##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:universalmotif.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings universalmotif_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/universalmotif.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘universalmotif/DESCRIPTION’ ... OK
* this is package ‘universalmotif’ version ‘1.25.1’
* 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 ‘universalmotif’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ArabidopsisPromoters.Rd: DNAStringSet
  add_multifreq.Rd: XStringSet
  create_motif.Rd: XStringSet, DNAStringSet, RNAStringSet, AAStringSet,
    BStringSet
  create_sequences.Rd: XStringSet
  enrich_motifs.Rd: XStringSet
  fontDFroboto.Rd: DataFrame-class
  get_bkg.Rd: XStringSet
  run_meme.Rd: XStringSet
  sample_sites.Rd: XStringSet
  scan_sequences.Rd: XStringSet, DNAString, MaskedXString,
    DNAStringSet, RNAStringSet
  sequence_complexity.Rd: XStringSet
  shuffle_sequences.Rd: XStringSet
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
convert_motifs 12.905  0.688  15.748
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/universalmotif.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL universalmotif
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘universalmotif’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c add_multifreq.cpp -o add_multifreq.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c calc_complexity.cpp -o calc_complexity.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c compare_motifs.cpp -o compare_motifs.o
In file included from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/aarch64-unknown-linux-gnu/bits/c++allocator.h:33,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/allocator.h:46,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/alloc_traits.h:39,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/ext/alloc_traits.h:34,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/hashtable_policy.h:39,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/hashtable.h:35,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/unordered_map.h:33,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/unordered_map:41,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/Rcpp/r/headers.h:66,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/RcppCommon.h:30,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include/Rcpp.h:27,
                 from compare_motifs.cpp:1:
In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = double]’,
    inlined from ‘static void std::allocator_traits<std::allocator<_Tp1> >::deallocate(allocator_type&, pointer, size_type) [with _Tp = double]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/alloc_traits.h:513:23,
    inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:389:19,
    inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:368:15,
    inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:738:7,
    inlined from ‘double compare_eucl(const list_num_t&, const list_num_t&, const str_t&, const vec_num_t&, const vec_num_t&)’ at compare_motifs.cpp:406:28:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*)’ called on pointer ‘<unknown>’ with nonzero offset [8, 9223372036854775800] [-Wfree-nonheap-object]
  172 |         _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n));
      |                                 ^
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = double]’,
    inlined from ‘static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = double]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/alloc_traits.h:478:28,
    inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:380:33,
    inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:398:44,
    inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:334:26,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:571:47,
    inlined from ‘double compare_eucl(const list_num_t&, const list_num_t&, const str_t&, const vec_num_t&, const vec_num_t&)’ at compare_motifs.cpp:406:47:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’
  151 |         return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
      |                                                       ^
In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = double]’,
    inlined from ‘static void std::allocator_traits<std::allocator<_Tp1> >::deallocate(allocator_type&, pointer, size_type) [with _Tp = double]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/alloc_traits.h:513:23,
    inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:389:19,
    inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:368:15,
    inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:738:7,
    inlined from ‘double compare_weucl(const list_num_t&, const list_num_t&, const str_t&, const vec_num_t&, const vec_num_t&, const vec_num_t&, const vec_num_t&)’ at compare_motifs.cpp:604:28:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*)’ called on pointer ‘<unknown>’ with nonzero offset [8, 9223372036854775800] [-Wfree-nonheap-object]
  172 |         _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n));
      |                                 ^
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = double]’,
    inlined from ‘static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = double]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/alloc_traits.h:478:28,
    inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:380:33,
    inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:398:44,
    inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:334:26,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_vector.h:571:47,
    inlined from ‘double compare_weucl(const list_num_t&, const list_num_t&, const str_t&, const vec_num_t&, const vec_num_t&, const vec_num_t&, const vec_num_t&)’ at compare_motifs.cpp:604:47:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’
  151 |         return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
      |                                                       ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c get_bkg.cpp -o get_bkg.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c motif_finder.cpp -o motif_finder.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c motif_peaks.cpp -o motif_peaks.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c motif_pvalue.cpp -o motif_pvalue.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c scan_sequences.cpp -o scan_sequences.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c shuffle_sequences.cpp -o shuffle_sequences.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c trim_motifs.cpp -o trim_motifs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c universalmotif-class.cpp -o universalmotif-class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c utils-exported.cpp -o utils-exported.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppThread/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c utils-internal.cpp -o utils-internal.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o universalmotif.so RcppExports.o add_multifreq.o calc_complexity.o compare_motifs.o get_bkg.o motif_finder.o motif_peaks.o motif_pvalue.o scan_sequences.o shuffle_sequences.o trim_motifs.o universalmotif-class.o utils-exported.o utils-internal.o -latomic -lpthread -L/home/biocbuild/R/R/lib -lR
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug universalmotif.so; fi
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-universalmotif/00new/universalmotif/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘convert_motifs’ with signature ‘motifs="MotifList"’: no definition for class “MotifList”
in method for ‘convert_motifs’ with signature ‘motifs="TFFMFirst"’: no definition for class “TFFMFirst”
in method for ‘convert_motifs’ with signature ‘motifs="PFMatrix"’: no definition for class “PFMatrix”
in method for ‘convert_motifs’ with signature ‘motifs="PWMatrix"’: no definition for class “PWMatrix”
in method for ‘convert_motifs’ with signature ‘motifs="ICMatrix"’: no definition for class “ICMatrix”
in method for ‘convert_motifs’ with signature ‘motifs="XMatrixList"’: no definition for class “XMatrixList”
in method for ‘convert_motifs’ with signature ‘motifs="pwm"’: no definition for class “pwm”
in method for ‘convert_motifs’ with signature ‘motifs="pcm"’: no definition for class “pcm”
in method for ‘convert_motifs’ with signature ‘motifs="pfm"’: no definition for class “pfm”
in method for ‘convert_motifs’ with signature ‘motifs="PWM"’: no definition for class “PWM”
in method for ‘convert_motifs’ with signature ‘motifs="Motif"’: no definition for class “Motif”
** 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 (universalmotif)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.228   0.017   0.437 

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> if (R.Version()$arch != "i386") {
+ 
+   library(testthat)
+   library(universalmotif)
+ 
+   test_check("universalmotif") 
+ 
+ } else TRUE
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 240 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 240 ]
> 
> proc.time()
   user  system elapsed 
 11.520   0.594  16.646