| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:30 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
|
To the developers/maintainers of the epialleleR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epialleleR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 587/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epialleleR 1.2.0 (landing page) Oleksii Nikolaienko
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: epialleleR |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epialleleR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings epialleleR_1.2.0.tar.gz |
| StartedAt: 2022-04-12 19:16:04 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 19:25:04 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 540.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: epialleleR.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epialleleR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings epialleleR_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/epialleleR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'epialleleR/DESCRIPTION' ... OK
* this is package 'epialleleR' version '1.2.0'
* 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 whether package 'epialleleR' can be installed ... WARNING
Found the following significant warnings:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:912:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:184:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:214:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/epialleleR.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 9.4Mb
sub-directories of 1Mb or more:
extdata 1.7Mb
libs 7.5Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... NOTE
GNU make is a SystemRequirements.
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/epialleleR/libs/i386/epialleleR.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/epialleleR/libs/x64/epialleleR.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Found 'rand', possibly from 'rand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
generateVcfReport 13.36 0.51 14.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
generateVcfReport 11.9 0.2 12.29
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/epialleleR.Rcheck/00check.log'
for details.
epialleleR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/epialleleR_1.2.0.tar.gz && rm -rf epialleleR.buildbin-libdir && mkdir epialleleR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=epialleleR.buildbin-libdir epialleleR_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL epialleleR_1.2.0.zip && rm epialleleR_1.2.0.tar.gz epialleleR_1.2.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 1716k 0 15987 0 0 133k 0 0:00:12 --:--:-- 0:00:12 133k
100 1716k 100 1716k 0 0 2006k 0 --:--:-- --:--:-- --:--:-- 2007k
install for i386
* installing *source* package 'epialleleR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_char_to_context.cpp -o rcpp_char_to_context.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_cx_report.cpp -o rcpp_cx_report.o
rcpp_cx_report.cpp: In function 'std::vector<int> rcpp_cx_report(Rcpp::DataFrame&, Rcpp::LogicalVector&, std::__cxx11::string)':
rcpp_cx_report.cpp:106:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int x=0; x<rname.size(); x++) {
~^~~~~~~~~~~~~
rcpp_cx_report.cpp:116:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int i=0; i<xm[x].size(); i++) {
~^~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:32,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'typename boost::container::dtl::enable_if_memtransfer_copy_assignable<I, F, F>::type boost::container::move_backward(I, I, F) [with I = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; typename boost::container::dtl::enable_if_memtransfer_copy_assignable<I, F, F>::type = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*]':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:2983:41: required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_expand_forward(T*, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy, boost::move_detail::true_type) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, boost::container::try_emplace_t, const long long unsigned int&, std::array<int, 16>&>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = unsigned int; boost::move_detail::true_type = boost::move_detail::integral_constant<bool, true>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:2826:10: required from 'boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::priv_insert_forward_range(const pointer&, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, boost::container::try_emplace_t, const long long unsigned int&, std::array<int, 16>&>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, false>; typename boost::container::allocator_traits<typename boost::container::real_allocator<T, A>::type>::pointer = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; boost::container::vector<T, Allocator, Options>::pointer = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; boost::container::vector<T, Allocator, Options>::size_type = unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:1866:87: required from 'boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::emplace(boost::container::vector<T, Allocator, Options>::const_iterator, Args&& ...) [with Args = {boost::container::try_emplace_t, const long long unsigned int&, std::array<int, 16>&}; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, false>; typename boost::container::allocator_traits<typename boost::container::real_allocator<T, A>::type>::pointer = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; boost::container::vector<T, Allocator, Options>::const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, true>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1020:20: required from 'std::pair<typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type::iterator, bool> boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::try_emplace(boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::const_iterator, KeyType&&, Args&& ...) [with KeyType = const long long unsigned int&; Args = {std::array<int, 16>&}; Value = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type::iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, false>; boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, true>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:968:89: required from 'boost::container::flat_map<Key, T, Compare, Allocator>::iterator boost::container::flat_map<Key, T, Compare, Allocator>::try_emplace(boost::container::flat_map<Key, T, Compare, Allocator>::const_iterator, const key_type&, Args&& ...) [with Args = {std::array<int, 16>&}; Key = long long unsigned int; T = std::array<int, 16>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; boost::container::flat_map<Key, T, Compare, Allocator>::iterator = boost::container::vec_iterator<std::pair<long long unsigned int, std::array<int, 16> >*, false>; boost::container::flat_map<Key, T, Compare, Allocator>::const_iterator = boost::container::vec_iterator<std::pair<long long unsigned int, std::array<int, 16> >*, true>; boost::container::flat_map<Key, T, Compare, Allocator>::key_type = long long unsigned int]'
rcpp_cx_report.cpp:121:55: required from here
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:912:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
std::memmove((boost::movelib::iterator_to_raw_pointer)(r), (boost::movelib::iterator_to_raw_pointer)(f), sizeof(value_type)*n);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} declared here
struct pair
^~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:32,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'F boost::container::dtl::memmove(I, I, F) [with I = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*]':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:325:23: required from 'typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type boost::container::uninitialized_move_alloc(Allocator&, I, I, F) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; I = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1205:59: required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; O = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; std::size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_new_allocation(T*, boost::container::vector<T, Allocator, Options>::size_type, T*, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:2610:7: required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(boost::container::vector<T, Allocator, Options>::size_type, boost::container::version_1) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:1570:10: required from 'void boost::container::vector<T, Allocator, Options>::reserve(boost::container::vector<T, Allocator, Options>::size_type) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:380:4: required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >, boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, void>; typename SequenceContainer::size_type = unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26: required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::size_type) [with Value = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::size_type = unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:9: required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(boost::container::flat_map<Key, T, Compare, Allocator>::size_type) [with Key = long long unsigned int; T = std::array<int, 16>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; boost::container::flat_map<Key, T, Compare, Allocator>::size_type = unsigned int]'
rcpp_cx_report.cpp:105:24: required from here
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:184:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
std::memmove(dest_raw, beg_raw, sizeof(value_type)*n);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'value_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} declared here
struct pair
^~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:32,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'I boost::container::dtl::memmove_n_source(I, std::size_t, F) [with I = boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; std::size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:553:32: required from 'typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type boost::container::uninitialized_copy_alloc_n_source(Allocator&, I, std::size_t, F) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; I = boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type = boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; std::size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:81:75: required from 'void boost::container::dtl::insert_range_proxy<Allocator, FwdIt, Iterator>::uninitialized_copy_n_and_update(Allocator&, Iterator, std::size_t) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; FwdIt = boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; Iterator = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; std::size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1208:4: required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; O = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; std::size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_new_allocation(T*, boost::container::vector<T, Allocator, Options>::size_type, T*, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:2610:7: required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(boost::container::vector<T, Allocator, Options>::size_type, boost::container::version_1) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:1570:10: required from 'void boost::container::vector<T, Allocator, Options>::reserve(boost::container::vector<T, Allocator, Options>::size_type) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:380:4: required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >, boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, void>; typename SequenceContainer::size_type = unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26: required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::size_type) [with Value = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::size_type = unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:9: required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(boost::container::flat_map<Key, T, Compare, Allocator>::size_type) [with Key = long long unsigned int; T = std::array<int, 16>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; boost::container::flat_map<Key, T, Compare, Allocator>::size_type = unsigned int]'
