Alicia Schep
| Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 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 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:35 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1313/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| motifmatchr 1.24.0 (landing page) Alicia Schep
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the motifmatchr package: - 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 Troubleshooting Build Report for more information. - 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. |
| Package: motifmatchr |
| Version: 1.24.0 |
| 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_1.24.0.tar.gz |
| StartedAt: 2024-03-03 21:58:17 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 22:04:03 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 345.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: motifmatchr.Rcheck |
| Warnings: 0 |
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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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/motifmatchr.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifmatchr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifmatchr’ version ‘1.24.0’
* 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 ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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-3.18-bioc/meat/motifmatchr.Rcheck/00check.log’
for details.
motifmatchr.Rcheck/00install.out
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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/4.3-x86_64/Resources/library’
* installing *source* package ‘motifmatchr’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/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-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/motif_0.cpp -o MOODS/motif_0.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./MOODS/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MOODS/match_types.cpp -o MOODS/match_types.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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)
motifmatchr.Rcheck/tests/testthat.Rout
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
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Platform: x86_64-apple-darwin20 (64-bit)
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> library(testthat)
> library(motifmatchr)
>
> test_check("motifmatchr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 50 ]
>
> proc.time()
user system elapsed
19.835 1.243 21.274
motifmatchr.Rcheck/motifmatchr-Ex.timings
| name | user | system | elapsed | |
| example_motifs | 0.004 | 0.002 | 0.005 | |
| matchMotifs | 0.660 | 0.056 | 0.724 | |
| motifCounts | 0.537 | 0.073 | 0.617 | |
| motifMatches | 0.452 | 0.048 | 0.506 | |
| motifScores | 0.417 | 0.039 | 0.460 | |
| pwmType | 0.007 | 0.001 | 0.008 | |