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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DNABarcodeCompatibility.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DNABarcodeCompatibility_1.27.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/DNABarcodeCompatibility.Rcheck’
* using R Under development (unstable) (2026-03-20 r89666)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-03-21 02:32:07 UTC
* using option ‘--no-vignettes’
* checking for file ‘DNABarcodeCompatibility/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DNABarcodeCompatibility’ version ‘1.27.0’
* 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 ‘DNABarcodeCompatibility’ can be installed ... OK
* used C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.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
Namespace in Imports field not imported from: ‘BH’
  All declared Imports should be used.
* 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 ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/DNABarcodeCompatibility.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DNABarcodeCompatibility
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘DNABarcodeCompatibility’ ...
** this is package ‘DNABarcodeCompatibility’ version ‘1.27.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DNABarcodes_init.c -o DNABarcodes_init.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cachedistance.cpp -o cachedistance.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c create_distance_func.cpp -o create_distance_func.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c distance_for_R.cpp -o distance_for_R.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c hammingdistance.cpp -o hammingdistance.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c levenshteindistance.cpp -o levenshteindistance.o
levenshteindistance.cpp:41:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   41 |   unsigned int distances[n+1][m+1];
      |                               ^~~
levenshteindistance.cpp:41:31: note: read of non-const variable 'm' is not allowed in a constant expression
levenshteindistance.cpp:39:10: note: declared here
   39 |   size_t m = sequence.length();
      |          ^
levenshteindistance.cpp:41:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   41 |   unsigned int distances[n+1][m+1];
      |                          ^~~
levenshteindistance.cpp:41:26: note: function parameter 'n' with unknown value cannot be used in a constant expression
levenshteindistance.cpp:36:119: note: declared here
   36 | bool LevenshteinDistance::is_seq_insertable(const std::vector<Sequence> &seqs, const Sequence &sequence, const size_t n, const unsigned int min_dist) {
      |                                                                                                                       ^
levenshteindistance.cpp:102:33: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  102 |     unsigned int distances[n+1][m+1];
      |                                 ^~~
levenshteindistance.cpp:102:33: note: read of non-const variable 'm' is not allowed in a constant expression
levenshteindistance.cpp:99:12: note: declared here
   99 |     size_t m = read.length();
      |            ^
levenshteindistance.cpp:102:28: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  102 |     unsigned int distances[n+1][m+1];
      |                            ^~~
levenshteindistance.cpp:102:28: note: read of non-const variable 'n' is not allowed in a constant expression
levenshteindistance.cpp:84:10: note: declared here
   84 |   size_t n = barcodes[1].length();
      |          ^
levenshteindistance.cpp:155:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  155 |   unsigned int distances[n+1][n+1];
      |                               ^~~
levenshteindistance.cpp:155:31: note: function parameter 'n' with unknown value cannot be used in a constant expression
levenshteindistance.cpp:148:112: note: declared here
  148 | unsigned int LevenshteinDistance::static_min_set_distance(const std::vector<Sequence> &sequences, const size_t n, const unsigned int cost_sub, const unsigned int cost_indel) {
      |                                                                                                                ^
levenshteindistance.cpp:155:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  155 |   unsigned int distances[n+1][n+1];
      |                          ^~~
levenshteindistance.cpp:155:26: note: function parameter 'n' with unknown value cannot be used in a constant expression
levenshteindistance.cpp:148:112: note: declared here
  148 | unsigned int LevenshteinDistance::static_min_set_distance(const std::vector<Sequence> &sequences, const size_t n, const unsigned int cost_sub, const unsigned int cost_indel) {
      |                                                                                                                ^
levenshteindistance.cpp:200:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  200 |   unsigned int distances[n+1][m+1];
      |                               ^~~
levenshteindistance.cpp:200:31: note: read of non-const variable 'm' is not allowed in a constant expression
levenshteindistance.cpp:196:10: note: declared here
  196 |   size_t m = sequence.length();
      |          ^
levenshteindistance.cpp:200:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  200 |   unsigned int distances[n+1][m+1];
      |                          ^~~
levenshteindistance.cpp:200:26: note: function parameter 'n' with unknown value cannot be used in a constant expression
levenshteindistance.cpp:192:135: note: declared here
  192 | unsigned int LevenshteinDistance::static_min_seq_distance(const std::vector< Sequence > &seqs, const Sequence &sequence, const size_t n, const unsigned int cost_sub, const unsigned int cost_indel) {
      |                                                                                                                                       ^
levenshteindistance.cpp:239:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  239 |   unsigned int distances[n+1][m+1];
      |                               ^~~
levenshteindistance.cpp:239:31: note: read of non-const variable 'm' is not allowed in a constant expression
levenshteindistance.cpp:237:10: note: declared here
  237 |   size_t m = sequence2.length();
      |          ^
levenshteindistance.cpp:239:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  239 |   unsigned int distances[n+1][m+1];
      |                          ^~~
