Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:45 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 362/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
clst 1.55.0 (landing page) Noah Hoffman
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the clst package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clst.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: clst |
Version: 1.55.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clst.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clst_1.55.0.tar.gz |
StartedAt: 2024-12-22 18:40:34 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 18:40:49 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 15.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: clst.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clst.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clst_1.55.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/clst.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘clst/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘clst’ version ‘1.55.0’ * 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 ‘clst’ can be installed ... OK * 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 ... NOTE Foreign function call to a different package: .C("ROC", ..., PACKAGE = "ROC") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE findPMMI: no visible binding for global variable ‘median’ findPMMI: no visible global function definition for ‘quantile’ getTally: no visible binding for global variable ‘median’ scaleDistPlot: no visible global function definition for ‘cmdscale’ simpleROC: no visible global function definition for ‘new’ template: no visible global function definition for ‘str’ Undefined global functions or variables: cmdscale median new quantile str Consider adding importFrom("methods", "new") importFrom("stats", "cmdscale", "median", "quantile") importFrom("utils", "str") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... WARNING Found the following file(s) containing GNU extensions: tests/unit/Makefile Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), $(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking include directives in Makefiles ... OK * 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 ‘runalltests.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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/clst.Rcheck/00check.log’ for details.
clst.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL clst ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘clst’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (clst)
clst.Rcheck/tests/runalltests.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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("RUnit") > > options(warn=1) > > dirs <- 'unit' > > testFilePat <- ".*_test\\.R$" > > allSuite <- defineTestSuite(name="allSuite", + dirs=dirs, + testFileRegexp=testFilePat, + rngKind="default", + rngNormalKind="default" + ) > > testData <- runTestSuite(allSuite) Executing test function test_strep01 ... classifier (depth 1): 149 elements in reference set classifier (depth 1): running findThreshold, method="mutinfo" findThreshold (depth 1): (in): method = mutinfo findThreshold (depth 1): (in): within: 463 between: 10563 findThreshold (depth 1): (out): D = 1.17 pmmi = 0.20 classifier (depth 1): bkpt = 1.175 classifier (depth 1): matches include S mitis, S pneumoniae, S pseudopneumoniae done successfully. Executing test function test_strep02 ... classifier (depth 1): 149 elements in reference set classifier (depth 1): running findThreshold, method="mutinfo" findThreshold (depth 1): (in): method = mutinfo findThreshold (depth 1): (in): within: 463 between: 10563 findThreshold (depth 1): (out): D = 1.17 pmmi = 0.20 classifier (depth 1): bkpt = 1.175 classifier (depth 1): matches include S mitis, S pneumoniae, S pseudopneumoniae done successfully. Executing test function test_strep03 ... classifier (depth 1): 149 elements in reference set classifier (depth 1): running findThreshold, method="mutinfo" findThreshold (depth 1): (in): method = mutinfo findThreshold (depth 1): (in): within: 471 between: 10555 findThreshold (depth 1): (out): D = 1.18 pmmi = 0.20 classifier (depth 1): bkpt = 1.181 classifier (depth 1): matches include S iniae done successfully. Executing test function test_bvseqs01 ... findLowestRank: all defined ranks: superkingdom, superphylum, phylum, class, subclass, order, suborder, family, genus, species_group, species_subgroup, species findLowestRank: lowest defined rank: 12 (species) classifyIter: starting rank is species classifyIter (depth 1): 425 reference objects in 