rcpp_cx_report.cpp:105:24: required from here
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:214:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
std::memmove(boost::movelib::iterator_to_raw_pointer(r), boost::movelib::iterator_to_raw_pointer(f), sizeof(value_type)*n);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} declared here
struct pair
^~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_fep.cpp -o rcpp_fep.o
rcpp_fep.cpp: In function 'std::vector<double> rcpp_fep(Rcpp::DataFrame&, std::vector<std::__cxx11::basic_string<char> >)':
rcpp_fep.cpp:21:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int x=0; x<A.size(); x++) {
~^~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o
rcpp_get_base_freqs.cpp: In function 'Rcpp::NumericMatrix rcpp_get_base_freqs(Rcpp::DataFrame&, std::vector<bool>, Rcpp::DataFrame&)':
rcpp_get_base_freqs.cpp:34:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int x=0; x<read_start.size(); x++) {
~^~~~~~~~~~~~~~~~~~
rcpp_get_base_freqs.cpp:39:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int i=cur_vcf; i<vcf_pos.size(); i++) {
~^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o
rcpp_get_xm_beta.cpp: In function 'std::vector<double> rcpp_get_xm_beta(Rcpp::DataFrame&, std::__cxx11::string, std::__cxx11::string)':
rcpp_get_xm_beta.cpp:16:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int x=0; x<xm.size(); x++) {
~^~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_match_target.cpp -o rcpp_match_target.o
rcpp_match_target.cpp: In function 'std::vector<int> rcpp_match_amplicon(Rcpp::DataFrame&, Rcpp::DataFrame&, int)':
rcpp_match_target.cpp:28:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int x=0; x<read_start.size(); x++) {
~^~~~~~~~~~~~~~~~~~
rcpp_match_target.cpp:33:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int i=0; i<ampl_start.size(); i++) {
~^~~~~~~~~~~~~~~~~~
rcpp_match_target.cpp: In function 'std::vector<int> rcpp_match_capture(Rcpp::DataFrame&, Rcpp::DataFrame&, int)':
rcpp_match_target.cpp:62:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int x=0; x<read_start.size(); x++) {
~^~~~~~~~~~~~~~~~~~
rcpp_match_target.cpp:67:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int i=0; i<capt_start.size(); i++) {
~^~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_read_bam.cpp -o rcpp_read_bam.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o
rcpp_threshold_reads.cpp: In function 'std::vector<bool> rcpp_threshold_reads(Rcpp::DataFrame&, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, unsigned int, double, double)':
rcpp_threshold_reads.cpp:26:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int x=0; x<xm.size(); x++) {
~^~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o epialleleR.dll tmp.def RcppExports.o rcpp_char_to_context.o rcpp_cx_report.o rcpp_fep.o rcpp_get_base_freqs.o rcpp_get_xm_beta.o rcpp_match_target.o rcpp_read_bam.o rcpp_threshold_reads.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/epialleleR.buildbin-libdir/00LOCK-epialleleR/00new/epialleleR/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'epialleleR'
finding HTML links ... done
generateBedEcdf html
finding level-2 HTML links ... done
generateBedReport html
generateCytosineReport html
generateVcfReport html
preprocessBam html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'epialleleR' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_char_to_context.cpp -o rcpp_char_to_context.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_cx_report.cpp -o rcpp_cx_report.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:32,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'typename boost::container::dtl::enable_if_memtransfer_copy_assignable<I, F, F>::type boost::container::move_backward(I, I, F) [with I = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; typename boost::container::dtl::enable_if_memtransfer_copy_assignable<I, F, F>::type = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*]':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:2983:41: required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_expand_forward(T*, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy, boost::move_detail::true_type) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, boost::container::try_emplace_t, const long long unsigned int&, std::array<int, 16>&>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long long unsigned int; boost::move_detail::true_type = boost::move_detail::integral_constant<bool, true>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:2826:10: required from 'boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::priv_insert_forward_range(const pointer&, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_emplace_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, boost::container::try_emplace_t, const long long unsigned int&, std::array<int, 16>&>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, false>; typename boost::container::allocator_traits<typename boost::container::real_allocator<T, A>::type>::pointer = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; boost::container::vector<T, Allocator, Options>::pointer = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; boost::container::vector<T, Allocator, Options>::size_type = long long unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:1866:87: required from 'boost::container::vector<T, Allocator, Options>::iterator boost::container::vector<T, Allocator, Options>::emplace(boost::container::vector<T, Allocator, Options>::const_iterator, Args&& ...) [with Args = {boost::container::try_emplace_t, const long long unsigned int&, std::array<int, 16>&}; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, false>; typename boost::container::allocator_traits<typename boost::container::real_allocator<T, A>::type>::pointer = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; boost::container::vector<T, Allocator, Options>::const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, true>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1020:20: required from 'std::pair<typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type::iterator, bool> boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::try_emplace(boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::const_iterator, KeyType&&, Args&& ...) [with KeyType = const long long unsigned int&; Args = {std::array<int, 16>&}; Value = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; typename boost::container::dtl::select_container_type<Value, AllocatorOrContainer>::type::iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, false>; boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::const_iterator = boost::container::vec_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*, true>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:968:89: required from 'boost::container::flat_map<Key, T, Compare, Allocator>::iterator boost::container::flat_map<Key, T, Compare, Allocator>::try_emplace(boost::container::flat_map<Key, T, Compare, Allocator>::const_iterator, const key_type&, Args&& ...) [with Args = {std::array<int, 16>&}; Key = long long unsigned int; T = std::array<int, 16>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; boost::container::flat_map<Key, T, Compare, Allocator>::iterator = boost::container::vec_iterator<std::pair<long long unsigned int, std::array<int, 16> >*, false>; boost::container::flat_map<Key, T, Compare, Allocator>::const_iterator = boost::container::vec_iterator<std::pair<long long unsigned int, std::array<int, 16> >*, true>; boost::container::flat_map<Key, T, Compare, Allocator>::key_type = long long unsigned int]'
rcpp_cx_report.cpp:121:55: required from here
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:912:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
std::memmove((boost::movelib::iterator_to_raw_pointer)(r), (boost::movelib::iterator_to_raw_pointer)(f), sizeof(value_type)*n);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} declared here
struct pair
^~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:32,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'F boost::container::dtl::memmove(I, I, F) [with I = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*]':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:325:23: required from 'typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type boost::container::uninitialized_move_alloc(Allocator&, I, I, F) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; I = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, F>::type = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1205:59: required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; O = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; std::size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_new_allocation(T*, boost::container::vector<T, Allocator, Options>::size_type, T*, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long long unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:2610:7: required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(boost::container::vector<T, Allocator, Options>::size_type, boost::container::version_1) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:1570:10: required from 'void boost::container::vector<T, Allocator, Options>::reserve(boost::container::vector<T, Allocator, Options>::size_type) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long long unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:380:4: required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >, boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26: required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::size_type) [with Value = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::size_type = long long unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:9: required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(boost::container::flat_map<Key, T, Compare, Allocator>::size_type) [with Key = long long unsigned int; T = std::array<int, 16>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; boost::container::flat_map<Key, T, Compare, Allocator>::size_type = long long unsigned int]'
rcpp_cx_report.cpp:105:24: required from here
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:184:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
std::memmove(dest_raw, beg_raw, sizeof(value_type)*n);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'value_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} declared here
struct pair
^~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:28,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:32,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp: In instantiation of 'I boost::container::dtl::memmove_n_source(I, std::size_t, F) [with I = boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; std::size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:553:32: required from 'typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type boost::container::uninitialized_copy_alloc_n_source(Allocator&, I, std::size_t, F) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; I = boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; typename boost::container::dtl::enable_if_memtransfer_copy_constructible<I, F, I>::type = boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; std::size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/advanced_insert_int.hpp:81:75: required from 'void boost::container::dtl::insert_range_proxy<Allocator, FwdIt, Iterator>::uninitialized_copy_n_and_update(Allocator&, Iterator, std::size_t) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; FwdIt = boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; Iterator = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; std::size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:1208:4: required from 'void boost::container::uninitialized_move_and_insert_alloc(Allocator&, F, F, F, O, std::size_t, InsertionProxy) [with Allocator = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; F = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; O = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*; InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; std::size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:3008:10: required from 'void boost::container::vector<T, Allocator, Options>::priv_insert_forward_range_new_allocation(T*, boost::container::vector<T, Allocator, Options>::size_type, T*, boost::container::vector<T, Allocator, Options>::size_type, InsertionProxy) [with InsertionProxy = boost::container::dtl::insert_range_proxy<boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, boost::move_iterator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>, boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>; T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long long unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:2610:7: required from 'void boost::container::vector<T, Allocator, Options>::priv_move_to_new_buffer(boost::container::vector<T, Allocator, Options>::size_type, boost::container::version_1) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long long unsigned int; boost::container::version_1 = boost::move_detail::integral_constant<unsigned int, 1>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/vector.hpp:1570:10: required from 'void boost::container::vector<T, Allocator, Options>::reserve(boost::container::vector<T, Allocator, Options>::size_type) [with T = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; A = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; Options = void; boost::container::vector<T, Allocator, Options>::size_type = long long unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:380:4: required from 'void boost::container::dtl::flat_tree_reserve(SequenceContainer&, typename SequenceContainer::size_type, boost::move_detail::true_) [with SequenceContainer = boost::container::vector<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >, boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >, void>; typename SequenceContainer::size_type = long long unsigned int; boost::move_detail::true_ = boost::move_detail::bool_<true>]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:1393:26: required from 'void boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::reserve(boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::size_type) [with Value = boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >; KeyOfValue = boost::container::dtl::select1st<long long unsigned int>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = boost::container::new_allocator<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> > >; boost::container::dtl::flat_tree<Value, KeyOfValue, Compare, AllocatorOrContainer>::size_type = long long unsigned int]'
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:712:9: required from 'void boost::container::flat_map<Key, T, Compare, Allocator>::reserve(boost::container::flat_map<Key, T, Compare, Allocator>::size_type) [with Key = long long unsigned int; T = std::array<int, 16>; Compare = std::less<long long unsigned int>; AllocatorOrContainer = void; boost::container::flat_map<Key, T, Compare, Allocator>::size_type = long long unsigned int]'
rcpp_cx_report.cpp:105:24: required from here
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/copy_move_algo.hpp:214:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
std::memmove(boost::movelib::iterator_to_raw_pointer(r), boost::movelib::iterator_to_raw_pointer(f), sizeof(value_type)*n);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/flat_tree.hpp:29,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/flat_map.hpp:29,
from rcpp_cx_report.cpp:3:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/container/detail/pair.hpp:218:8: note: 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >*>::element_type' {aka 'struct boost::container::dtl::pair<long long unsigned int, std::array<int, 16> >'} declared here
struct pair
^~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_fep.cpp -o rcpp_fep.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_match_target.cpp -o rcpp_match_target.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_read_bam.cpp -o rcpp_read_bam.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++17 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o epialleleR.dll tmp.def RcppExports.o rcpp_char_to_context.o rcpp_cx_report.o rcpp_fep.o rcpp_get_base_freqs.o rcpp_get_xm_beta.o rcpp_match_target.o rcpp_read_bam.o rcpp_threshold_reads.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/epialleleR.buildbin-libdir/epialleleR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'epialleleR' as epialleleR_1.2.0.zip
* DONE (epialleleR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'epialleleR' successfully unpacked and MD5 sums checked
|
epialleleR.Rcheck/tests_i386/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> BiocGenerics:::testPackage("epialleleR")
Reading BED file [0.060s]
Reading BAM file [0.020s]
Computing ECDFs for within- and out-of-context per-read beta values [0.060s]
Reading BED file [0.010s]
Reading BAM file [0.020s]
Computing ECDFs for within- and out-of-context per-read beta values [0.040s]
Reading BED file [0.030s]
Reading BAM file [0.000s]
Preparing amplicon report [0.050s]
Reading BED file [0.040s]
Reading BAM file [0.010s]
Thresholding reads [0.000s]
Preparing amplicon report [0.030s]
Writing the report [0.000s]
Reading BED file [0.030s]
Reading BAM file [0.020s]
Thresholding reads [0.000s]
Preparing amplicon report [0.030s]
Reading BAM file [0.030s]
Thresholding reads [0.000s]
Preparing cytosine report [0.120s]
Reading BAM file [0.040s]
Thresholding reads [0.000s]
Preparing cytosine report [0.140s]
Writing the report [0.000s]
Reading BAM file [0.030s]
Thresholding reads [0.000s]
Preparing cytosine report [0.120s]
Reading BED file [0.020s]
Reading VCF file [0.900s]
Reading BAM file [0.020s]
Extracting base frequences [0.090s]
Reading VCF file [0.290s]
Reading BAM file [0.020s]
Extracting base frequencesAlready preprocessed VCF supplied as an input. Options 'bed' and 'zero.based.bed' will have no effect.
