| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-23 12:07 -0400 (Thu, 23 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" | 4894 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4684 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4629 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 2166/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.21.2 (landing page) Nicholas Cooley
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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: 1.21.2 |
| 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_1.21.2.tar.gz |
| StartedAt: 2025-10-22 22:23:43 -0400 (Wed, 22 Oct 2025) |
| EndedAt: 2025-10-22 22:26:20 -0400 (Wed, 22 Oct 2025) |
| EllapsedTime: 157.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SynExtend.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.21.2.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 ‘1.21.2’
* 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 ... OK
* 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
SuperTree.Rd: Treeline
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 shell scripts ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SummarizePairs 27.867 0.862 28.999
BlockExpansion 20.252 0.476 21.986
ExpandDiagonal 16.532 0.551 17.318
SelectByK 11.198 0.265 11.652
SuperTree 7.412 0.299 7.759
* 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: 3 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 ‘1.21.2’
** 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 -DCOMPILING_SYNEXTEND_VIA_R -fPIC -falign-functions=64 -Wall -g -O2 -c calcMIR2C.c -o calcMIR2C.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DCOMPILING_SYNEXTEND_VIA_R -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 -DCOMPILING_SYNEXTEND_VIA_R -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 -DCOMPILING_SYNEXTEND_VIA_R -fPIC -falign-functions=64 -Wall -g -O2 -c dendrapply.c -o dendrapply.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DCOMPILING_SYNEXTEND_VIA_R -fPIC -falign-functions=64 -Wall -g -O2 -c HitConsensus.c -o HitConsensus.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DCOMPILING_SYNEXTEND_VIA_R -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 -DCOMPILING_SYNEXTEND_VIA_R -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 -DCOMPILING_SYNEXTEND_VIA_R -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 -DCOMPILING_SYNEXTEND_VIA_R -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 -DCOMPILING_SYNEXTEND_VIA_R -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 -DCOMPILING_SYNEXTEND_VIA_R -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 -DCOMPILING_SYNEXTEND_VIA_R -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.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DCOMPILING_SYNEXTEND_VIA_R -fPIC -falign-functions=64 -Wall -g -O2 -c ExoLabel/ExoLabel.c -o ExoLabel/ExoLabel.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DCOMPILING_SYNEXTEND_VIA_R -fPIC -falign-functions=64 -Wall -g -O2 -c ExoLabel/FileHandlers.c -o ExoLabel/FileHandlers.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DCOMPILING_SYNEXTEND_VIA_R -fPIC -falign-functions=64 -Wall -g -O2 -c ExoLabel/PrefixTrie.c -o ExoLabel/PrefixTrie.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DCOMPILING_SYNEXTEND_VIA_R -fPIC -falign-functions=64 -Wall -g -O2 -c ExoLabel/LoserTree.c -o ExoLabel/LoserTree.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c utilfuncs.f95 -o utilfuncs.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c tabulate_mod.f95 -o tabulate_mod.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c cart_methods.f95 -o cart_methods.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 calcMIR2C.o CDend.o CShuffle.o dendrapply.o HitConsensus.o HungarianAlgo.o MoranI.o NucleotideCounts.o R_init_synextend.o RandomForest.o SEutils.o XORRand.o ExoLabel/ExoLabel.o ExoLabel/FileHandlers.o ExoLabel/PrefixTrie.o ExoLabel/LoserTree.o cart_methods.o tabulate_mod.o utilfuncs.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
+
+ file_fxns <- list(
+ none=\(x) {},
+ gz=\(x){ system(paste("gzip", "-f", x))}
+ )
+ file_endings <- c("", ".gz")
+
+ for(i in seq_along(file_fxns)){
+ cat("File Compression:", names(file_fxns)[i], '\n')
+
+ to_process <- paste0(c(tf1, tf2), file_endings[i])
+ elf1 <- to_process[1]
+ elf2 <- to_process[2]
+
+ cat("\tSmall 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$w - loop) < WEIGHT_TOLERANCE] + 3*WEIGHT_TOLERANCE
+ write.table(df, tf1, row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t')
+ file_fxns[[i]](tf1)
+ testExo(elf1, add_self_loops=loop)
+ }
+ cat("passed.\n")
+
+ cat("\tLarger graphs:...")
+ for(loop in c(0, 0.5)){
+ df <- generate_random_graph(10000, 25000)
+ if(any(abs(df$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')
+ file_fxns[[i]](tf1)
+ testExo(elf1, add_self_loops=loop)
+ }
+ cat("passed.\n")
+
+
+ cat("\tDirected Edges...")
+ testExo(elf1, mode="directed")
+ cat("passed.\n")
+
+ cat("\tNo fast sort...")
+ testExo(elf1, use_fast_sort=FALSE)
+ cat("passed.\n")
+
+ ## I'll just use the same graph here
+ cat("\tDifferent separator...")
+ write.table(df, tf1, row.names=FALSE, col.names=FALSE, quote=FALSE, sep=',')
+ file_fxns[[i]](tf1)
+ testExo(elf1, sep=',')
+ cat("passed.\n")
+
+ cat("\tMulti-file input...")
+ 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')
+ file_fxns[[i]](tf1)
+ file_fxns[[i]](tf2)
+ testExo(c(elf1, elf2))
+ cat("passed.\n")
+
+ cat("\tHeaders...")