93 starting groups [470, 471, 575, 562, 838_2, 28127, 838_3, 838_4, 838_7, 28125, 838_1, 28130, 838_6, 820, 28123, 2098, 2130, 134821, 1624, 1249, 1582, 47715, 1254, 97478, 1613, 1633, 181675, 1596, 147802, 109790, 47770, 1587, 1318, 1338, 1328, 1311, 1335, 1309, 1304, 1305, 1303, 28037, 1351, 1352, 33945, 87541, 1377, 1280, 29388, 1282, 1290, 1283, 1292, 186802_1, 187101, 40543, 849, 851, 186802_2, 186802_3, 39948_2, 39948_1, 906_2, 906_1, 1261, 33037, 33036, 33033, 1260, 33030, 33031, 38284, 103621, 184870, 2052, 2051, 2702, 1685, 216816, 1681, 419015, 82135, 1383, 358, 294, 303, 47885, 47880, 70775, 76759, 78327, 316, 287] classify (depth 1): classifier (depth 1): 425 elements in reference set classifier (depth 1): running findThreshold, method="mutinfo" findThreshold (depth 1): (in): method = mutinfo findThreshold (depth 1): (in): within: 797 between: 89303 findThreshold (depth 1): (out): D = 0.09 pmmi = 0.05 classifier (depth 1): bkpt = 0.090 classifier (depth 1): matches include classify (depth 1): threshIsValid: TRUE classify (depth 1): moreThanOneMatch: FALSE classify (depth 1): remainingGroupsLargeEnough: FALSE classify (depth 1): remainingNotAllMatches: TRUE classify (depth 1): stopping at depth 1 classifyIter (depth 1): no matches - redefining groups at rank 11 (species_subgroup) classifyIter (depth 2): 5 reference objects in 1 starting groups [578833] classifyIter (depth 2): only one group met screening criteria - setting dStart to 0.0888 classify (depth 1): classifier (depth 1): 5 elements in reference set classifier (depth 1): setting D to dStart=0.089 classifier (depth 1): bkpt = 0.089 classifier (depth 1): matches include classify (depth 1): threshIsValid: TRUE classify (depth 1): moreThanOneMatch: FALSE classify (depth 1): remainingGroupsLargeEnough: FALSE classify (depth 1): remainingNotAllMatches: TRUE classify (depth 1): stopping at depth 1 classifyIter (depth 2): no matches - redefining groups at rank 10 (species_group) classifyIter (depth 3): 60 reference objects in 6 starting groups [655183, 671232, 136843, 136845, 136846, 136841] classify (depth 1): classifier (depth 1): 60 elements in reference set classifier (depth 1): running findThreshold, method="mutinfo" findThreshold (depth 1): (in): method = mutinfo findThreshold (depth 1): (in): within: 520 between: 1250 findThreshold (depth 1): (out): D = 0.29 pmmi = 0.29 classifier (depth 1): bkpt = 0.286 classifier (depth 1): matches include classify (depth 1): threshIsValid: TRUE classify (depth 1): moreThanOneMatch: FALSE classify (depth 1): remainingGroupsLargeEnough: FALSE classify (depth 1): remainingNotAllMatches: TRUE classify (depth 1): stopping at depth 1 classifyIter (depth 3): no matches - redefining groups at rank 9 (genus) classifyIter (depth 4): 422 reference objects in 35 starting groups [469, 160674, 561, 838, 816, 836, 2093, 2129, 1578, 46255, 1253, 1301, 1350, 1375, 1279, 1378, 168808, 848, 39948, 906, 1257, 165779, 150022, 162289, 1716, 1654, 184869, 2050, 2701, 1678, 419014, 84111, 1380, 357, 286] classify (depth 1): classifier (depth 1): 422 elements in reference set classifier (depth 1): running findThreshold, method="mutinfo" findThreshold (depth 1): (in): method = mutinfo findThreshold (depth 1): (in): within: 5585 between: 83246 findThreshold (depth 1): (out): D = 0.51 pmmi = 0.22 classifier (depth 1): bkpt = 0.510 classifier (depth 1): matches include 286, 469 classify (depth 1): threshIsValid: TRUE classify (depth 1): moreThanOneMatch: TRUE classify (depth 1): remainingGroupsLargeEnough: TRUE classify (depth 1): remainingNotAllMatches: TRUE classify (depth 1): running classify from depth 1 classify (depth 2): classifier (depth 2): 54 elements in reference set classifier (depth 2): running findThreshold, method="mutinfo" findThreshold (depth 2): (in): method = mutinfo findThreshold (depth 2): (in): within: 1026 between: 405 findThreshold (depth 2): (out): D = 0.33 pmmi = 0.85 classifier (depth 2): bkpt = 0.330 classifier (depth 2): matches include 469 classify (depth 2): threshIsValid: TRUE classify (depth 2): moreThanOneMatch: FALSE classify (depth 2): remainingGroupsLargeEnough: TRUE classify (depth 2): remainingNotAllMatches: TRUE classify (depth 2): stopping at depth 2 classifyIter (depth 4): matchCount = 1 --> breaking ============================================================ matches: 469 ============================================================ --------------- rank species (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.09 pmmi = 0.049 matches: below above score match min median max 470 2 2 0.44 0 0.04 0.07 0.10 471 1 4 0.18 0 0.09 0.12 0.16 294 0 5 0.00 0 0.42 