##############################################################################
##############################################################################
###
### 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) (2025-10-20 r88955)
* 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    59.677  0.133  59.815
BlockExpansion    54.784  0.916  55.713
ExpandDiagonal    34.622  0.154  34.803
SelectByK         30.368  0.207  30.576
SuperTree         27.979  0.090  28.069
predict.EvoWeaver  8.134  0.057   8.191
gffToDataFrame     7.608  0.003   7.627
* 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.

##############################################################################
##############################################################################
###
### 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 -Werror=format-security -c  utilfuncs.f95 -o utilfuncs.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c  tabulate_mod.f95 -o tabulate_mod.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gfortran  -fpic  -g -O2  -Wall -Werror=format-security -c  cart_methods.f95 -o cart_methods.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
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) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 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 
 16.819   2.470  19.279