Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-17 12:07 -0400 (Fri, 17 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
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 2164/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SynExtend 1.21.1 (landing page) Nicholas Cooley
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the SynExtend package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SynExtend.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: SynExtend |
Version: 1.21.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SynExtend_1.21.1.tar.gz |
StartedAt: 2025-10-16 22:24:56 -0400 (Thu, 16 Oct 2025) |
EndedAt: 2025-10-16 22:28:12 -0400 (Thu, 16 Oct 2025) |
EllapsedTime: 196.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: SynExtend.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SynExtend_1.21.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SynExtend.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SynExtend/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SynExtend’ version ‘1.21.1’ * package encoding: UTF-8 * 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 ‘SynExtend’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’ * used SDK: ‘MacOSX11.3.1.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Missing object imported by a ':::' call: ‘DECIPHER:::.detectCores’ Unexported objects imported by ':::' calls: ‘DECIPHER:::.getSubMatrix’ ‘DECIPHER:::.nucleotideSubstitutionMatrix’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE SuperTree: no visible global function definition for ‘TreeLine’ Undefined global functions or variables: TreeLine * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: AAHitScoping.Rd: SearchIndex ApproximateBackground.Rd: translate, FindSynteny BlockByRank.Rd: FindSynteny BlockExpansion.Rd: FindSynteny BlockReconciliation.Rd: FindSynteny, Synteny-class CheckAgainstReport.Rd: readDNAStringSet ClusterByK.Rd: FindSynteny CompetePairs.Rd: FindSynteny DisjointSet.Rd: FindSynteny, Synteny-class EstimRearrScen.Rd: Synteny-class, FindSynteny ExpandDiagonal.Rd: AlignPairs, FindSynteny ExtractBy.Rd: FindSynteny, Synteny-class HitConsensus.Rd: FindSynteny NucleotideOverlap.Rd: FindSynteny, Synteny-class PairSummaries.Rd: FindSynteny, Synteny-class PrepareSeqs.Rd: FindSynteny SelectByK.Rd: FindSynteny SequenceSimilarity.Rd: AlignSeqs, AlignProfiles, AlignTranslation, DistanceMatrix SummarizePairs.Rd: AlignPairs, getGeneticCode, IndexSeqs, SearchIndex, FindSynteny Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking usage of KIND in Fortran files ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘SynExtend-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: SuperTree > ### Title: Create a Species Tree from Gene Trees > ### Aliases: SuperTree > > ### ** Examples > > # Loads a list of dendrograms > # each is a gene tree from Streptomyces genomes > data("SuperTreeEx", package="SynExtend") > > # Notice that the labels of the tree are in #_#_# format > # See the man page for SuperTreeEx for more info > labs <- labels(exData[[1]]) > if(interactive()) print(labs) > > # The first number corresponds to the species, > # so we need to trim the rest in each leaf label > namefun <- function(x) gsub("([0-9A-Za-z]*)_.