0.47 0.51 303 0 5 0.00 0 0.45 0.47 0.54 47880 0 5 0.00 0 0.46 0.47 0.50 70775 0 5 0.00 0 0.46 0.47 0.50 76759 0 5 0.00 0 0.45 0.48 0.51 78327 0 5 0.00 0 0.46 0.48 0.54 (... plus 85 groups not shown) --------------- rank species_subgroup (depth 1) -------------------- thresh: prob = classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09 method = user D = 0.09 pmmi = matches: below above score match min median max 578833 0 5 0 0 0.5 0.52 0.54 --------------- rank species_group (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.29 pmmi = 0.287 matches: below above score match min median max 136843 0 5 0 0 0.42 0.47 0.51 136845 0 30 0 0 0.45 0.48 0.62 136846 0 5 0 0 0.50 0.52 0.54 136841 0 5 0 0 0.57 0.59 0.62 655183 0 5 0 0 1.50 1.51 1.51 671232 0 10 0 0 1.62 1.66 1.71 --------------- rank genus (depth 2) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.33 pmmi = 0.845 matches: 469 below above score match min median max 469 9 0 0.95 1 0.04 0.1 0.16 286 0 45 0.00 0 0.42 0.5 0.62 ---------------------------------------------- ============================================================ matches: Acinetobacter ============================================================ --------------- rank species (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.09 pmmi = 0.049 matches: below above score match min median max Acinetobacter baumannii 2 2 0.44 0 0.04 0.07 0.10 Acinetobacter calcoaceticus 1 4 0.18 0 0.09 0.12 0.16 Pseudomonas fluorescens 0 5 0.00 0 0.42 0.47 0.51 Pseudomonas putida 0 5 0.00 0 0.45 0.47 0.54 Pseudomonas fulva 0 5 0.00 0 0.46 0.47 0.50 Pseudomonas plecoglossicida 0 5 0.00 0 0.46 0.47 0.50 Pseudomonas monteilii 0 5 0.00 0 0.45 0.48 0.51 Pseudomonas mosselii 0 5 0.00 0 0.46 0.48 0.54 (... plus 85 groups not shown) --------------- rank species_subgroup (depth 1) -------------------- thresh: prob = classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09 method = user D = 0.09 pmmi = matches: below above score match min median max Pseudomonas stutzeri subgroup 0 5 0 0 0.5 0.52 0.54 --------------- rank species_group (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.29 pmmi = 0.287 matches: below above score match min median max Pseudomonas fluorescens group 0 5 0 0 0.42 0.47 0.51 Pseudomonas putida group 0 30 0 0 0.45 0.48 0.62 Pseudomonas stutzeri group 0 5 0 0 0.50 0.52 0.54 Pseudomonas aeruginosa group 0 5 0 0 0.57 0.59 0.62 Lactobacillus casei group 0 5 0 0 1.50 1.51 1.51 Streptococcus anginosus group 0 10 0 0 1.62 1.66 1.71 --------------- rank genus (depth 2) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.33 pmmi = 0.845 matches: Acinetobacter below above score match min median max Acinetobacter 9 0 0.95 1 0.04 0.1 0.16 Pseudomonas 0 45 0.00 0 0.42 0.5 0.62 ---------------------------------------------- [1] "unit_output/test_bvseqs01.pdf" Timing stopped at: 0.222 0.018 0.241 Error in xyplot(x ~ y, data = data.frame(x = 1:10, y = 1:10)) : could not find function "xyplot" done successfully. Executing test function test_bvseqs02 ... findThreshold (depth 1): (in): method = mutinfo findThreshold (depth 1): (in): within: 5594 between: 83659 findThreshold (depth 1): (out): D = 0.51 pmmi = 0.22 findLowestRank: all defined ranks: superkingdom, superphylum, phylum, class, subclass, order, suborder, family, genus, species_group, species_subgroup, species findLowestRank: lowest defined rank: 12 (species) classifyIter: starting rank is species classifyIter (depth 1): 425 reference objects in 93 starting groups [470, 471, 575, 562, 838_2, 28127, 838_3, 838_4, 838_7, 28125, 838_1, 28130, 838_6, 820, 28123, 2098, 2130, 134821, 1624, 1249, 1582, 47715, 1254, 97478, 1613, 1633, 181675, 1596, 147802, 109790, 47770, 1587, 1318, 1338, 1328, 1311, 1335, 1309, 1304, 1305, 1303, 28037, 1351, 1352, 33945, 87541, 1377, 1280, 29388, 1282, 1290, 1283, 1292, 186802_1, 187101, 40543, 849, 851, 186802_2, 186802_3, 39948_2, 39948_1, 906_2, 906_1, 1261, 33037, 33036, 33033, 1260, 33030, 33031, 38284, 103621, 184870, 2052, 2051, 2702, 1685, 216816, 1681, 419015, 82135, 1383, 358, 294, 303, 47885, 47880, 70775, 76759, 78327, 316, 287] classify (depth 1): classifier (depth 1): 425 elements in reference set classifier (depth 1): setting D to dStart=0.510 classifier (depth 1): bkpt = 0.510 classifier (depth 1): matches include 294, 303, 470, 471, 47880, 70775, 78327 classify (depth 1): threshIsValid: TRUE classify (depth 1): moreThanOneMatch: TRUE classify (depth 1): remainingGroupsLargeEnough: TRUE classify (depth 1): remainingNotAllMatches: TRUE classify (depth 1): running classify from depth 1 classify (depth 2): classifier (depth 2): 34 elements in reference set