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This page was generated on 2025-10-02 11:40 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4831
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4612
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4584
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 2149/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SynExtend 1.20.2  (landing page)
Nicholas Cooley
Snapshot Date: 2025-09-29 13:40 -0400 (Mon, 29 Sep 2025)
git_url: https://git.bioconductor.org/packages/SynExtend
git_branch: RELEASE_3_21
git_last_commit: 6d3d7fc
git_last_commit_date: 2025-05-19 12:53:58 -0400 (Mon, 19 May 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  


CHECK results for SynExtend on merida1

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.

raw results


Summary

Package: SynExtend
Version: 1.20.2
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_1.20.2.tar.gz
StartedAt: 2025-09-30 11:13:37 -0400 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 11:33:07 -0400 (Tue, 30 Sep 2025)
EllapsedTime: 1170.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SynExtend.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.20.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SynExtend.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.20.2’
* 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 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        220.943  5.494 234.411
ExampleStreptomycesData 151.987  3.332 158.244
BlockExpansion          127.616  1.702 134.404
SummarizePairs          112.765  2.576 117.116
SelectByK                70.123  1.034  71.660
ExpandDiagonal           67.644  2.393  71.883
gffToDataFrame           20.473  0.058  20.808
predict.EvoWeaver        19.581  0.402  20.691
PairSummaries             8.422  0.080   8.697
WithinSetCompetition      8.113  0.060   8.299
* 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-3.21-bioc/meat/SynExtend.Rcheck/00check.log’
for details.


Installation output

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 ‘1.20.2’
** 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)

Tests output

SynExtend.Rcheck/tests/test_ExoLabel.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "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: GenomeInfoDb

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 
 17.927   5.438  25.427 

Example timings

SynExtend.Rcheck/SynExtend-Ex.timings

nameusersystemelapsed
AAHitScoping0.0000.0010.000
ApproximateBackground0.1450.0140.162
BlastSeqs000
BlockByRank1.6880.0161.725
BlockExpansion127.616 1.702134.404
BlockReconciliation000
BuiltInEnsembles220.943 5.494234.411
CIDist_NullDist0.0020.0040.006
CheckAgainstReport0.0010.0010.001
ClusterByK2.7380.0262.827
CompetePairs1.9080.0201.965
DPhyloStatistic0.0690.0040.073
DecisionTree-class0.0860.0040.092
DisjointSet0.1720.0100.183
Endosymbionts_GeneCalls0.0300.0070.038
Endosymbionts_LinkedFeatures0.0360.0060.043
Endosymbionts_Pairs010.0510.0070.058
Endosymbionts_Pairs020.0520.0060.061
Endosymbionts_Pairs030.0460.0060.052
Endosymbionts_Sets0.0060.0060.012
Endosymbionts_Synteny0.0080.0060.014
EstimRearrScen3.3560.0383.426
EstimateExoLabel0.0050.0010.006
EvoWeaver0.0060.0010.008
EvoWeb0.1700.0090.180
ExampleStreptomycesData151.987 3.332158.244
ExoLabel0.0360.0250.063
ExpandDiagonal67.644 2.39371.883
ExtractBy0.5870.0180.617
FastQFromSRR0.0010.0000.001
FindSets0.0020.0010.006
FitchParsimony0.1680.0070.176
Generic0.0030.0040.008
HitConsensus0.0000.0000.001
MakeBlastDb000
MoransI0.0020.0010.002
NormVec0.0000.0010.001
NucleotideOverlap1.3360.0161.365
OneSite0.0010.0010.001
PairSummaries8.4220.0808.697
PhyloDistance-CI0.0090.0030.013
PhyloDistance-JRF0.0070.0010.010
PhyloDistance-KF0.0050.0000.005
PhyloDistance-RF0.0050.0010.006
PhyloDistance0.0080.0010.010
PrepareSeqs3.0620.0943.230
RandForest0.0260.0010.028
RejectionBy0.0000.0010.001
SelectByK70.123 1.03471.660
SequenceSimilarity0.1190.0160.138
SubSetPairs0.6930.0730.773
SummarizePairs112.765 2.576117.116
SuperTree0.6030.0160.623
SuperTreeEx0.0190.0020.021
WithinSetCompetition8.1130.0608.299
dendrapply0.2500.0320.283
gffToDataFrame20.473 0.05820.808
plot.EvoWeb2.4530.0632.547
predict.EvoWeaver19.581 0.40220.691
simMat0.0620.0090.071
subset-dendrogram0.5840.0150.606