Ioannis Vardaxis
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/MACPET |
| git_branch: RELEASE_3_13 |
| git_last_commit: 2e34842 |
| git_last_commit_date: 2021-05-19 12:33:30 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:10 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the MACPET package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MACPET.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1016/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MACPET 1.12.0 (landing page) Ioannis Vardaxis
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MACPET |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MACPET.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MACPET_1.12.0.tar.gz |
| StartedAt: 2021-10-15 01:16:32 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:23:14 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 402.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MACPET.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MACPET.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MACPET_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MACPET.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MACPET/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MACPET' version '1.12.0'
* 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 'MACPET' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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-3.13-bioc/R/library/MACPET/libs/i386/MACPET.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/MACPET/libs/x64/MACPET.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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
MACPETUlt 6.81 0.43 27.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MACPETUlt 6.42 0.2 25.56
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/MACPET.Rcheck/00check.log'
for details.
MACPET.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MACPET_1.12.0.tar.gz && rm -rf MACPET.buildbin-libdir && mkdir MACPET.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MACPET.buildbin-libdir MACPET_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MACPET_1.12.0.zip && rm MACPET_1.12.0.tar.gz MACPET_1.12.0.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
100 851k 100 851k 0 0 2245k 0 --:--:-- --:--:-- --:--:-- 2252k
install for i386
* installing *source* package 'MACPET' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Stage_0_FastqFilteringSubFunctions.cpp -o Stage_0_FastqFilteringSubFunctions.o
Stage_0_FastqFilteringSubFunctions.cpp: In function 'SEXPREC* FilterFastqYield_fun_Rcpp(int&, std::vector<std::__cxx11::basic_string<char> >&, Rcpp::NumericVector&, std::vector<std::__cxx11::basic_string<char> >&, Rcpp::NumericVector&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&)':
Stage_0_FastqFilteringSubFunctions.cpp:55:36: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
~~~~~~~~~~~~~~~~~~~~~~~~^~~~
Stage_0_FastqFilteringSubFunctions.cpp:55:66: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
~~~~~~~~~~~~~~~~~~~~~~~~^~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:187,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_3_PeakFinderSubFunctions.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h: In function 'Rcpp::List PrepLocFit_Rcpp(Rcpp::DataFrame&, const DataFrame&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:442:13: warning: 'ChromSize' may be used uninitialized in this function [-Wmaybe-uninitialized]
r_vector_start<RTYPE>(x)[0] = object;
^~~~~~~~~~~~~~
Stage_3_PeakFinderSubFunctions.cpp:61:9: note: 'ChromSize' was declared here
int ChromSize;//initiate to find them.
^~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
Stage_4_InteractionsSubFunctions.cpp: In function 'SEXPREC* Get_NewPeakSummit_fun_Rcpp(const NumericVector&, const NumericVector&, const NumericVector&, const NumericVector&, const int&, const int&)':
Stage_4_InteractionsSubFunctions.cpp:47:39: warning: 'PeakSummit_opt' may be used uninitialized in this function [-Wmaybe-uninitialized]
PeakSummitNew[MergedPeakCount]=PeakSummit_opt;
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o MACPET.dll tmp.def RcppExports.o Stage_0_FastqFilteringSubFunctions.o Stage_3_PeakFinderSubFunctions.o Stage_4_InteractionsSubFunctions.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/MACPET.buildbin-libdir/00LOCK-MACPET/00new/MACPET/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MACPET'
finding HTML links ... done
AnalysisStatistics html
ConvertToPE_BAM html
ConvertToPSelf html
GenomeMap-class html
GetShortestPath html
GetSignInteractions html
MACPET html
finding level-2 HTML links ... done
MACPETUlt html
MACPET_GenomeMapData.rda html
MACPET_pinterData.rda html
MACPET_pintraData.rda html
MACPET_pselfData.rda html
MACPET_psfitData.rda html
PInter-class html
PIntra-class html
PSFit-class html
PSelf-class html
PeaksToGRanges html
PeaksToNarrowPeak html
SampleChIAPETData.bam html
SampleChIAPETDataRead_1.bam html
SampleChIAPETDataRead_2.bam html
TagsToGInteractions html
exportPeaks html
plot html
summary 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 'MACPET' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Stage_0_FastqFilteringSubFunctions.cpp -o Stage_0_FastqFilteringSubFunctions.o
Stage_0_FastqFilteringSubFunctions.cpp: In function 'SEXPREC* FilterFastqYield_fun_Rcpp(int&, std::vector<std::__cxx11::basic_string<char> >&, Rcpp::NumericVector&, std::vector<std::__cxx11::basic_string<char> >&, Rcpp::NumericVector&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&)':
Stage_0_FastqFilteringSubFunctions.cpp:55:36: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
~~~~~~~~~~~~~~~~~~~~~~~~^~~~
Stage_0_FastqFilteringSubFunctions.cpp:55:66: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
~~~~~~~~~~~~~~~~~~~~~~~~^~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:187,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_3_PeakFinderSubFunctions.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h: In function 'Rcpp::List PrepLocFit_Rcpp(Rcpp::DataFrame&, const DataFrame&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:442:13: warning: 'ChromSize' may be used uninitialized in this function [-Wmaybe-uninitialized]
r_vector_start<RTYPE>(x)[0] = object;
^~~~~~~~~~~~~~
Stage_3_PeakFinderSubFunctions.cpp:61:9: note: 'ChromSize' was declared here
int ChromSize;//initiate to find them.
^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
Stage_4_InteractionsSubFunctions.cpp: In function 'SEXPREC* Get_NewPeakSummit_fun_Rcpp(const NumericVector&, const NumericVector&, const NumericVector&, const NumericVector&, const int&, const int&)':
Stage_4_InteractionsSubFunctions.cpp:47:39: warning: 'PeakSummit_opt' may be used uninitialized in this function [-Wmaybe-uninitialized]
PeakSummitNew[MergedPeakCount]=PeakSummit_opt;
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o MACPET.dll tmp.def RcppExports.o Stage_0_FastqFilteringSubFunctions.o Stage_3_PeakFinderSubFunctions.o Stage_4_InteractionsSubFunctions.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/MACPET.buildbin-libdir/MACPET/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MACPET' as MACPET_1.12.0.zip
* DONE (MACPET)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MACPET' successfully unpacked and MD5 sums checked
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MACPET.Rcheck/examples_i386/MACPET-Ex.timings
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MACPET.Rcheck/examples_x64/MACPET-Ex.timings
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