Jitao David Zhang
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/rqubic |
| Branch: RELEASE_3_11 |
| Last Commit: 555a638 |
| Last Changed Date: 2020-04-27 14:26:34 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:38 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE rqubic PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1535/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rqubic 1.34.0 Jitao David Zhang
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: rqubic |
| Version: 1.34.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:rqubic.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings rqubic_1.34.0.tar.gz |
| StartedAt: 2020-10-17 05:00:43 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:01:37 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 54.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rqubic.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:rqubic.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings rqubic_1.34.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/rqubic.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rqubic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rqubic’ version ‘1.34.0’
* 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 ... WARNING
Found the following significant warnings:
bicluster.c:354:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
See ‘/home/biocbuild/bbs-3.11-bioc/meat/rqubic.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.11-bioc/meat/rqubic.Rcheck/00check.log’
for details.
rqubic.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL rqubic
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘rqubic’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bicluster.c -o bicluster.o
bicluster.c: In function ‘seed_intersect_r’:
bicluster.c:354:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
if (flag=ss) (*m_cnt)++;
^~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c discretize.c -o discretize.o
In file included from discretize.c:9:0:
rqubic.h:61:20: warning: ‘MINCOL_ATT_NAME’ defined but not used [-Wunused-variable]
static const char *MINCOL_ATT_NAME="minimumCol";
^~~~~~~~~~~~~~~
rqubic.h:60:20: warning: ‘EDGELIST_ATT_NAME’ defined but not used [-Wunused-variable]
static const char *EDGELIST_ATT_NAME="edgelist";
^~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fib.c -o fib.o
In file included from fib.c:35:0:
rqubic.h:61:20: warning: ‘MINCOL_ATT_NAME’ defined but not used [-Wunused-variable]
static const char *MINCOL_ATT_NAME="minimumCol";
^~~~~~~~~~~~~~~
rqubic.h:60:20: warning: ‘EDGELIST_ATT_NAME’ defined but not used [-Wunused-variable]
static const char *EDGELIST_ATT_NAME="edgelist";
^~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c graph.c -o graph.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rqubic.c -o rqubic.o
In file included from rqubic.c:5:0:
rqubic.h:61:20: warning: ‘MINCOL_ATT_NAME’ defined but not used [-Wunused-variable]
static const char *MINCOL_ATT_NAME="minimumCol";
^~~~~~~~~~~~~~~
rqubic.h:60:20: warning: ‘EDGELIST_ATT_NAME’ defined but not used [-Wunused-variable]
static const char *EDGELIST_ATT_NAME="edgelist";
^~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o rqubic.so bicluster.o discretize.o fib.o graph.o rqubic.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(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
2.033 0.100 2.118
rqubic.Rcheck/tests/rqubic_implementations.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(rqubic)
> library(Biobase)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
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 1.34.0"
$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] 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
[[6]]
[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
[[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
3.173 0.116 3.274
rqubic.Rcheck/tests/test_read.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(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
1.633 0.093 1.711
rqubic.Rcheck/tests/test_utilities.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> 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
0.225 0.036 0.246
rqubic.Rcheck/rqubic-Ex.timings
| name | user | system | elapsed | |
| QUBICBiclusterSet-class | 0.001 | 0.000 | 0.001 | |
| combineBiclusts-methods | 1.778 | 0.004 | 1.782 | |
| discretize | 0.210 | 0.016 | 0.226 | |
| eSetDimName | 0.071 | 0.000 | 0.072 | |
| fcFilter | 0.592 | 0.000 | 0.591 | |
| features-methods | 0.128 | 0.019 | 0.159 | |
| generateSeeds-methods | 0.068 | 0.000 | 0.068 | |
| parseQubicBlocks | 0.056 | 0.008 | 0.068 | |
| quBicluster | 0.513 | 0.013 | 0.524 | |
| readBiclusterResults | 0.074 | 0.011 | 0.087 | |
| writeQubicInputFile | 0.043 | 0.001 | 0.043 | |