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CHECK report for CoGAPS on malbec2

This page was generated on 2019-10-16 11:58:41 -0400 (Wed, 16 Oct 2019).

Package 320/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 3.4.1
Elana J. Fertig
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CoGAPS
Branch: RELEASE_3_9
Last Commit: 01d5480
Last Changed Date: 2019-06-26 14:45:46 -0400 (Wed, 26 Jun 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CoGAPS
Version: 3.4.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CoGAPS_3.4.1.tar.gz
StartedAt: 2019-10-16 00:41:30 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:46:34 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 304.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CoGAPS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CoGAPS_3.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CoGAPS.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘3.4.1’
* 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 ‘CoGAPS’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 27.7Mb
  sub-directories of 1Mb or more:
    extdata  19.6Mb
    libs      7.4Mb
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/CoGAPS/libs/CoGAPS.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.

Installation output

CoGAPS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CoGAPS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘CoGAPS’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++11 accepts -g... (cached) yes
checking for C++ compiler vendor... gnu
checking for a sed that does not truncate output... /bin/sed
checking for C++ compiler version... 7.4.0
checking for OpenMP flag of C++ compiler... -fopenmp
building on gnu compiler version 7.4.0
Using AVX instructions if available
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c Cogaps.cpp -o Cogaps.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c GapsParameters.cpp -o GapsParameters.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c GapsResult.cpp -o GapsResult.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c GapsRunner.cpp -o GapsRunner.o
In file included from include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from include/boost/shared_ptr.hpp:17,
                 from include/boost/date_time/gregorian/greg_month.hpp:14,
                 from include/boost/date_time/gregorian/greg_ymd.hpp:16,
                 from include/boost/date_time/gregorian/greg_calendar.hpp:17,
                 from include/boost/date_time/gregorian/gregorian_types.hpp:19,
                 from include/boost/date_time/posix_time/posix_time_config.hpp:18,
                 from include/boost/date_time/posix_time/posix_time_system.hpp:13,
                 from include/boost/date_time/posix_time/ptime.hpp:12,
                 from include/boost/date_time/posix_time/posix_time.hpp:15,
                 from GapsRunner.cpp:17:
include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from data_structures/../utils/GapsAssert.h:7,
                 from data_structures/../utils/Archive.h:4,
                 from data_structures/Matrix.h:4,
                 from GapsParameters.h:4,
                 from GapsStatistics.h:4,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from include/boost/shared_ptr.hpp:17:0,
                 from include/boost/date_time/gregorian/greg_month.hpp:14,
                 from include/boost/date_time/gregorian/greg_ymd.hpp:16,
                 from include/boost/date_time/gregorian/greg_calendar.hpp:17,
                 from include/boost/date_time/gregorian/gregorian_types.hpp:19,
                 from include/boost/date_time/posix_time/posix_time_config.hpp:18,
                 from include/boost/date_time/posix_time/posix_time_system.hpp:13,
                 from include/boost/date_time/posix_time/ptime.hpp:12,
                 from include/boost/date_time/posix_time/posix_time.hpp:15,
                 from GapsRunner.cpp:17:
include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template 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++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from data_structures/../utils/GapsAssert.h:7,
                 from data_structures/../utils/Archive.h:4,
                 from data_structures/Matrix.h:4,
                 from GapsParameters.h:4,
                 from GapsStatistics.h:4,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from include/boost/shared_ptr.hpp:17:0,
                 from include/boost/date_time/gregorian/greg_month.hpp:14,
                 from include/boost/date_time/gregorian/greg_ymd.hpp:16,
                 from include/boost/date_time/gregorian/greg_calendar.hpp:17,
                 from include/boost/date_time/gregorian/gregorian_types.hpp:19,
                 from include/boost/date_time/posix_time/posix_time_config.hpp:18,
                 from include/boost/date_time/posix_time/posix_time_system.hpp:13,
                 from include/boost/date_time/posix_time/ptime.hpp:12,
                 from include/boost/date_time/posix_time/posix_time.hpp:15,
                 from GapsRunner.cpp:17:
include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from data_structures/../utils/GapsAssert.h:7,
                 from data_structures/../utils/Archive.h:4,
                 from data_structures/Matrix.h:4,
                 from GapsParameters.h:4,
                 from GapsStatistics.h:4,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from include/boost/shared_ptr.hpp:17:0,
                 from include/boost/date_time/gregorian/greg_month.hpp:14,
                 from include/boost/date_time/gregorian/greg_ymd.hpp:16,
                 from include/boost/date_time/gregorian/greg_calendar.hpp:17,
                 from include/boost/date_time/gregorian/gregorian_types.hpp:19,
                 from include/boost/date_time/posix_time/posix_time_config.hpp:18,
                 from include/boost/date_time/posix_time/posix_time_system.hpp:13,