*", "\\1", x) > namefun(labs) # trims to just first number [1] "218" "268" "174" "258" "217" "20" "21" "19" "222" "10" "212" "38" [13] "40" "270" "26" "91" "36" "33" "272" "7" "299" "180" "184" "144" [25] "29" "250" "236" "223" "95" "235" "42" "73" "164" "138" "244" "259" [37] "118" "294" "90" "94" "225" "161" "114" "17" "288" "283" "106" "232" [49] "128" "198" "277" "87" "271" "275" "82" "61" "71" "159" "186" "166" [61] "58" "57" "56" "55" "53" "52" "50" "261" "196" "49" "216" "229" [73] "80" "214" "213" "243" "254" "154" "113" "30" "228" "165" "136" "160" [85] "231" "150" "149" "183" "147" "14" "47" "68" "173" "101" "100" "107" [97] "108" "109" "110" "81" "269" "65" "44" "20" "19" "21" "5" "267" [109] "281" "105" "297" "11" "264" "171" "168" "133" "117" "175" "46" "265" [121] "139" "300" "121" "4" "24" "103" "282" "278" "276" "263" "262" "203" [133] "63" "296" "208" "180" "97" "102" "174" "169" "15" "163" "179" "215" [145] "205" "132" "170" "268" "66" "142" "156" "145" "162" "93" "190" "152" [157] "285" "187" "206" "247" "243" "23" "153" "227" "13" "167" "219" "131" [169] "148" "77" "140" "279" "238" "41" "253" "210" "9" "69" "301" "85" [181] "241" "37" "35" "34" "28" "257" "146" "242" "152" "182" "134" "141" [193] "242" "75" "252" "280" "120" "60" "54" "51" "72" "31" "191" "123" [205] "122" "292" "127" "155" "254" "154" "59" "8" "246" "104" "202" "204" [217] "289" "274" "172" "201" "226" "192" "224" "6" "233" "76" "112" "211" [229] "260" "119" "39" "251" "195" "151" "143" "111" "293" "256" "188" "92" [241] "176" "70" "83" "124" "158" "67" "299" "129" "116" "218" "12" "125" [253] "27" "45" "291" "286" "248" "200" "130" "96" "126" "295" "181" "89" [265] "62" "217" "194" "197" "273" "184" "79" "137" "88" "64" "258" "237" [277] "234" "189" "98" "207" "99" "221" "287" "185" "115" "48" "43" "78" [289] "178" "86" "199" "22" "84" "266" "230" "250" "29" "290" "245" "193" [301] "18" "74" "25" "220" "298" "32" "3" "2" "16" "209" "177" "135" [313] "239" "249" "240" > > # This function replaces gene identifiers with species identifiers > # we pass it to NAMEFUN > # Note NAMEFUN should take in a character vector and return a character vector > tree <- SuperTree(exData, NAMEFUN=namefun) Compiling species... | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Done. Constructing species-level distance matrix... | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Done. Building species tree... Error in TreeLine(myDistMatrix = dmat, method = "NJ", verbose = Verbose, : could not find function "TreeLine" Calls: SuperTree Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed BuiltInEnsembles 33.063 2.886 36.367 SummarizePairs 27.862 1.310 29.499 ExampleStreptomycesData 23.133 1.819 25.185 BlockExpansion 20.215 0.513 21.445 ExpandDiagonal 16.180 0.751 17.078 SelectByK 11.320 0.411 12.044 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test_ExoLabel.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 ERROR, 4 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/SynExtend.Rcheck/00check.log’ for details.
SynExtend.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SynExtend ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘SynExtend’ ... ** this is package ‘SynExtend’ version ‘1.21.1’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’ using SDK: ‘MacOSX11.3.1.sdk’ clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CDend.c -o CDend.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CShuffle.c -o CShuffle.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c HungarianAlgo.c -o HungarianAlgo.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LoserTree.c -o LoserTree.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MoranI.c -o MoranI.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c NucleotideCounts.c -o NucleotideCounts.o NucleotideCounts.c:267:7: warning: unused variable 'nthreads' [-Wunused-variable] int nthreads = INTEGER(NTHREADS)[0]; ^ 1 warning generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OnDiskLP.c -o OnDiskLP.