 395 403 410 413 431 440 462 471 473 476 486 497 [[2]] [1] 1 5 6 7 8 12 13 14 16 17 20 21 24 25 26 29 34 55 56 [20] 66 67 68 72 77 79 92 94 97 102 108 124 125 141 143 145 154 155 158 [39] 160 161 166 185 186 190 202 211 212 213 214 215 216 227 233 244 245 246 256 [58] 258 268 278 297 308 312 315 316 319 321 325 331 335 338 344 354 359 367 374 [77] 375 379 382 387 389 395 397 403 408 413 439 440 454 462 479 486 [[3]] [1] 5 16 20 25 26 29 34 36 39 68 75 76 92 129 134 166 173 180 190 [20] 191 204 213 216 224 230 237 285 307 317 319 325 334 343 356 360 374 385 389 [39] 437 440 458 460 473 491 [[4]] [1] 1 6 7 21 36 53 58 59 74 75 84 118 121 126 128 137 147 167 177 [20] 181 184 186 189 200 201 211 222 223 224 235 237 238 242 253 259 265 268 275 [39] 276 290 296 298 311 315 321 325 327 332 335 336 337 350 361 366 369 388 393 [58] 396 403 415 419 423 426 432 433 445 447 451 467 471 476 478 482 493 498 [[5]] [1] 40 58 66 84 89 117 130 132 134 142 143 169 171 194 201 207 208 214 219 [20] 223 235 236 242 249 252 259 277 282 283 284 285 289 290 294 296 308 321 327 [39] 340 350 353 354 363 366 368 369 379 397 398 416 426 435 451 454 467 470 478 [58] 482 487 488 493 494 [[6]] [1] 1 9 14 16 20 23 48 49 50 55 58 60 62 64 66 67 79 86 102 [20] 138 140 158 165 167 180 186 190 195 227 230 257 268 271 277 280 288 306 307 [39] 329 330 332 335 336 345 350 358 365 374 383 384 392 413 416 419 434 445 447 [58] 458 465 480 487 490 [[7]] [1] 9 11 31 41 49 55 56 60 62 67 68 100 104 105 109 123 131 141 147 [20] 152 158 167 168 178 195 199 203 206 207 210 212 217 227 234 252 260 264 269 [39] 273 295 318 323 330 335 346 354 357 360 363 386 447 457 462 466 471 488 489 [58] 490 492 [[8]] [1] 33 39 40 41 42 46 52 53 54 58 76 78 80 81 96 126 128 147 192 [20] 199 201 224 235 251 260 262 265 273 283 284 285 287 289 301 305 347 357 361 [39] 369 399 426 428 431 432 433 435 441 448 451 [[9]] [1] 3 9 13 43 49 58 90 93 95 102 103 107 143 156 158 159 170 172 183 [20] 209 228 248 251 255 257 294 299 301 314 335 336 352 371 373 380 388 400 407 [39] 417 418 423 445 447 448 457 468 478 490 492 [[10]] [1] 55 62 67 72 96 111 129 133 167 178 195 201 207 227 234 238 239 243 246 [20] 252 258 264 269 292 295 309 311 322 330 333 335 337 343 353 357 358 382 395 [39] 401 424 457 471 485 499 [[11]] [1] 1 16 36 51 55 57 62 67 121 129 134 140 158 167 178 186 227 237 264 [20] 268 269 295 298 325 330 332 343 350 379 447 460 470 471 487 488 [[12]] [1] 12 17 47 48 51 85 91 100 102 127 141 143 195 206 212 223 271 287 307 [20] 316 344 354 355 366 413 451 464 470 492 [[13]] [1] 14 17 58 59 75 93 102 107 126 138 173 201 240 269 273 319 323 338 356 [20] 407 408 417 418 466 467 492 500 [[14]] [1] 13 41 75 144 147 151 170 182 199 208 250 258 260 294 343 357 408 421 428 [20] 430 438 452 467 468 [[15]] [1] 46 96 224 253 265 277 285 289 354 361 366 369 382 435 451 457 463 467 [[16]] [1] 39 40 41 42 192 199 260 262 283 285 289 294 386 454 492 [[17]] [1] 42 58 96 224 238 265 269 326 361 366 435 441 456 > conditions(exp.blocks) [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S" [20] "T" "U" "V" "W" "X" "Y" "Z" > BCconditionCount(exp.blocks) [1] 3 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > > proc.time() user system elapsed 3.997 0.376 4.674
rqubic.Rcheck/tests/test_read.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(rqubic) > source("test_utilities.R") > > bf1 <- getTestFile("bic_1.out") > bfn <- getTestFile("bic_null.out") > bf3 <- getTestFile("bic_3.out") > > bi1 <- readBiclusterResults(bf1) > bi3 <- readBiclusterResults(bf3) > class(bicn <- readBiclusterResults(bfn)) ## show method prints error [1] "Biclust" attr(,"package") [1] "biclust" > > ## combine > combineBiclusts(bi3, bi3) An object of class Biclust call: NULL Number of Clusters found: 6 First 5 Cluster sizes: BC 1 BC 2 BC 3 BC 4 BC 5 Number of Rows: 2 1 2 2 1 Number of Columns: 2 2 1 2 2 > > ## combine with empty bicluster objects > combineBiclusts(bi3, bi3, bicn) An object of class Biclust call: NULL Number of Clusters found: 6 First 5 Cluster sizes: BC 1 BC 2 BC 3 BC 4 BC 5 Number of Rows: 2 1 2 2 1 Number of Columns: 2 2 1 2 2 > > proc.time() user system elapsed 3.360 0.329 3.917
rqubic.Rcheck/tests/test_utilities.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > getTestFile <- function(filename, package="rqubic") { + res <- system.file("extdata", filename, + package=package) + if(file.exists(res)) + return(res) + res <- sprintf("../inst/extdata/%s", filename) + if(file.exists(res)) + return(res) + stop(sprintf("%s cannot be found either in installed pack directory or in the source directory", + filename)) + } > > proc.time() user system elapsed 0.348 0.112 0.431
rqubic.Rcheck/rqubic-Ex.timings
name | user | system | elapsed | |
QUBICBiclusterSet-class | 0.003 | 0.002 | 0.004 | |
combineBiclusts-methods | 1.545 | 0.041 | 1.712 | |
discretize | 0.091 | 0.013 | 0.108 | |
eSetDimName | 0.096 | 0.012 | 0.118 | |
fcFilter | 0.459 | 0.019 | 0.499 | |
features-methods | 0.241 | 0.033 | 0.302 | |
generateSeeds-methods | 0.062 | 0.009 | 0.078 | |
parseQubicBlocks | 0.140 | 0.014 | 0.169 | |
quBicluster | 0.445 | 0.023 | 0.508 | |
readBiclusterResults | 0.093 | 0.027 | 0.133 | |
writeQubicInputFile | 0.050 | 0.007 | 0.066 | |