Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-07 12:08 -0400 (Thu, 07 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4815 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
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 2126/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SynExtend 1.21.1 (landing page) Nicholas Cooley
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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: 2025-08-07 00:40:51 -0400 (Thu, 07 Aug 2025) |
EndedAt: 2025-08-07 00:50:24 -0400 (Thu, 07 Aug 2025) |
EllapsedTime: 572.8 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_1.21.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SynExtend.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * 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 14.0.0 (clang-1400.0.29.202)’ * used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘DECIPHER:::.detectCores’ ‘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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BuiltInEnsembles 95.299 3.284 99.398 ExampleStreptomycesData 66.949 1.880 69.412 BlockExpansion 65.363 1.522 67.794 SummarizePairs 61.792 3.650 66.132 ExpandDiagonal 36.015 2.779 39.396 SelectByK 35.174 1.153 36.620 gffToDataFrame 8.876 0.065 8.985 predict.EvoWeaver 8.576 0.236 8.880 * 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-x86_64/Resources/library’ * installing *source* package ‘SynExtend’ ... ** this is package ‘SynExtend’ version ‘1.21.1’ ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CDend.c -o CDend.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CShuffle.c -o CShuffle.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c HungarianAlgo.c -o HungarianAlgo.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LoserTree.c -o LoserTree.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MoranI.c -o MoranI.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c 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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OnDiskLP.c -o OnDiskLP.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PrefixTrie.c -o PrefixTrie.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_synextend.c -o R_init_synextend.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RandomForest.c -o RandomForest.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SEutils.c -o SEutils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c 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 x86_64 -fPIC -Wall -g -O2 -c _fortran_tabulate.f95 -o _fortran_tabulate.o /opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c _fortran_utils.f95 -o _fortran_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c calcMIR2C.c -o calcMIR2C.o /opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c cart_fort.f95 -o cart_fort.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dendrapply.c -o dendrapply.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o 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/x86_64-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-x86_64/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 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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 10.571 3.064 13.931
SynExtend.Rcheck/SynExtend-Ex.timings
name | user | system | elapsed | |
AAHitScoping | 0.000 | 0.000 | 0.001 | |
ApproximateBackground | 0.092 | 0.010 | 0.104 | |
BlastSeqs | 0 | 0 | 0 | |
BlockByRank | 0.677 | 0.009 | 0.691 | |
BlockExpansion | 65.363 | 1.522 | 67.794 | |
BlockReconciliation | 0.000 | 0.001 | 0.000 | |
BuiltInEnsembles | 95.299 | 3.284 | 99.398 | |
CIDist_NullDist | 0.001 | 0.002 | 0.004 | |
CheckAgainstReport | 0 | 0 | 0 | |
ClusterByK | 1.578 | 0.029 | 1.619 | |
CompetePairs | 0.637 | 0.013 | 0.654 | |
DPhyloStatistic | 0.034 | 0.001 | 0.036 | |
DecisionTree-class | 0.041 | 0.004 | 0.045 | |
DisjointSet | 0.076 | 0.004 | 0.081 | |
Endosymbionts_GeneCalls | 0.014 | 0.001 | 0.016 | |
Endosymbionts_LinkedFeatures | 0.016 | 0.002 | 0.019 | |
Endosymbionts_Pairs01 | 0.027 | 0.002 | 0.030 | |
Endosymbionts_Pairs02 | 0.027 | 0.002 | 0.030 | |
Endosymbionts_Pairs03 | 0.027 | 0.002 | 0.030 | |
Endosymbionts_Sets | 0.004 | 0.001 | 0.006 | |
Endosymbionts_Synteny | 0.005 | 0.002 | 0.008 | |
EstimRearrScen | 1.839 | 0.032 | 1.886 | |
EstimateExoLabel | 0.003 | 0.001 | 0.004 | |
EvoWeaver | 0.003 | 0.001 | 0.005 | |
EvoWeb | 0.085 | 0.005 | 0.091 | |
ExampleStreptomycesData | 66.949 | 1.880 | 69.412 | |
ExoLabel | 0.018 | 0.014 | 0.035 | |
ExpandDiagonal | 36.015 | 2.779 | 39.396 | |
ExtractBy | 0.318 | 0.010 | 0.330 | |
FastQFromSRR | 0.000 | 0.001 | 0.001 | |
FindSets | 0.002 | 0.001 | 0.003 | |
FitchParsimony | 0.070 | 0.003 | 0.075 | |
Generic | 0.002 | 0.002 | 0.003 | |
HitConsensus | 0.000 | 0.001 | 0.000 | |
MakeBlastDb | 0.000 | 0.001 | 0.001 | |
MoransI | 0.001 | 0.001 | 0.001 | |
NormVec | 0.000 | 0.001 | 0.000 | |
NucleotideOverlap | 0.584 | 0.010 | 0.598 | |
OneSite | 0.000 | 0.001 | 0.001 | |
PairSummaries | 3.791 | 0.059 | 3.876 | |
PhyloDistance-CI | 0.004 | 0.002 | 0.006 | |
PhyloDistance-JRF | 0.003 | 0.000 | 0.004 | |
PhyloDistance-KF | 0.002 | 0.000 | 0.002 | |
PhyloDistance-RF | 0.001 | 0.000 | 0.002 | |
PhyloDistance | 0.004 | 0.001 | 0.005 | |
PrepareSeqs | 1.550 | 0.064 | 1.636 | |
RandForest | 0.026 | 0.007 | 0.037 | |
RejectionBy | 0 | 0 | 0 | |
SelectByK | 35.174 | 1.153 | 36.620 | |
SequenceSimilarity | 0.064 | 0.003 | 0.069 | |
SubSetPairs | 0.325 | 0.043 | 0.370 | |
SummarizePairs | 61.792 | 3.650 | 66.132 | |
SuperTree | 0.225 | 0.011 | 0.243 | |
SuperTreeEx | 0.010 | 0.001 | 0.011 | |
WithinSetCompetition | 3.125 | 0.047 | 3.186 | |
dendrapply | 0.121 | 0.015 | 0.136 | |
gffToDataFrame | 8.876 | 0.065 | 8.985 | |
plot.EvoWeb | 0.954 | 0.038 | 0.999 | |
predict.EvoWeaver | 8.576 | 0.236 | 8.880 | |
simMat | 0.017 | 0.003 | 0.020 | |
subset-dendrogram | 0.361 | 0.011 | 0.376 | |