                 from include/boost/date_time/posix_time/ptime.hpp:12,
                 from include/boost/date_time/posix_time/posix_time.hpp:15,
                 from GapsRunner.cpp:17:
include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from data_structures/../utils/GapsAssert.h:7,
                 from data_structures/../utils/Archive.h:4,
                 from data_structures/Matrix.h:4,
                 from GapsParameters.h:4,
                 from GapsStatistics.h:4,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from include/boost/shared_ptr.hpp:17:0,
                 from include/boost/date_time/gregorian/greg_month.hpp:14,
                 from include/boost/date_time/gregorian/greg_ymd.hpp:16,
                 from include/boost/date_time/gregorian/greg_calendar.hpp:17,
                 from include/boost/date_time/gregorian/gregorian_types.hpp:19,
                 from include/boost/date_time/posix_time/posix_time_config.hpp:18,
                 from include/boost/date_time/posix_time/posix_time_system.hpp:13,
                 from include/boost/date_time/posix_time/ptime.hpp:12,
                 from include/boost/date_time/posix_time/posix_time.hpp:15,
                 from GapsRunner.cpp:17:
include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from data_structures/../utils/GapsAssert.h:7,
                 from data_structures/../utils/Archive.h:4,
                 from data_structures/Matrix.h:4,
                 from GapsParameters.h:4,
                 from GapsStatistics.h:4,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from include/boost/shared_ptr.hpp:17:0,
                 from include/boost/date_time/gregorian/greg_month.hpp:14,
                 from include/boost/date_time/gregorian/greg_ymd.hpp:16,
                 from include/boost/date_time/gregorian/greg_calendar.hpp:17,
                 from include/boost/date_time/gregorian/gregorian_types.hpp:19,
                 from include/boost/date_time/posix_time/posix_time_config.hpp:18,
                 from include/boost/date_time/posix_time/posix_time_system.hpp:13,
                 from include/boost/date_time/posix_time/ptime.hpp:12,
                 from include/boost/date_time/posix_time/posix_time.hpp:15,
                 from GapsRunner.cpp:17:
include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from data_structures/../utils/GapsAssert.h:7,
                 from data_structures/../utils/Archive.h:4,
                 from data_structures/Matrix.h:4,
                 from GapsParameters.h:4,
                 from GapsStatistics.h:4,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from include/boost/shared_ptr.hpp:17:0,
                 from include/boost/date_time/gregorian/greg_month.hpp:14,
                 from include/boost/date_time/gregorian/greg_ymd.hpp:16,
                 from include/boost/date_time/gregorian/greg_calendar.hpp:17,
                 from include/boost/date_time/gregorian/gregorian_types.hpp:19,
                 from include/boost/date_time/posix_time/posix_time_config.hpp:18,
                 from include/boost/date_time/posix_time/posix_time_system.hpp:13,
                 from include/boost/date_time/posix_time/ptime.hpp:12,
                 from include/boost/date_time/posix_time/posix_time.hpp:15,
                 from GapsRunner.cpp:17:
include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from data_structures/../utils/GapsAssert.h:7,
                 from data_structures/../utils/Archive.h:4,
                 from data_structures/Matrix.h:4,
                 from GapsParameters.h:4,
                 from GapsStatistics.h:4,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c GapsStatistics.cpp -o GapsStatistics.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c data_structures/HashSets.cpp -o data_structures/HashSets.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c data_structures/Matrix.cpp -o data_structures/Matrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c data_structures/Vector.cpp -o data_structures/Vector.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c file_parser/CsvParser.cpp -o file_parser/CsvParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c file_parser/FileParser.cpp -o file_parser/FileParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c file_parser/GctParser.cpp -o file_parser/GctParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c file_parser/TsvParser.cpp -o file_parser/TsvParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c gibbs_sampler/DenseStoragePolicy.cpp -o gibbs_sampler/DenseStoragePolicy.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c gibbs_sampler/SparseStoragePolicy.cpp -o gibbs_sampler/SparseStoragePolicy.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c math/Math.cpp -o math/Math.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c math/MatrixMath.cpp -o math/MatrixMath.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c math/Random.cpp -o math/Random.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c math/VectorMath.cpp -o math/VectorMath.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o CoGAPS.so Cogaps.o GapsParameters.o GapsResult.o GapsRunner.o GapsStatistics.o RcppExports.o test-runner.o atomic/AtomicDomain.o atomic/ProposalQueue.o data_structures/HashSets.o data_structures/HybridMatrix.o data_structures/HybridVector.o data_structures/Matrix.o data_structures/SparseIterator.o data_structures/SparseMatrix.o data_structures/SparseVector.o data_structures/Vector.o file_parser/CsvParser.o file_parser/FileParser.o file_parser/GctParser.o file_parser/TsvParser.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseStoragePolicy.o gibbs_sampler/SparseStoragePolicy.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.o -fopenmp /home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-CoGAPS/00new/CoGAPS/libs
** R
** data
** 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 (CoGAPS)

