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CHECK report for MACPET on malbec1

This page was generated on 2019-03-15 11:17:55 -0400 (Fri, 15 Mar 2019).

Package 863/1649HostnameOS / ArchINSTALLBUILDCHECK
MACPET 1.2.0
Ioannis Vardaxis
Snapshot Date: 2019-03-14 17:00:06 -0400 (Thu, 14 Mar 2019)
URL: https://git.bioconductor.org/packages/MACPET
Branch: RELEASE_3_8
Last Commit: 7c55f69
Last Changed Date: 2018-10-30 11:42:08 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MACPET
Version: 1.2.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MACPET.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MACPET_1.2.0.tar.gz
StartedAt: 2019-03-15 01:38:32 -0400 (Fri, 15 Mar 2019)
EndedAt: 2019-03-15 01:43:14 -0400 (Fri, 15 Mar 2019)
EllapsedTime: 282.1 seconds
RetCode: 0
Status:  OK 
CheckDir: MACPET.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MACPET.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MACPET_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/MACPET.Rcheck’
* using R version 3.5.2 (2018-12-20)
* 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 ‘1.2.0’
* 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 for sufficient/correct file permissions ... 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
* 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 or elapsed time > 5s
           user system elapsed
MACPETUlt 6.424  0.768   9.285
plot      5.740  0.020   5.791
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/MACPET.Rcheck/00check.log’
for details.

Installation output

MACPET.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL MACPET
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘MACPET’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include" -I"/home/biocbuild/bbs-3.8-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::__cxx11::string&, std::__cxx11::string&, int&, int&, int&)’:
Stage_0_FastqFilteringSubFunctions.cpp:55:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
                                    ^
Stage_0_FastqFilteringSubFunctions.cpp:55:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
                                                                  ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:187:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_3_PeakFinderSubFunctions.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h: In function ‘Rcpp::List PrepLocFit_Rcpp(Rcpp::DataFrame&, const DataFrame&)’:
/home/biocbuild/bbs-3.8-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.
         ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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 /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: 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:47:54: warning: ‘PeakSummit_opt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         PeakSummitNew[MergedPeakCount]=PeakSummit_opt;
                                                      ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-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-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (MACPET)

Tests output

Example timings

MACPET.Rcheck/MACPET-Ex.timings

nameusersystemelapsed
AnalysisStatistics0.2080.0040.393
ConvertToPE_BAM3.3720.0723.575
ConvertToPSelf0.2480.0320.295
GetShortestPath0.1040.0040.110
GetSignInteractions0.0680.0120.077
MACPETUlt6.4240.7689.285
PeaksToGRanges2.7400.7000.069
PeaksToNarrowPeak0.1400.0000.139
TagsToGInteractions0.0880.0040.090
exportPeaks0.0120.0000.011
plot5.7400.0205.791
summary0.7680.0000.789