+ testExo(c(elf1, elf2), header=TRUE)
+ testExo(c(elf1, elf2), header=10L)
+ cat("passed.\n")
+
+ cat("\tLarger weights...")
+ df[,3] <- df[,3] * 1000
+ write.table(df, tf1, row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t')
+ file_fxns[[i]](tf1)
+ testExo(elf1)
+ cat("passed.\n")
+
+ file.remove(elf1)
+ file.remove(elf2)
+ }
+
+ 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
File Compression: none
Small graphs:...passed.
Larger graphs:...passed.
Directed Edges...passed.
No fast sort...passed.
Different separator...passed.
Multi-file input...passed.
Headers...passed.
Larger weights...passed.
File Compression: gz
Small graphs:...passed.
Larger graphs:...passed.
Directed Edges...passed.
No fast sort...passed.
Different separator...passed.
Multi-file input...passed.
Headers...passed.
Larger weights...passed.
All checks passed!
>
> proc.time()
user system elapsed
7.706 3.256 11.325
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 | 0.185 | 0.001 | 0.202 | |
| BlockExpansion | 20.252 | 0.476 | 21.986 | |
| BlockReconciliation | 0 | 0 | 0 | |
| BuiltInEnsembles | 0.716 | 0.043 | 0.762 | |
| CIDist_NullDist | 0.001 | 0.001 | 0.001 | |
| CheckAgainstReport | 0 | 0 | 0 | |
| ClusterByK | 0.825 | 0.017 | 0.841 | |
| CompetePairs | 0.204 | 0.001 | 0.206 | |
| DPhyloStatistic | 0.012 | 0.001 | 0.013 | |
| DecisionTree-class | 0.012 | 0.001 | 0.013 | |
| DisjointSet | 0.027 | 0.001 | 0.034 | |
| Endosymbionts_GeneCalls | 0.007 | 0.001 | 0.008 | |
| Endosymbionts_LinkedFeatures | 0.009 | 0.001 | 0.010 | |
| Endosymbionts_Pairs01 | 0.014 | 0.001 | 0.015 | |
| Endosymbionts_Pairs02 | 0.015 | 0.001 | 0.015 | |
| Endosymbionts_Pairs03 | 0.012 | 0.001 | 0.012 | |
| Endosymbionts_Sets | 0.001 | 0.001 | 0.002 | |
| Endosymbionts_Synteny | 0.003 | 0.001 | 0.003 | |
| EstimRearrScen | 0.498 | 0.008 | 0.527 | |
| EstimateExoLabel | 0.001 | 0.000 | 0.001 | |
| EvoWeaver | 0.001 | 0.001 | 0.001 | |
| EvoWeb | 0.026 | 0.002 | 0.029 | |
| ExampleStreptomycesData | 0.017 | 0.001 | 0.020 | |
| ExoLabel | 0.006 | 0.004 | 0.010 | |
| ExpandDiagonal | 16.532 | 0.551 | 17.318 | |
| ExtractBy | 0.155 | 0.005 | 0.160 | |
| FastQFromSRR | 0 | 0 | 0 | |
| FindSets | 0 | 0 | 0 | |
| FitchParsimony | 0.019 | 0.001 | 0.020 | |
| Generic | 0.001 | 0.002 | 0.002 | |
| HitConsensus | 0 | 0 | 0 | |
| MakeBlastDb | 0 | 0 | 0 | |
| MoransI | 0.000 | 0.000 | 0.001 | |
| NormVec | 0.000 | 0.001 | 0.000 | |
| NucleotideOverlap | 0.181 | 0.001 | 0.183 | |
| OneSite | 0 | 0 | 0 | |
| PairSummaries | 1.621 | 0.031 | 1.659 | |
| PhyloDistance-CI | 0.001 | 0.001 | 0.002 | |
| PhyloDistance-JRF | 0.001 | 0.000 | 0.001 | |
| PhyloDistance-KF | 0.001 | 0.000 | 0.001 | |
| PhyloDistance-RF | 0.001 | 0.000 | 0.000 | |
| PhyloDistance | 0.001 | 0.000 | 0.001 | |
| PrepareSeqs | 0.558 | 0.023 | 0.593 | |
| RandForest | 0.005 | 0.000 | 0.005 | |
| RejectionBy | 0 | 0 | 0 | |
| SelectByK | 11.198 | 0.265 | 11.652 | |
| SequenceSimilarity | 0.026 | 0.002 | 0.029 | |
| SubSetPairs | 0.107 | 0.029 | 0.136 | |
| SummarizePairs | 27.867 | 0.862 | 28.999 | |
| SuperTree | 7.412 | 0.299 | 7.759 | |
| SuperTreeEx | 0.004 | 0.001 | 0.004 | |
| WithinSetCompetition | 0.955 | 0.004 | 0.967 | |
| dendrapply | 0.028 | 0.005 | 0.034 | |
| gffToDataFrame | 2.262 | 0.031 | 2.389 | |
| plot.EvoWeb | 0.343 | 0.015 | 0.360 | |
| predict.EvoWeaver | 3.082 | 0.261 | 3.363 | |
| simMat | 0.005 | 0.001 | 0.006 | |
| subset-dendrogram | 0.186 | 0.005 | 0.205 | |