Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-09-27 12:05 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 2145/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SynExtend 1.21.1  (landing page)
Nicholas Cooley
Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 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: 2025-09-27 00:40:26 -0400 (Sat, 27 Sep 2025)
EndedAt: 2025-09-27 00:50:02 -0400 (Sat, 27 Sep 2025)
EllapsedTime: 575.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SynExtend.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 Patched (2025-09-10 r88807)
* 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: ‘MacOSX11.3.1.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        94.197  3.402  98.385
ExampleStreptomycesData 66.513  1.822  68.853
BlockExpansion          64.904  1.473  68.705
SummarizePairs          61.923  3.135  65.616
ExpandDiagonal          36.729  2.440  39.666
SelectByK               37.164  1.126  38.603
predict.EvoWeaver       10.564  0.186  10.812
gffToDataFrame          10.312  0.064  10.429
* 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: ‘MacOSX11.3.1.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 Patched (2025-09-10 r88807) -- "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 
 10.648   3.301  14.354 

Example timings

SynExtend.Rcheck/SynExtend-Ex.timings

nameusersystemelapsed
AAHitScoping0.0000.0000.001
ApproximateBackground0.1020.0110.118
BlastSeqs000
BlockByRank0.6780.0100.694
BlockExpansion64.904 1.47368.705
BlockReconciliation000
BuiltInEnsembles94.197 3.40298.385
CIDist_NullDist0.0020.0020.004
CheckAgainstReport0.0000.0000.001
ClusterByK1.5810.0351.630
CompetePairs0.6410.0130.656
DPhyloStatistic0.0360.0020.038
DecisionTree-class0.0380.0020.040
DisjointSet0.0680.0030.072
Endosymbionts_GeneCalls0.0160.0030.017
Endosymbionts_LinkedFeatures0.0250.0020.026
Endosymbionts_Pairs010.0320.0020.034
Endosymbionts_Pairs020.0290.0030.032
Endosymbionts_Pairs030.0230.0020.025
Endosymbionts_Sets0.0030.0020.005
Endosymbionts_Synteny0.0050.0010.007
EstimRearrScen1.7340.0261.772
EstimateExoLabel0.0010.0000.002
EvoWeaver0.0030.0010.004
EvoWeb0.0780.0040.082
ExampleStreptomycesData66.513 1.82268.853
ExoLabel0.0200.0140.036
ExpandDiagonal36.729 2.44039.666
ExtractBy0.3420.0120.359
FastQFromSRR000
FindSets0.0020.0010.002
FitchParsimony0.0650.0030.068
Generic0.0020.0020.005
HitConsensus0.0000.0000.001
MakeBlastDb000
MoransI0.0010.0010.001
NormVec0.0010.0000.000
NucleotideOverlap0.6500.0130.670
OneSite0.0000.0010.001
PairSummaries4.1010.0704.221
PhyloDistance-CI0.0050.0010.007
PhyloDistance-JRF0.0050.0000.005
PhyloDistance-KF0.0030.0000.003
PhyloDistance-RF0.0030.0000.003
PhyloDistance0.0050.0010.005
PrepareSeqs1.6080.0621.695
RandForest0.0160.0010.017
RejectionBy000
SelectByK37.164 1.12638.603
SequenceSimilarity0.0660.0050.073
SubSetPairs0.6660.0590.729
SummarizePairs61.923 3.13565.616
SuperTree0.2210.0110.233
SuperTreeEx0.0080.0010.009
WithinSetCompetition3.1940.0163.222
dendrapply0.1170.0130.130
gffToDataFrame10.312 0.06410.429
plot.EvoWeb1.1310.0311.169
predict.EvoWeaver10.564 0.18610.812
simMat0.0160.0040.019
subset-dendrogram0.3710.0100.386