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PrefixTrie.c -o PrefixTrie.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_synextend.c -o R_init_synextend.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RandomForest.c -o RandomForest.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SEutils.c -o SEutils.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XORRand.c -o XORRand.o XORRand.c:67:7: warning: unused variable 'threads' [-Wunused-variable] int threads = INTEGER(NTHREADS)[0]; ^ 1 warning generated. /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c _fortran_tabulate.f95 -o _fortran_tabulate.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c _fortran_utils.f95 -o _fortran_utils.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c calcMIR2C.c -o calcMIR2C.o /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c cart_fort.f95 -o cart_fort.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dendrapply.c -o dendrapply.o clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SynExtend.so CDend.o CShuffle.o HungarianAlgo.o LoserTree.o MoranI.o NucleotideCounts.o OnDiskLP.o PrefixTrie.o R_init_synextend.o RandomForest.o SEutils.o XORRand.o _fortran_tabulate.o _fortran_utils.o calcMIR2C.o cart_fort.o dendrapply.o -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-SynExtend/00new/SynExtend/libs ** R ** data ** 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 (SynExtend)
SynExtend.Rcheck/tests/test_ExoLabel.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 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. > generate_random_graph <- function(nverts, nedges){ + require(igraph, quietly=TRUE) + alph <- AA_STANDARD + num_required <- ceiling(log(nverts, length(alph))) + num_required <- max(num_required, 3) + sample_names <- mkAllStrings(alph, num_required) + labs <- sample(sample_names, nverts) + g <- sample_gnm(nverts, nedges) + df <- as_data_frame(g, what="edges") + data.frame(v1=labs[df[,1]], v2=labs[df[,2]], w=runif(nedges)) + } > > run_status_tests <- function(){ + if(!require(igraph)){ + cat("Skipping tests, igraph is not available.\n") + invisible(TRUE) + } + require(SynExtend) + tf1 <- tempfile() + tf2 <- tempfile() + WEIGHT_TOLERANCE <- 0.001 + testExo <- SynExtend:::.testExoLabel + cat("Small graphs:...") + for(loop in c(0, 0.25, 0.5)){ + df <- generate_random_graph(10, 25) + if(any(abs(df$w - loop) < WEIGHT_TOLERANCE)) + df$w[abs(df$w - loop) < WEIGHT_TOLERANCE] <- df$w[abs(df$w - loop) < WEIGHT_TOLERANCE] + 3*WEIGHT_TOLERANCE + write.table(df, tf1, row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t') + testExo(tf1, add_self_loops=loop) + } + cat("passed.\n") + + cat("Larger graphs:...") + for(loop in c(0, 0.5)){ + df <- generate_random_graph(10000, 25000) + if(any(abs(df$w - loop) < WEIGHT_TOLERANCE)) + df$w[abs(df$w - loop) < WEIGHT_TOLERANCE] <- df$w[abs(df$w - loop) < WEIGHT_TOLERANCE] + 3*WEIGHT_TOLERANCE + write.table(df, tf1, row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t') + testExo(tf1, add_self_loops=loop) + } + cat("passed.\n") + + + cat("Directed Edges...") + testExo(tf1, mode="directed") + cat("passed.\n") + + cat("No fast sort...") + testExo(tf1, use_fast_sort=FALSE) + cat("passed.\n") + + ## I'll just use the same graph here + cat("Different separator...") + write.table(df, tf1, row.names=FALSE, col.names=FALSE, quote=FALSE, sep=',') + testExo(tf1, sep=',') + cat("passed.