classifier (depth 2): running findThreshold, method="mutinfo" findThreshold (depth 2): (in): method = mutinfo findThreshold (depth 2): (in): within: 66 between: 495 findThreshold (depth 2): (out): D = 0.12 pmmi = 0.09 classifier (depth 2): bkpt = 0.121 classifier (depth 2): matches include 470 classify (depth 2): threshIsValid: TRUE classify (depth 2): moreThanOneMatch: FALSE classify (depth 2): remainingGroupsLargeEnough: TRUE classify (depth 2): remainingNotAllMatches: TRUE classify (depth 2): stopping at depth 2 classifyIter (depth 1): matchCount = 1 --> breaking ============================================================ matches: 470 ============================================================ --------------- rank species (depth 2) -------------------- thresh: prob = 0.5 classifer: minScore = 0.65 doffset = 0.5 dStart = NA method = mutinfo D = 0.12 pmmi = 0.092 matches: 470 below above score match min median max 470 4 0 0.89 1 0.04 0.07 0.10 471 3 2 0.55 0 0.09 0.12 0.16 294 0 5 0.00 0 0.42 0.47 0.51 303 0 5 0.00 0 0.45 0.47 0.54 47880 0 5 0.00 0 0.46 0.47 0.50 70775 0 5 0.00 0 0.46 0.47 0.50 78327 0 5 0.00 0 0.46 0.48 0.54 ---------------------------------------------- ============================================================ matches: Acinetobacter baumannii ============================================================ --------------- rank species (depth 2) -------------------- thresh: prob = 0.5 classifer: minScore = 0.65 doffset = 0.5 dStart = NA method = mutinfo D = 0.12 pmmi = 0.092 matches: Acinetobacter baumannii below above score match min median max Acinetobacter baumannii 4 0 0.89 1 0.04 0.07 0.10 Acinetobacter calcoaceticus 3 2 0.55 0 0.09 0.12 0.16 Pseudomonas fluorescens 0 5 0.00 0 0.42 0.47 0.51 Pseudomonas putida 0 5 0.00 0 0.45 0.47 0.54 Pseudomonas fulva 0 5 0.00 0 0.46 0.47 0.50 Pseudomonas plecoglossicida 0 5 0.00 0 0.46 0.47 0.50 Pseudomonas mosselii 0 5 0.00 0 0.46 0.48 0.54 ---------------------------------------------- [1] "unit_output/test_bvseqs02.pdf" done successfully. Executing test function test_bvseqs03 ... findThreshold (depth 1): (in): method = mutinfo findThreshold (depth 1): (in): within: 6691 between: 82985 findThreshold (depth 1): (out): D = 0.48 pmmi = 0.24 findLowestRank: all defined ranks: superkingdom, superphylum, phylum, class, subclass, order, suborder, family, genus, species_group, species_subgroup, species findLowestRank: lowest defined rank: 12 (species) classifyIter: starting rank is species classifyIter (depth 1): 425 reference objects in 93 starting groups [470, 471, 575, 562, 838_2, 28127, 838_3, 838_4, 838_7, 28125, 838_1, 28130, 838_6, 820, 28123, 2098, 2130, 134821, 1624, 1249, 1582, 47715, 1254, 97478, 1613, 1633, 181675, 1596, 147802, 109790, 47770, 1587, 1318, 1338, 1328, 1311, 1335, 1309, 1304, 1305, 1303, 28037, 1351, 1352, 33945, 87541, 1377, 1280, 29388, 1282, 1290, 1283, 1292, 186802_1, 187101, 40543, 849, 851, 186802_2, 186802_3, 39948_2, 39948_1, 906_2, 906_1, 1261, 33037, 33036, 33033, 1260, 33030, 33031, 38284, 103621, 184870, 2052, 2051, 2702, 1685, 216816, 1681, 419015, 82135, 1383, 358, 294, 303, 47885, 47880, 70775, 76759, 78327, 316, 287] classify (depth 1): classifier (depth 1): 425 elements in reference set classifier (depth 1): setting D to dStart=0.480 classifier (depth 1): bkpt = 0.480 classifier (depth 1): matches include 294, 303, 470, 471, 47880, 70775 classify (depth 1): threshIsValid: TRUE classify (depth 1): moreThanOneMatch: TRUE classify (depth 1): remainingGroupsLargeEnough: TRUE classify (depth 1): remainingNotAllMatches: TRUE classify (depth 1): running classify from depth 1 classify (depth 2): classifier (depth 2): 29 elements in reference set classifier (depth 2): running findThreshold, method="mutinfo" findThreshold (depth 2): (in): method = mutinfo findThreshold (depth 2): (in): within: 56 between: 350 findThreshold (depth 2): (out): D = 0.21 pmmi = 0.12 classifier (depth 2): bkpt = 0.210 classifier (depth 2): matches include 470, 471 classify (depth 2): threshIsValid: TRUE classify (depth 2): moreThanOneMatch: TRUE classify (depth 2): remainingGroupsLargeEnough: TRUE classify (depth 2): remainingNotAllMatches: TRUE classify (depth 2): running classify from depth 2 classify (depth 3): classifier (depth 3): 9 elements in reference set classifier (depth 3): running findThreshold, method="mutinfo" findThreshold (depth 3): (in): method = mutinfo findThreshold (depth 3): (in): within: 16 between: 20 findThreshold (depth 3): (out): D = NA pmmi = -0.04 classifier (depth 3): bkpt = NA classifier (depth 3): matches include classify (depth 3): threshIsValid: FALSE classify (depth 3): moreThanOneMatch: