Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-01-14 13:05:22 -0500 (Fri, 14 Jan 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.2 (2021-11-01) -- "Bird Hippie" | 4327 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.2 (2021-11-01) -- "Bird Hippie" | 4076 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.2 (2021-11-01) -- "Bird Hippie" | 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 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 1029/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MACPET 1.14.0 (landing page) Ioannis Vardaxis
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: 1.14.0 |
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MACPET.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MACPET_1.14.0.tar.gz |
StartedAt: 2022-01-13 08:17:51 -0500 (Thu, 13 Jan 2022) |
EndedAt: 2022-01-13 08:21:52 -0500 (Thu, 13 Jan 2022) |
EllapsedTime: 241.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MACPET.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MACPET.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MACPET_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MACPET.Rcheck’ * using R version 4.1.2 (2021-11-01) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MACPET/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MACPET’ version ‘1.14.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MACPET’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: libs 6.7Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PeaksToGRanges 10.399 3.558 0.137 MACPETUlt 6.339 0.785 10.884 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/MACPET.Rcheck/00check.log’ for details.
MACPET.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL MACPET ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘MACPET’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | 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-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | 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-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | 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-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | 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-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.14-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | 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-3.14-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-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)
MACPET.Rcheck/MACPET-Ex.timings
name | user | system | elapsed | |
AnalysisStatistics | 0.054 | 0.000 | 0.054 | |
ConvertToPE_BAM | 2.255 | 0.080 | 2.334 | |
ConvertToPSelf | 1.070 | 0.009 | 1.078 | |
GetShortestPath | 0.077 | 0.000 | 0.077 | |
GetSignInteractions | 0.109 | 0.000 | 0.109 | |
MACPETUlt | 6.339 | 0.785 | 10.884 | |
PeaksToGRanges | 10.399 | 3.558 | 0.137 | |
PeaksToNarrowPeak | 0.250 | 0.052 | 0.301 | |
TagsToGInteractions | 0.087 | 0.016 | 0.102 | |
exportPeaks | 0.009 | 0.000 | 0.009 | |
plot | 2.472 | 0.436 | 2.909 | |
summary | 0.437 | 0.000 | 0.437 | |