Reading BAM file [0.030s]
Thresholding reads [0.000s]
Extracting base frequences [0.220s]
Writing the report [0.060s]
Reading BED file [0.030s]
Reading VCF file [0.910s]
Reading BAM file [0.010s]
Extracting base frequences [0.110s]
Already preprocessed BAM supplied as an input. Options 'min.mapq', 'min.baseq', 'skip.duplicates' and 'nthreads' will have no effect.
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
RUNIT TEST PROTOCOL -- Tue Apr 12 19:24:26 2022
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
epialleleR RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
20.42 1.59 25.00
|
epialleleR.Rcheck/tests_x64/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> BiocGenerics:::testPackage("epialleleR")
Reading BED file [0.110s]
Reading BAM file [0.000s]
Computing ECDFs for within- and out-of-context per-read beta values [0.080s]
Reading BED file [0.020s]
Reading BAM file [0.010s]
Computing ECDFs for within- and out-of-context per-read beta values [0.030s]
Reading BED file [0.020s]
Reading BAM file [0.010s]
Preparing amplicon report [0.020s]
Reading BED file [0.010s]
Reading BAM file [0.020s]
Thresholding reads [0.000s]
Preparing amplicon report [0.030s]
Writing the report [0.000s]
Reading BED file [0.010s]
Reading BAM file [0.000s]
Thresholding reads [0.000s]
Preparing amplicon report [0.030s]
Reading BAM file [0.030s]
Thresholding reads [0.000s]
Preparing cytosine report [0.070s]
Reading BAM file [0.050s]
Thresholding reads [0.000s]
Preparing cytosine report [0.090s]
Writing the report [0.000s]
Reading BAM file [0.030s]
Thresholding reads [0.000s]
Preparing cytosine report [0.090s]
Reading BED file [0.030s]
Reading VCF file [0.960s]
Reading BAM file [0.010s]
Extracting base frequences [0.130s]
Reading VCF file [0.420s]
Reading BAM file [0.010s]
Extracting base frequencesAlready preprocessed VCF supplied as an input. Options 'bed' and 'zero.based.bed' will have no effect.
Reading BAM file [0.030s]
Thresholding reads [0.000s]
Extracting base frequences [0.160s]
Writing the report [0.010s]
Reading BED file [0.020s]
Reading VCF file [0.750s]
Reading BAM file [0.010s]
Extracting base frequences [0.080s]
Already preprocessed BAM supplied as an input. Options 'min.mapq', 'min.baseq', 'skip.duplicates' and 'nthreads' will have no effect.
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
RUNIT TEST PROTOCOL -- Tue Apr 12 19:24:53 2022
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
epialleleR RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
24.89 1.12 26.45
|
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epialleleR.Rcheck/examples_i386/epialleleR-Ex.timings
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epialleleR.Rcheck/examples_x64/epialleleR-Ex.timings
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