FALSE classify (depth 3): remainingGroupsLargeEnough: FALSE classify (depth 3): remainingNotAllMatches: TRUE classify (depth 3): stopping at depth 3 classify (depth 3): no matches on final iteration, returning previous result classifyIter (depth 1): no matches - redefining groups at rank 11 (species_subgroup) classifyIter (depth 2): 5 reference objects in 1 starting groups [578833] classifyIter (depth 2): only one group met screening criteria - setting dStart to 0.0888 classify (depth 1): classifier (depth 1): 5 elements in reference set classifier (depth 1): setting D to dStart=0.089 classifier (depth 1): bkpt = 0.089 classifier (depth 1): matches include classify (depth 1): threshIsValid: TRUE classify (depth 1): moreThanOneMatch: FALSE classify (depth 1): remainingGroupsLargeEnough: FALSE classify (depth 1): remainingNotAllMatches: TRUE classify (depth 1): stopping at depth 1 classifyIter (depth 2): no matches - redefining groups at rank 10 (species_group) classifyIter (depth 3): 60 reference objects in 6 starting groups [655183, 671232, 136843, 136845, 136846, 136841] classify (depth 1): classifier (depth 1): 60 elements in reference set classifier (depth 1): running findThreshold, method="mutinfo" findThreshold (depth 1): (in): method = mutinfo findThreshold (depth 1): (in): within: 520 between: 1250 findThreshold (depth 1): (out): D = 0.29 pmmi = 0.29 classifier (depth 1): bkpt = 0.286 classifier (depth 1): matches include classify (depth 1): threshIsValid: TRUE classify (depth 1): moreThanOneMatch: FALSE classify (depth 1): remainingGroupsLargeEnough: FALSE classify (depth 1): remainingNotAllMatches: TRUE classify (depth 1): stopping at depth 1 classifyIter (depth 3): no matches - redefining groups at rank 9 (genus) classifyIter (depth 4): 422 reference objects in 35 starting groups [469, 160674, 561, 838, 816, 836, 2093, 2129, 1578, 46255, 1253, 1301, 1350, 1375, 1279, 1378, 168808, 848, 39948, 906, 1257, 165779, 150022, 162289, 1716, 1654, 184869, 2050, 2701, 1678, 419014, 84111, 1380, 357, 286] classify (depth 1): classifier (depth 1): 422 elements in reference set classifier (depth 1): running findThreshold, method="mutinfo" findThreshold (depth 1): (in): method = mutinfo findThreshold (depth 1): (in): within: 5585 between: 83246 findThreshold (depth 1): (out): D = 0.51 pmmi = 0.22 classifier (depth 1): bkpt = 0.510 classifier (depth 1): matches include 286, 469 classify (depth 1): threshIsValid: TRUE classify (depth 1): moreThanOneMatch: TRUE classify (depth 1): remainingGroupsLargeEnough: TRUE classify (depth 1): remainingNotAllMatches: TRUE classify (depth 1): running classify from depth 1 classify (depth 2): classifier (depth 2): 54 elements in reference set classifier (depth 2): running findThreshold, method="mutinfo" findThreshold (depth 2): (in): method = mutinfo findThreshold (depth 2): (in): within: 1026 between: 405 findThreshold (depth 2): (out): D = 0.33 pmmi = 0.85 classifier (depth 2): bkpt = 0.330 classifier (depth 2): matches include 469 classify (depth 2): threshIsValid: TRUE classify (depth 2): moreThanOneMatch: FALSE classify (depth 2): remainingGroupsLargeEnough: TRUE classify (depth 2): remainingNotAllMatches: TRUE classify (depth 2): stopping at depth 2 classifyIter (depth 4): matchCount = 1 --> breaking ============================================================ matches: 469 ============================================================ --------------- rank species (depth 2) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.21 pmmi = 0.120 matches: 470, 471 below above score match min median max 471 5 0 0.91 1 0.09 0.12 0.16 470 4 0 0.89 1 0.04 0.07 0.10 294 0 5 0.00 0 0.42 0.47 0.51 303 0 5 0.00 0 0.45 0.47 0.54 47880 0 5 0.00 0 0.46 0.47 0.50 70775 0 5 0.00 0 0.46 0.47 0.50 --------------- rank species_subgroup (depth 1) -------------------- thresh: prob = classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09 method = user D = 0.09 pmmi = matches: below above score match min median max 578833 0 5 0 0 0.5 0.52 0.54 --------------- rank species_group (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.29 pmmi = 0.287 matches: below above score match min median max 136843 0 5 0 0 0.42 0.47 0.51 136845 0 30 0 0 0.45 0.48 0.62 136846 0 5 0 0 0.50 0.52 0.54 136841 0 5 0 0 0.57 0.59 0.62 655183 0 5 0 0 1.50 1.51 1.51 671232 0 10 0 0 1.62 1.66 1.71 --------------- rank genus (depth 2) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.33 pmmi = 0.845 matches: 469 below above score match min median max 469 9 0 0.95 1 0.04 0.1 0.16 286 0 45 0.00 0 0.42 0.5 0.62 ---------------------------------------------- ============================================================ matches: Acinetobacter ============================================================ --------------- rank species (depth 2) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.21 pmmi = 0.120 matches: Acinetobacter baumannii, Acinetobacter calcoaceticus below above score match min median max Acinetobacter calcoaceticus 5 0 0.91 1 0.09 0.12 0.16 Acinetobacter baumannii 4 0 0.89 1 0.04 0.07 0.10 Pseudomonas fluorescens 0 5 0.00 0 0.42 0.47 0.51 Pseudomonas putida 0 5 0.00 0 0.45 0.47 0.54 Pseudomonas fulva 0 5 0.00 0 0.46 0.47 0.50 Pseudomonas plecoglossicida 0 5 0.00 0 0.46 0.47 0.50 --------------- rank species_subgroup (depth 1) -------------------- thresh: prob = classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09 method = user D = 0.09 pmmi = matches: below above score match min median max Pseudomonas stutzeri subgroup 0 5 0 0 0.5 0.52 0.54 --------------- rank species_group (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.29 pmmi = 0.287 matches: below above score match min median max Pseudomonas fluorescens group 0 5 0 0 0.42 0.47 0.51 Pseudomonas putida group 0 30 0 0 0.45 0.48 0.62 Pseudomonas stutzeri group 0 5 0 0 0.50 0.52 0.54 Pseudomonas aeruginosa group 0 5 0 0 0.57 0.59 0.62 Lactobacillus casei group 0 5 0 0 1.50 1.51 1.51 Streptococcus anginosus group 0 10 0 0 1.62 1.66 1.71 --------------- rank genus (depth 2) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.33 pmmi = 0.845 matches: Acinetobacter below above score match min median max Acinetobacter 9 0 0.95 1 0.04 0.1 0.16 Pseudomonas 0 45 0.00 0 0.42 0.5 0.62 ---------------------------------------------- [1] "unit_output/test_bvseqs03.pdf" Timing stopped at: 0.108 0.011 0.118 Error in xyplot(x ~ y, data = data.frame(x = 1:10, y = 1:10)) : could not find function "xyplot" done successfully. Executing test function test_strep01 ... classify (depth 1): classifier (depth 1): 149 elements in reference set classifier (depth 1): running findThreshold, method="mutinfo" findThreshold (depth 1): (in): method = mutinfo findThreshold (depth 1): (in): within: 463 between: 10563 findThreshold (depth 1): (out): D = 1.17 pmmi = 0.20 classifier (depth 1): bkpt = 1.175 classifier (depth 1): matches include S mitis, S pneumoniae, S pseudopneumoniae classify (depth 1): threshIsValid: TRUE classify (depth 1): moreThanOneMatch: TRUE classify (depth 1): remainingGroupsLargeEnough: TRUE classify (depth 1): remainingNotAllMatches: TRUE classify (depth 1): running classify from depth 1 classify (depth 2): classifier (depth 2): 14 elements in reference set classifier (depth 2): running findThreshold, method="mutinfo" findThreshold (depth 2): (in): method = mutinfo findThreshold (depth 2): (in): within: 42 between: 49 findThreshold (depth 2): (out): D = 0.46 pmmi = 0.30 classifier (depth 2): bkpt = 0.460 classifier (depth 2): matches include S mitis, S pseudopneumoniae classify (depth 2): threshIsValid: TRUE classify (depth 2): moreThanOneMatch: TRUE classify (depth 2): remainingGroupsLargeEnough: TRUE classify (depth 2): remainingNotAllMatches: TRUE classify (depth 2): running classify from depth 2 classify (depth 3): classifier (depth 3): 10 elements in reference set classifier (depth 3): running findThreshold, method="mutinfo" findThreshold (depth 3): (in): method = mutinfo findThreshold (depth 3): (in): within: 36 between: 9 findThreshold (depth 3): (out): D = NA pmmi = -0.05 classifier (depth 3): bkpt = NA classifier (depth 3): matches include classify (depth 3): threshIsValid: FALSE classify (depth 3): moreThanOneMatch: FALSE classify (depth 3): remainingGroupsLargeEnough: FALSE classify (depth 3): remainingNotAllMatches: TRUE classify (depth 3): stopping at depth 3 classify (depth 3): no matches on final iteration, returning previous result [1] "unit_output/test_strep01.pdf" done successfully. Executing test function test_actino ... done successfully. Executing test function test_bvseqs ... done successfully. Executing test function test_strep ... done successfully. Executing test function test_ROC ... Timing stopped at: 0.002 0 0.002 Error in package.version("ROC") : could not find function "package.version" done successfully. Executing test function test_findPMMI_strep01 ... done successfully. Executing test function test_findPMMI_strep02 ... done successfully. Executing test function test_findThreshold_strep01 ... done successfully. Executing test function test_getThresh_01 ... done successfully. Executing test function test_getThresh_02 ... done successfully. Executing test function test_plotDistances_strep01 ... [1] "unit_output/test_plotDistances_strep01.pdf" done