\n") + + cat("Multi-file input...") + tf2 <- tempfile() + df <- generate_random_graph(50000, 100000) + write.table(df[1:50000,], tf1, row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t') + write.table(df[50000:100000,], tf2, row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t') + testExo(c(tf1, tf2)) + cat("passed.\n") + + cat("Larger weights...") + df[,3] <- df[,3] * 1000 + write.table(df, tf1, row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t') + testExo(tf1) + cat("passed.\n") + + file.remove(tf1) + file.remove(tf2) + + cat("\nAll checks passed!\n") + invisible(TRUE) + } > > run_status_tests() Loading required package: igraph Attaching package: 'igraph' The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Loading required package: SynExtend Loading required package: DECIPHER Loading required package: Biostrings Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:igraph': components, union The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:igraph': normalize, path 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: XVector Loading required package: Seqinfo Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'SynExtend' The following object is masked from 'package:stats': dendrapply Small graphs:...passed. Larger graphs:...passed. Directed Edges...passed. No fast sort...passed. Different separator...passed. Multi-file input...passed. Larger weights...passed. All checks passed! > > proc.time() user system elapsed 3.420 1.032 4.620
SynExtend.Rcheck/SynExtend-Ex.timings
name | user | system | elapsed | |
AAHitScoping | 0 | 0 | 0 | |
ApproximateBackground | 0.029 | 0.002 | 0.032 | |
BlastSeqs | 0 | 0 | 0 | |
BlockByRank | 0.183 | 0.002 | 0.186 | |
BlockExpansion | 20.215 | 0.513 | 21.445 | |
BlockReconciliation | 0 | 0 | 0 | |
BuiltInEnsembles | 33.063 | 2.886 | 36.367 | |
CIDist_NullDist | 0.001 | 0.001 | 0.002 | |
CheckAgainstReport | 0 | 0 | 0 | |
ClusterByK | 0.816 | 0.018 | 0.862 | |
CompetePairs | 0.206 | 0.003 | 0.218 | |
DPhyloStatistic | 0.012 | 0.000 | 0.013 | |
DecisionTree-class | 0.012 | 0.001 | 0.013 | |
DisjointSet | 0.026 | 0.001 | 0.027 | |
Endosymbionts_GeneCalls | 0.007 | 0.001 | 0.008 | |
Endosymbionts_LinkedFeatures | 0.009 | 0.001 | 0.011 | |
Endosymbionts_Pairs01 | 0.014 | 0.001 | 0.015 | |
Endosymbionts_Pairs02 | 0.014 | 0.001 | 0.015 | |
Endosymbionts_Pairs03 | 0.011 | 0.001 | 0.012 | |
Endosymbionts_Sets | 0.001 | 0.001 | 0.002 | |
Endosymbionts_Synteny | 0.002 | 0.000 | 0.003 | |
EstimRearrScen | 0.488 | 0.009 | 0.498 | |
EstimateExoLabel | 0.000 | 0.000 | 0.001 | |
EvoWeaver | 0.001 | 0.000 | 0.001 | |
EvoWeb | 0.026 | 0.001 | 0.028 | |
ExampleStreptomycesData | 23.133 | 1.819 | 25.185 | |
ExoLabel | 0.006 | 0.003 | 0.010 | |
ExpandDiagonal | 16.180 | 0.751 | 17.078 | |
ExtractBy | 0.158 | 0.006 | 0.165 | |
FastQFromSRR | 0 | 0 | 0 | |
FindSets | 0.000 | 0.000 | 0.001 | |
FitchParsimony | 0.164 | 0.010 | 0.177 | |
Generic | 0.001 | 0.001 | 0.002 | |
HitConsensus | 0 | 0 | 0 | |
MakeBlastDb | 0 | 0 | 0 | |
MoransI | 0.001 | 0.000 | 0.000 | |
NormVec | 0.000 | 0.000 | 0.001 | |
NucleotideOverlap | 0.173 | 0.005 | 0.178 | |
OneSite | 0.001 | 0.000 | 0.000 | |
PairSummaries | 1.467 | 0.030 | 1.530 | |
PhyloDistance-CI | 0.002 | 0.001 | 0.002 | |
PhyloDistance-JRF | 0.001 | 0.000 | 0.001 | |
PhyloDistance-KF | 0 | 0 | 0 | |
PhyloDistance-RF | 0.000 | 0.000 | 0.001 | |
PhyloDistance | 0.001 | 0.001 | 0.001 | |
PrepareSeqs | 0.555 | 0.023 | 0.586 | |
RandForest | 0.005 | 0.000 | 0.005 | |
RejectionBy | 0 | 0 | 0 | |
SelectByK | 11.320 | 0.411 | 12.044 | |
SequenceSimilarity | 0.025 | 0.001 | 0.027 | |
SubSetPairs | 0.130 | 0.026 | 0.158 | |
SummarizePairs | 27.862 | 1.310 | 29.499 | |