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 15:05:44 -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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MACPET |
| StartedAt: 2021-10-14 06:23:14 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 06:24:18 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 63.9 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MACPET
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘MACPET’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -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::string&, std::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 unsigned int’} and ‘int’ [-Wsign-compare]
55 | 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 unsigned int’} and ‘int’ [-Wsign-compare]
55 | if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
/home/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]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
/home/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]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
/home/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]
465 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
/home/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]
478 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
/home/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]
561 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
/home/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]
570 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
/home/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>&&)’:
/home/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]
572 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | 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]
47 | PeakSummitNew[MergedPeakCount]=PeakSummit_opt;
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o MACPET.so RcppExports.o Stage_0_FastqFilteringSubFunctions.o Stage_3_PeakFinderSubFunctions.o Stage_4_InteractionsSubFunctions.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-MACPET/00new/MACPET/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MACPET)