successfully. Executing test function test_plotDistances_strep02 ... [1] "unit_output/test_plotDistances_strep02.pdf" done successfully. Executing test function test_plotMutinfo_strep01 ... [1] "unit_output/test_plotMutinfo_strep01.pdf" done successfully. Executing test function test_partition_01 ... done successfully. Executing test function test_bvseqs01 ... ============================================================ matches: 469 ============================================================ --------------- rank species (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.09 pmmi = 0.049 matches: below above score match min median max 470 2 2 0.44 0 0.04 0.07 0.10 471 1 4 0.18 0 0.09 0.12 0.16 294 0 5 0.00 0 0.42 0.47 0.51 303 0 5 0.00 0 0.45 0.47 0.54 47880 0 5 0.00 0 0.46 0.47 0.50 70775 0 5 0.00 0 0.46 0.47 0.50 76759 0 5 0.00 0 0.45 0.48 0.51 78327 0 5 0.00 0 0.46 0.48 0.54 (... plus 85 groups not shown) --------------- rank species_subgroup (depth 1) -------------------- thresh: prob = classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09 method = user D = 0.09 pmmi = matches: below above score match min median max 578833 0 5 0 0 0.5 0.52 0.54 --------------- rank species_group (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.29 pmmi = 0.287 matches: below above score match min median max 136843 0 5 0 0 0.42 0.47 0.51 136845 0 30 0 0 0.45 0.48 0.62 136846 0 5 0 0 0.50 0.52 0.54 136841 0 5 0 0 0.57 0.59 0.62 655183 0 5 0 0 1.50 1.51 1.51 671232 0 10 0 0 1.62 1.66 1.71 --------------- rank genus (depth 2) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.33 pmmi = 0.845 matches: 469 below above score match min median max 469 9 0 0.95 1 0.04 0.1 0.16 286 0 45 0.00 0 0.42 0.5 0.62 ---------------------------------------------- ============================================================ matches: Acinetobacter ============================================================ --------------- rank species (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.09 pmmi = 0.049 matches: below above score match min median max Acinetobacter baumannii 2 2 0.44 0 0.04 0.07 0.10 Acinetobacter calcoaceticus 1 4 0.18 0 0.09 0.12 0.16 Pseudomonas fluorescens 0 5 0.00 0 0.42 0.47 0.51 Pseudomonas putida 0 5 0.00 0 0.45 0.47 0.54 Pseudomonas fulva 0 5 0.00 0 0.46 0.47 0.50 Pseudomonas plecoglossicida 0 5 0.00 0 0.46 0.47 0.50 Pseudomonas monteilii 0 5 0.00 0 0.45 0.48 0.51 Pseudomonas mosselii 0 5 0.00 0 0.46 0.48 0.54 (... plus 85 groups not shown) --------------- rank species_subgroup (depth 1) -------------------- thresh: prob = classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09 method = user D = 0.09 pmmi = matches: below above score match min median max Pseudomonas stutzeri subgroup 0 5 0 0 0.5 0.52 0.54 --------------- rank species_group (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.29 pmmi = 0.287 matches: below above score match min median max Pseudomonas fluorescens group 0 5 0 0 0.42 0.47 0.51 Pseudomonas putida group 0 30 0 0 0.45 0.48 0.62 Pseudomonas stutzeri group 0 5 0 0 0.50 0.52 0.54 Pseudomonas aeruginosa group 0 5 0 0 0.57 0.59 0.62 Lactobacillus casei group 0 5 0 0 1.50 1.51 1.51 Streptococcus anginosus group 0 10 0 0 1.62 1.66 1.71 --------------- rank genus (depth 2) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.33 pmmi = 0.845 matches: Acinetobacter below above score match min median max Acinetobacter 9 0 0.95 1 0.04 0.1 0.16 Pseudomonas 0 45 0.00 0 0.42 0.5 0.62 ---------------------------------------------- ============================================================ matches: Acinetobacter ============================================================ --------------- rank species (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.09 pmmi = 0.049 matches: below above score match min median max Ac...r baumannii 2 2 0.44 0 0.04 0.07 0.10 Ac...lcoaceticus 1 4 0.18 0 0.09 0.12 0.16 Ps...fluorescens 0 5 0.00 0 0.42 0.47 0.51 Ps...onas putida 0 5 0.00 0 0.45 0.47 0.54 Ps...monas fulva 0 5 0.00 0 0.46 0.47 0.50 Ps...oglossicida 0 5 0.00 0 0.46 0.47 0.50 Ps...s monteilii 0 5 0.00 0 0.45 0.48 0.51 Ps...as mosselii 0 5 0.00 0 0.46 0.48 0.54 (... plus 85 groups not shown) --------------- rank species_subgroup (depth 1) -------------------- thresh: prob = classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09 method = user D = 0.09 pmmi = matches: below above score match min median max Ps...ri subgroup 0 5 0 0 0.5 0.52 0.54 --------------- rank species_group (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.29 pmmi = 0.287 matches: below above score match min median max Ps...scens group 0 5 0 0 0.42 0.47 0.51 Ps...utida