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This page was generated on 2025-09-06 12:06 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 2133/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SynExtend 1.21.1  (landing page)
Nicholas Cooley
Snapshot Date: 2025-09-05 13:45 -0400 (Fri, 05 Sep 2025)
git_url: https://git.bioconductor.org/packages/SynExtend
git_branch: devel
git_last_commit: 66702ff
git_last_commit_date: 2025-05-19 12:03:56 -0400 (Mon, 19 May 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SynExtend on lconway

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: 1.21.1
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: 2025-09-06 00:17:15 -0400 (Sat, 06 Sep 2025)
EndedAt: 2025-09-06 00:26:44 -0400 (Sat, 06 Sep 2025)
EllapsedTime: 569.0 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_1.21.1.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        96.665  3.044 100.292
ExampleStreptomycesData 67.896  1.759  70.074
BlockExpansion          66.070  1.401  68.080
SummarizePairs          63.079  2.938  66.460
ExpandDiagonal          35.928  2.343  38.560
SelectByK               35.262  0.893  36.326
predict.EvoWeaver        8.429  0.198   8.678
gffToDataFrame           8.289  0.054   8.389
* 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.


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 ‘1.21.1’
** 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)

Tests output

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 
 10.496   2.891  13.557 

Example timings

SynExtend.Rcheck/SynExtend-Ex.timings

nameusersystemelapsed
AAHitScoping0.0000.0010.000
ApproximateBackground0.0930.0100.106
BlastSeqs000
BlockByRank0.6450.0090.660
BlockExpansion66.070 1.40168.080
BlockReconciliation000
BuiltInEnsembles 96.665 3.044100.292
CIDist_NullDist0.0010.0020.002
CheckAgainstReport000
ClusterByK1.6040.0291.640
CompetePairs0.6330.0090.644
DPhyloStatistic0.0430.0010.045
DecisionTree-class0.0430.0010.044
DisjointSet0.0790.0030.084
Endosymbionts_GeneCalls0.0140.0010.016
Endosymbionts_LinkedFeatures0.0180.0020.019
Endosymbionts_Pairs010.0300.0030.032
Endosymbionts_Pairs020.0330.0020.036
Endosymbionts_Pairs030.0250.0010.027
Endosymbionts_Sets0.0040.0020.006
Endosymbionts_Synteny0.0040.0020.007
EstimRearrScen1.7750.0161.797
EstimateExoLabel0.0020.0000.003
EvoWeaver0.0020.0000.003
EvoWeb0.0890.0030.093
ExampleStreptomycesData67.896 1.75970.074
ExoLabel0.0160.0120.032
ExpandDiagonal35.928 2.34338.560
ExtractBy0.3320.0100.364
FastQFromSRR000
FindSets0.0010.0000.001
FitchParsimony0.0750.0030.079
Generic0.0020.0020.004
HitConsensus000
MakeBlastDb000
MoransI0.0010.0010.002
NormVec0.0000.0000.001
NucleotideOverlap0.5480.0060.558
OneSite0.0010.0000.001
PairSummaries3.8040.0533.880
PhyloDistance-CI0.0040.0010.006
PhyloDistance-JRF0.0030.0000.004
PhyloDistance-KF0.0010.0010.002
PhyloDistance-RF0.0020.0000.002
PhyloDistance0.0030.0000.003
PrepareSeqs1.5860.0481.646
RandForest0.0230.0040.028
RejectionBy000
SelectByK35.262 0.89336.326
SequenceSimilarity0.0660.0030.071
SubSetPairs0.3430.0500.395
SummarizePairs63.079 2.93866.460
SuperTree0.2190.0100.231
SuperTreeEx0.0110.0010.012
WithinSetCompetition2.9510.0473.013
dendrapply0.1140.0140.130
gffToDataFrame8.2890.0548.389
plot.EvoWeb0.9400.0360.984
predict.EvoWeaver8.4290.1988.678
simMat0.0150.0040.020
subset-dendrogram0.3810.0100.394