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This page was generated on 2024-04-18 11:32:14 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 1313/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifmatchr 1.24.0  (landing page)
Alicia Schep
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/motifmatchr
git_branch: RELEASE_3_18
git_last_commit: 4051143
git_last_commit_date: 2023-10-24 10:57:39 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'TFBSTools' which is only available as a source package that needs compilation

INSTALL results for motifmatchr on kjohnson1


To the developers/maintainers of the motifmatchr package:
- 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: motifmatchr
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL motifmatchr
StartedAt: 2024-04-16 10:56:28 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 10:57:43 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 75.1 seconds
RetCode: 0
Status:   OK  

Command output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘motifmatchr’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/unordered_map:411:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__hash_table:15:
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2084:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
    delete __ptr;
    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2345:7: note: in instantiation of member function 'std::default_delete<MOODS::scan::Motif>::operator()' requested here
      __ptr_.second()(__tmp);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2299:19: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::reset' requested here
  ~unique_ptr() { reset(); }
                  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:92: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::~unique_ptr' requested here
    _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                                                           ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1578:21: note: in instantiation of member function 'std::allocator<std::unique_ptr<MOODS::scan::Motif>>::destroy' requested here
                __a.destroy(__p);
                    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1419:14: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::__destroy<std::unique_ptr<MOODS::scan::Motif>>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:428:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::destroy<std::unique_ptr<MOODS::scan::Motif>>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:371:29: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:465:9: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:551:5: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::~__vector_base' requested here
    ~vector()
    ^
./MOODS/scanner.h:31:11: note: in instantiation of member function 'std::vector<std::unique_ptr<MOODS::scan::Motif>>::~vector' requested here
    class Scanner {
          ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/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:
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2084:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
    delete __ptr;
    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2345:7: note: in instantiation of member function 'std::default_delete<MOODS::scan::Motif>::operator()' requested here
      __ptr_.second()(__tmp);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2299:19: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::reset' requested here
  ~unique_ptr() { reset(); }
                  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:92: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::~unique_ptr' requested here
    _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                                                           ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1578:21: note: in instantiation of member function 'std::allocator<std::unique_ptr<MOODS::scan::Motif>>::destroy' requested here
                __a.destroy(__p);
                    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1419:14: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::__destroy<std::unique_ptr<MOODS::scan::Motif>>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:428:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::destroy<std::unique_ptr<MOODS::scan::Motif>>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:371:29: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:465:9: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:497:5: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::~__vector_base' requested here
    vector() _NOEXCEPT_(is_nothrow_default_constructible<allocator_type>::value)
    ^
MOODS/scanner.cpp:28:14: note: in instantiation of member function 'std::vector<std::unique_ptr<MOODS::scan::Motif>>::vector' requested here
    Scanner::Scanner(unsigned int window_size){
             ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/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]
            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++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/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]
        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/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/algorithm:643:
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2084:5: warning: delete called on 'MOODS::scan::Motif' that is abstract but has non-virtual destructor [-Wdelete-abstract-non-virtual-dtor]
    delete __ptr;
    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2345:7: note: in instantiation of member function 'std::default_delete<MOODS::scan::Motif>::operator()' requested here
      __ptr_.second()(__tmp);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:2299:19: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::reset' requested here
  ~unique_ptr() { reset(); }
                  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1686:92: note: in instantiation of member function 'std::unique_ptr<MOODS::scan::Motif>::~unique_ptr' requested here
    _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                                                           ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1578:21: note: in instantiation of member function 'std::allocator<std::unique_ptr<MOODS::scan::Motif>>::destroy' requested here
                __a.destroy(__p);
                    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1419:14: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::__destroy<std::unique_ptr<MOODS::scan::Motif>>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:428:25: note: in instantiation of function template specialization 'std::allocator_traits<std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::destroy<std::unique_ptr<MOODS::scan::Motif>>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_address(--__soon_to_be_end));
                        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:371:29: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:465:9: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::clear' requested here
        clear();
        ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/vector:551:5: note: in instantiation of member function 'std::__vector_base<std::unique_ptr<MOODS::scan::Motif>, std::allocator<std::unique_ptr<MOODS::scan::Motif>>>::~__vector_base' requested here
    ~vector()
    ^
./MOODS/scanner.h:31:11: note: in instantiation of member function 'std::vector<std::unique_ptr<MOODS::scan::Motif>>::~vector' requested here
    class Scanner {
          ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/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++11 -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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/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)