##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SynExtend_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SynExtend.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.23.0’
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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 ... INFO
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 59.680  0.149  60.028
BlockExpansion 55.230  0.782  56.036
ExpandDiagonal 34.320  0.170  34.500
SelectByK      30.652  0.232  30.895
SuperTree      28.269  0.116  28.405
gffToDataFrame  7.459  0.006   7.466
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/SynExtend.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL SynExtend
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘SynExtend’ ...
** this is package ‘SynExtend’ version ‘1.23.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c calcMIR2C.c -o calcMIR2C.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c CDend.c -o CDend.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c CShuffle.c -o CShuffle.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c dendrapply.c -o dendrapply.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c HitConsensus.c -o HitConsensus.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c HungarianAlgo.c -o HungarianAlgo.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c MoranI.c -o MoranI.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c NucleotideCounts.c -o NucleotideCounts.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c R_init_synextend.c -o R_init_synextend.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c RandomForest.c -o RandomForest.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c SEutils.c -o SEutils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c XORRand.c -o XORRand.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c ExoLabel/ExoLabel.c -o ExoLabel/ExoLabel.o
ExoLabel/ExoLabel.c: In function ‘R_LPOOM_cluster’:
ExoLabel/ExoLabel.c:1882:5: warning: ‘debug_weights’ may be used uninitialized [-Wmaybe-uninitialized]
 1882 |     SET_VECTOR_ELT(LIST_VAL, 1, debug_weights);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ExoLabel/ExoLabel.c:1777:8: note: ‘debug_weights’ was declared here
 1777 |   SEXP debug_weights, debug_degrees;
      |        ^~~~~~~~~~~~~
ExoLabel/ExoLabel.c:1883:5: warning: ‘debug_degrees’ may be used uninitialized [-Wmaybe-uninitialized]
 1883 |     SET_VECTOR_ELT(LIST_VAL, 2, debug_degrees);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ExoLabel/ExoLabel.c:1777:23: note: ‘debug_degrees’ was declared here
 1777 |   SEXP debug_weights, debug_degrees;
      |                       ^~~~~~~~~~~~~
ExoLabel/ExoLabel.c:1884:5: warning: ‘debug_disjoint_sizes’ may be used uninitialized [-Wmaybe-uninitialized]
 1884 |     SET_VECTOR_ELT(LIST_VAL, 3, debug_disjoint_sizes);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ExoLabel/ExoLabel.c:1826:8: note: ‘debug_disjoint_sizes’ was declared here
 1826 |   SEXP debug_disjoint_sizes;
      |        ^~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c ExoLabel/FileHandlers.c -o ExoLabel/FileHandlers.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c ExoLabel/PrefixTrie.c -o ExoLabel/PrefixTrie.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -DCOMPILING_SYNEXTEND_VIA_R -fpic  -g -O2  -Wall -Werror=format-security -c ExoLabel/LoserTree.c -o ExoLabel/LoserTree.o
gfortran  -fpic  -g -O2  -Wall -c  utilfuncs.f95 -o utilfuncs.o
gfortran  -fpic  -g -O2  -Wall -c  tabulate_mod.f95 -o tabulate_mod.o
gfortran  -fpic  -g -O2  -Wall -c  cart_methods.f95 -o cart_methods.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/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 -fopenmp -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-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)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 16.977   2.518  19.487