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This page was generated on 2021-10-15 15:06:43 -0400 (Fri, 15 Oct 2021).

CHECK results for motifmatchr on machv2

To the developers/maintainers of the motifmatchr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifmatchr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1184/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifmatchr 1.14.0  (landing page)
Alicia Schep
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/motifmatchr
git_branch: RELEASE_3_13
git_last_commit: b395fda
git_last_commit_date: 2021-05-19 12:28:12 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: motifmatchr
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:motifmatchr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings motifmatchr_1.14.0.tar.gz
StartedAt: 2021-10-14 21:23:03 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 21:28:43 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 339.3 seconds
RetCode: 0
Status:   OK  
CheckDir: motifmatchr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:motifmatchr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings motifmatchr_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/motifmatchr.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifmatchr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifmatchr’ version ‘1.14.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘motifmatchr’ can be installed ... OK
* 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 R 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 ... NOTE
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 in ‘inst/doc’ ... 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-3.13-bioc/meat/motifmatchr.Rcheck/00check.log’
for details.



Installation output

motifmatchr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL motifmatchr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘motifmatchr’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -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/4.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/r/headers.h:66:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/unordered_map:384:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/__hash_table:16:
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2335:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
    delete __ptr;
    ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2648:7: note: in instantiation of member function 'std::__1::default_delete<MOODS::scan::Motif>::operator()' requested here
      __ptr_.second()(__tmp);
      ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2602:19: note: in instantiation of member function 'std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >::reset' requested here
  ~unique_ptr() { reset(); }
                  ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1880:64: note: in instantiation of member function 'std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >::~unique_ptr' requested here
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1742:18: note: in instantiation of member function 'std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >::destroy' requested here
            {__a.destroy(__p);}
                 ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1595:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::__destroy<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::destroy<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/scanner.cpp -o MOODS/scanner.o
In file included from MOODS/scanner.cpp:12:
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2335:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
    delete __ptr;
    ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2648:7: note: in instantiation of member function 'std::__1::default_delete<MOODS::scan::Motif>::operator()' requested here
      __ptr_.second()(__tmp);
      ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2602:19: note: in instantiation of member function 'std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >::reset' requested here
  ~unique_ptr() { reset(); }
                  ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1880:64: note: in instantiation of member function 'std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >::~unique_ptr' requested here
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1742:18: note: in instantiation of member function 'std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >::destroy' requested here
            {__a.destroy(__p);}
                 ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1595:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::__destroy<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::destroy<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:464:28: note: in instantiation of member function 'std::__1::__vector_base<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::~__vector_base' requested here
class _LIBCPP_TEMPLATE_VIS vector
                           ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/motif_h.cpp -o MOODS/motif_h.o
MOODS/motif_h.cpp:256:25: warning: '&' within '^' [-Wbitwise-op-parentheses]
            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
            CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
                        ^
                   (                     )
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/motif_0.cpp -o MOODS/motif_0.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -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]
        bool done = 0;
             ^
MOODS/moods_scan.cpp:252:33: warning: '&' within '|' [-Wbitwise-op-parentheses]
                    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
                    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/usr/include/c++/v1/vector:270:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/algorithm:644:
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2335:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
    delete __ptr;
    ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2648:7: note: in instantiation of member function 'std::__1::default_delete<MOODS::scan::Motif>::operator()' requested here
      __ptr_.second()(__tmp);
      ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2602:19: note: in instantiation of member function 'std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >::reset' requested here
  ~unique_ptr() { reset(); }
                  ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1880:64: note: in instantiation of member function 'std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >::~unique_ptr' requested here
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1742:18: note: in instantiation of member function 'std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >::destroy' requested here
            {__a.destroy(__p);}
                 ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:1595:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::__destroy<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::destroy<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > >' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/usr/include/c++/v1/vector:464:28: note: in instantiation of member function 'std::__1::__vector_base<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> >, std::__1::allocator<std::__1::unique_ptr<MOODS::scan::Motif, std::__1::default_delete<MOODS::scan::Motif> > > >::~__vector_base' requested here
class _LIBCPP_TEMPLATE_VIS vector
                           ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c MOODS/match_types.cpp -o MOODS/match_types.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/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)

Tests output

motifmatchr.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 
 22.380   1.008  23.389 

Example timings

motifmatchr.Rcheck/motifmatchr-Ex.timings

nameusersystemelapsed
example_motifs0.0030.0020.005
matchMotifs0.8460.0360.883
motifCounts0.6720.0640.738
motifMatches1.3020.0311.333
motifScores0.4340.0190.453
pwmType0.0080.0020.010