group 0 30 0 0 0.45 0.48 0.62 Ps...tzeri group 0 5 0 0 0.50 0.52 0.54 Ps...inosa group 0 5 0 0 0.57 0.59 0.62 La...casei group 0 5 0 0 1.50 1.51 1.51 St...nosus group 0 10 0 0 1.62 1.66 1.71 --------------- rank genus (depth 2) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.33 pmmi = 0.845 matches: Acinetobacter below above score match min median max Acinetobacter 9 0 0.95 1 0.04 0.1 0.16 Pseudomonas 0 45 0.00 0 0.42 0.5 0.62 ---------------------------------------------- done successfully. Executing test function test_strep01 ... ============================================================ matches: S mitis, S pseudopneumoniae ============================================================ --------------- rank (depth 1) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 1.17 pmmi = 0.199 matches: S mitis, S pneumoniae, S pseudopneumoniae below above score match min median max S mitis 9 0 0.95 1 0.00 0.38 0.58 S pneumoniae 4 0 0.89 1 0.56 0.60 0.97 S pseudopneumoniae 1 0 0.67 1 0.39 0.39 0.39 S australis 0 1 0.00 0 2.00 2.00 2.00 S infantis 0 2 0.00 0 2.23 2.42 2.61 S peroris 0 1 0.00 0 2.43 2.43 2.43 S sanguinis 0 5 0.00 0 3.74 4.04 5.73 S cristatus 0 1 0.00 0 4.61 4.61 4.61 (... plus 42 groups not shown) --------------- rank (depth 2) -------------------- thresh: prob = 0.5 classifer: minScore = 0.45 doffset = 0.5 dStart = NA method = mutinfo D = 0.46 pmmi = 0.300 matches: S mitis, S pseudopneumoniae below above score match min median max S mitis 7 2 0.74 1 0.00 0.38 0.58 S pseudopneumoniae 1 0 0.67 1 0.39 0.39 0.39 S pneumoniae 0 4 0.00 0 0.56 0.60 0.97 ---------------------------------------------- done successfully. > > printTextProtocol(testData, showDetails=TRUE) RUNIT TEST PROTOCOL -- Sun Dec 22 18:40:46 2024 *********************************************** Number of test functions: 22 Number of errors: 3 Number of failures: 0 1 Test Suite : allSuite - 22 test functions, 3 errors, 0 failures ERROR in test_bvseqs01: Error in xyplot(x ~ y, data = data.frame(x = 1:10, y = 1:10)) : could not find function "xyplot" ERROR in test_bvseqs03: Error in xyplot(x ~ y, data = data.frame(x = 1:10, y = 1:10)) : could not find function "xyplot" ERROR in test_ROC: Error in package.version("ROC") : could not find function "package.version" Details *************************** Test Suite: allSuite Test function regexp: ^test.+ Test file regexp: .*_test\.R$ Involved directory: unit --------------------------- Test file: unit/classifier_test.R test_strep01: (3 checks) ... OK (0.01 seconds) test_strep02: (3 checks) ... OK (0.01 seconds) test_strep03: (3 checks) ... OK (0.01 seconds) --------------------------- Test file: unit/classifyIter_test.R test_bvseqs01: ERROR !! Error in xyplot(x ~ y, data = data.frame(x = 1:10, y = 1:10)) : could not find function "xyplot" test_bvseqs02: (0 checks) ... OK (0.08 seconds) test_bvseqs03: ERROR !! Error in xyplot(x ~ y, data = data.frame(x = 1:10, y = 1:10)) : could not find function "xyplot" --------------------------- Test file: unit/classify_test.R test_strep01: (0 checks) ... OK (0.06 seconds) --------------------------- Test file: unit/data_test.R test_actino: (2 checks) ... OK (0 seconds) test_bvseqs: (2 checks) ... OK (0.01 seconds) test_strep: (2 checks) ... OK (0 seconds) --------------------------- Test file: unit/dependencies_test.R test_ROC: ERROR !! Error in package.version("ROC") : could not find function "package.version" --------------------------- Test file: unit/findThreshold_test.R test_findPMMI_strep01: (0 checks) ... OK (0.02 seconds) test_findPMMI_strep02: (0 checks) ... OK (0.02 seconds) test_findThreshold_strep01: (1 checks) ... OK (0.01 seconds) test_getThresh_01: (2 checks) ... OK (0 seconds) test_getThresh_02: (4 checks) ... OK (0 seconds) test_plotDistances_strep01: (0 checks) ... OK (0.03 seconds) test_plotDistances_strep02: (0 checks) ... OK (0.06 seconds) test_plotMutinfo_strep01: (0 checks) ... OK (0.04 seconds) --------------------------- Test file: unit/partition_test.R test_partition_01: (2 checks) ... OK (0 seconds) --------------------------- Test file: unit/print_test.R test_bvseqs01: (0 checks) ... OK (0.08 seconds) test_strep01: (0 checks) ... OK (0.01 seconds) > > #q(runLast=FALSE) > > proc.time() user system elapsed 0.870 0.094 0.967
clst.Rcheck/clst-Ex.timings
name | user | system | elapsed | |
actino | 0.000 | 0.000 | 0.001 | |
bvseqs | 0 | 0 | 0 | |
classify | 0.041 | 0.003 | 0.045 | |
clst-package | 0.032 | 0.002 | 0.033 | |
findThreshold | 0.012 | 0.001 | 0.013 | |
plotDistances | 0.105 | 0.002 | 0.108 | |
printClst | 0.001 | 0.000 | 0.002 | |
scaleDistPlot | 1.905 | 0.038 | 1.944 | |
strep | 0 | 0 | 0 | |