Tests output

CoGAPS.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> library(testthat)
> library(CoGAPS)
> 
> test_check("CoGAPS")

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples
[1] 0

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 3 is starting!
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    worker 4 is starting!
    worker 2 is finished! Time: 00:00:00
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    worker 2 is finished! Time: 00:00:00
    worker 1 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 4 is starting!
    worker 1 is finished! Time: 00:00:00
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    worker 1 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running single-cell CoGAPS on 9 genes and 1363 samples
    worker 1 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 4 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 4 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running single-cell CoGAPS on 9 genes and 1363 samples
    worker 1 is starting!
    worker 3 is starting!
    worker 4 is starting!
    worker 2 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 1 is starting!
    worker 3 is starting!
    worker 4 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 1 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 4 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 4 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 4 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 1 is starting!
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    worker 4 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples with parameters:

-- Standard Parameters --
nPatterns            3 
nIterations          175 
seed                 42 
singleCell           TRUE 
sparseOptimization   TRUE 
distributed          genome-wide 

-- Sparsity Parameters --
alpha          0.01 
maxGibbsMass   100 

-- Distributed CoGAPS Parameters -- 
nSets          5 
cut            4 
minNS          3 
maxNS          8 

Creating subsets...using provided indexed subsets
set sizes (min, mean, max): (200, 200, 200)
Running Final Stage...

Loading Data...Done! (00:00:00)
    worker 1 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 4 is starting!
    worker 5 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    worker 5 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples with parameters:

-- Standard Parameters --
nPatterns            3 
nIterations          175 
seed                 42 
singleCell           TRUE 
sparseOptimization   TRUE 
distributed          genome-wide 

-- Sparsity Parameters --
alpha          0.01 
maxGibbsMass   100 

-- Distributed CoGAPS Parameters -- 
nSets          5 
cut            4 
minNS          3 
maxNS          8 

Creating subsets...using provided indexed subsets
set sizes (min, mean, max): (200, 200, 200)
Running Final Stage...

Loading Data...Done! (00:00:00)
    worker 1 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 4 is starting!
    worker 5 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    worker 5 is finished! Time: 00:00:00
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 75 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
561.515   6.998 136.872

Example timings

CoGAPS.Rcheck/CoGAPS-Ex.timings

nameusersystemelapsed
CoGAPS1.0860.0200.555
CogapsParams0.0030.0000.003
GWCoGAPS0.0000.0000.001
binaryA-methods0.0330.0000.034
buildReport0.0010.0000.000
calcZ-methods0.0340.0000.034
checkpointsEnabled000
getClusteredPatterns-methods0.0350.0000.035
getCorrelationToMeanPattern-methods0.0310.0040.034
getFeatureLoadings-methods0.0500.0120.062
getMeanChiSq-methods0.0340.0000.034
getOriginalParameters-methods0.0260.0080.034
getParam-methods0.0010.0000.001
getRetinaSubset1.3600.2401.726
getSampleFactors-methods0.0290.0040.033
getSubsets-methods0.0300.0040.034
getUnmatchedPatterns-methods0.0330.0000.034
getVersion-methods0.0310.0040.034
plotResiduals-methods0.0330.0000.033
reconstructGene-methods0.0330.0000.033
scCoGAPS000
setAnnotationWeights-methods0.0020.0000.002
setDistributedParams-methods0.0020.0000.002
setFixedPatterns-methods0.0350.0000.036
setParam-methods0.0020.0000.001