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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifmatchr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifmatchr_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/motifmatchr.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* 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: 2026-05-07 01:21:09 UTC
* using option ‘--no-vignettes’
* checking for file ‘motifmatchr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifmatchr’ version ‘1.34.0’
* 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 ‘motifmatchr’ can be installed ... NOTE
Found the following notes/warnings:
  SystemRequirements specified C++11: support has been removed
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/motifmatchr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking C++ specification ... NOTE
  Obsolete C++11 standard request will be ignored
* 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 ... OK
* 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 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 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/motifmatchr.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL motifmatchr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘motifmatchr’ ...
** this is package ‘motifmatchr’ version ‘1.34.0’
** using staged installation
** libs
specified C++11
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/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. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c r_interface.cpp -o r_interface.o
In file included from r_interface.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:39:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/unordered_map:595:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__hash_table:29:
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:78:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
   78 |     delete __ptr;
      |     ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:300:7: note: in instantiation of member function 'std::default_delete<MOODS::scan::Motif>::operator()' requested here
  300 |       __deleter_(__tmp);
      |       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:269:71: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::reset' requested here
  269 |   _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
      |                                                                       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/construct_at.h:66:11: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::~unique_ptr' requested here
   66 |   __loc->~_Tp();
      |           ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/scanner.cpp -o MOODS/scanner.o
In file included from MOODS/scanner.cpp:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/memory:947:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/inout_ptr.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/shared_ptr.h:35:
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:78:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
   78 |     delete __ptr;
      |     ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:300:7: note: in instantiation of member function 'std::default_delete<MOODS::scan::Motif>::operator()' requested here
  300 |       __deleter_(__tmp);
      |       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:269:71: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::reset' requested here
  269 |   _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
      |                                                                       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/construct_at.h:66:11: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::~unique_ptr' requested here
   66 |   __loc->~_Tp();
      |           ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/motif_h.cpp -o MOODS/motif_h.o
MOODS/motif_h.cpp:256:25: warning: '&' within '^' [-Wbitwise-op-parentheses]
  256 |             CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
      |                    ~~~~~^~~~~~~~~~~~~~~~~ ~
MOODS/motif_h.cpp:256:25: note: place parentheses around the '&' expression to silence this warning
  256 |             CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
      |                         ^
      |                    (                     )
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/motif_0.cpp -o MOODS/motif_0.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o
MOODS/moods_scan.cpp:97:14: warning: unused variable 'done' [-Wunused-variable]
   97 |         bool done = 0;
      |              ^~~~
MOODS/moods_scan.cpp:252:33: warning: '&' within '|' [-Wbitwise-op-parentheses]
  252 |                     CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
      |                            ~~~~~^~~~~~~~~~~~~~~~~ ~
MOODS/moods_scan.cpp:252:33: note: place parentheses around the '&' expression to silence this warning
  252 |                     CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
      |                                 ^
      |                            (                     )
In file included from MOODS/moods_scan.cpp:3:
In file included from MOODS/moods.h:5:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/vector:352:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/algorithm:1854:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__algorithm/for_each.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__ranges/movable_box.h:21:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/optional:1302:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/memory:947:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/inout_ptr.h:16:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/shared_ptr.h:35:
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:78:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
   78 |     delete __ptr;
      |     ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:300:7: note: in instantiation of member function 'std::default_delete<MOODS::scan::Motif>::operator()' requested here
  300 |       __deleter_(__tmp);
      |       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/unique_ptr.h:269:71: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::reset' requested here
  269 |   _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX23 ~unique_ptr() { reset(); }
      |                                                                       ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/__memory/construct_at.h:66:11: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::~unique_ptr' requested here
   66 |   __loc->~_Tp();
      |           ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MOODS/match_types.cpp -o MOODS/match_types.o
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 motifmatchr.so ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-motifmatchr/00new/motifmatchr/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 (motifmatchr)

R version 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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.

> library(testthat)
> library(motifmatchr)
> 
> test_check("motifmatchr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 50 ]
> 
> proc.time()
   user  system elapsed 
  6.145   0.268   6.442