levenshteindistance.cpp:239:26: note: read of non-const variable 'n' is not allowed in a constant expression
levenshteindistance.cpp:236:10: note: declared here
  236 |   size_t n = sequence1.length();
      |          ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c phaseshiftdist.cpp -o phaseshiftdist.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sequence.cpp -o sequence.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o
sequencelevenshteindistance.cpp:38:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   38 |   unsigned int distances[n+1][m+1];
      |                               ^~~
sequencelevenshteindistance.cpp:38:31: note: read of non-const variable 'm' is not allowed in a constant expression
sequencelevenshteindistance.cpp:34:10: note: declared here
   34 |   size_t m = sequence.length();
      |          ^
sequencelevenshteindistance.cpp:38:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   38 |   unsigned int distances[n+1][m+1];
      |                          ^~~
sequencelevenshteindistance.cpp:38:26: note: function parameter 'n' with unknown value cannot be used in a constant expression
sequencelevenshteindistance.cpp:33:127: note: declared here
   33 | bool SequenceLevenshteinDistance::is_seq_insertable(const std::vector<Sequence> &seqs, const Sequence &sequence, const size_t n, const unsigned int min_dist) {
      |                                                                                                                               ^
sequencelevenshteindistance.cpp:115:33: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  115 |     unsigned int distances[n+1][m+1];
      |                                 ^~~
sequencelevenshteindistance.cpp:115:33: note: read of non-const variable 'm' is not allowed in a constant expression
sequencelevenshteindistance.cpp:112:12: note: declared here
  112 |     size_t m = read.length();
      |            ^
sequencelevenshteindistance.cpp:115:28: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  115 |     unsigned int distances[n+1][m+1];
      |                            ^~~
sequencelevenshteindistance.cpp:115:28: note: read of non-const variable 'n' is not allowed in a constant expression
sequencelevenshteindistance.cpp:97:10: note: declared here
   97 |   size_t n = barcodes[1].length();
      |          ^
sequencelevenshteindistance.cpp:180:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  180 |   unsigned int distances[n+1][n+1];
      |                               ^~~
sequencelevenshteindistance.cpp:180:31: note: function parameter 'n' with unknown value cannot be used in a constant expression
sequencelevenshteindistance.cpp:175:120: note: declared here
  175 | unsigned int SequenceLevenshteinDistance::static_min_set_distance(const std::vector<Sequence> &sequences, const size_t n, const unsigned int cost_sub, const unsigned int cost_indel) {
      |                                                                                                                        ^
sequencelevenshteindistance.cpp:180:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  180 |   unsigned int distances[n+1][n+1];
      |                          ^~~
sequencelevenshteindistance.cpp:180:26: note: function parameter 'n' with unknown value cannot be used in a constant expression
sequencelevenshteindistance.cpp:175:120: note: declared here
  175 | unsigned int SequenceLevenshteinDistance::static_min_set_distance(const std::vector<Sequence> &sequences, const size_t n, const unsigned int cost_sub, const unsigned int cost_indel) {
      |                                                                                                                        ^
sequencelevenshteindistance.cpp:236:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  236 |   unsigned int distances[n+1][m+1];
      |                               ^~~
sequencelevenshteindistance.cpp:236:31: note: read of non-const variable 'm' is not allowed in a constant expression
sequencelevenshteindistance.cpp:230:10: note: declared here
  230 |   size_t m = sequence.length();
      |          ^
sequencelevenshteindistance.cpp:236:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  236 |   unsigned int distances[n+1][m+1];
      |                          ^~~
sequencelevenshteindistance.cpp:236:26: note: function parameter 'n' with unknown value cannot be used in a constant expression
sequencelevenshteindistance.cpp:229:141: note: declared here
  229 | unsigned int SequenceLevenshteinDistance::static_min_seq_distance(const std::vector<Sequence> &seqs, const Sequence &sequence, const size_t n, const unsigned int cost_sub, const unsigned int cost_indel) {
      |                                                                                                                                             ^
sequencelevenshteindistance.cpp:287:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  287 |   unsigned int distances[n+1][m+1];
      |                               ^~~
sequencelevenshteindistance.cpp:287:31: note: read of non-const variable 'm' is not allowed in a constant expression
sequencelevenshteindistance.cpp:285:10: note: declared here
  285 |   size_t m = sequence2.length();
      |          ^
sequencelevenshteindistance.cpp:287:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  287 |   unsigned int distances[n+1][m+1];
      |                          ^~~
sequencelevenshteindistance.cpp:287:26: note: read of non-const variable 'n' is not allowed in a constant expression
sequencelevenshteindistance.cpp:284:10: note: declared here
  284 |   size_t n = sequence1.length();
      |          ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o DNABarcodeCompatibility.so DNABarcodes_init.o RcppExports.o cachedistance.o create_distance_func.o distance_for_R.o hammingdistance.o levenshteindistance.o phaseshiftdist.o sequence.o sequencelevenshteindistance.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-DNABarcodeCompatibility/00new/DNABarcodeCompatibility/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (DNABarcodeCompatibility)

R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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Type 'license()' or 'licence()' for distribution details.

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> library(testthat)
> library(DNABarcodeCompatibility)
> 
> test_check("DNABarcodeCompatibility")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  0.470   0.074   0.550