Elana J. Fertig
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CoGAPS |
| Branch: RELEASE_3_8 |
| Last Commit: 0bb2e91 |
| Last Changed Date: 2019-02-23 12:13:39 -0400 (Sat, 23 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:55:17 -0400 (Tue, 16 Apr 2019).
| Package 304/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CoGAPS 3.2.40 Elana J. Fertig
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CoGAPS |
| Version: 3.2.40 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CoGAPS_3.2.40.tar.gz |
| StartedAt: 2019-04-15 23:08:52 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:12:23 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 210.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CoGAPS.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CoGAPS_3.2.40.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CoGAPS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘3.2.40’
* 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 20.9Mb
sub-directories of 1Mb or more:
extdata 19.6Mb
* 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 ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/CoGAPS/libs/CoGAPS.so’:
Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_printf’, possibly from ‘printf’ (C)
Found ‘_putchar’, possibly from ‘putchar’ (C)
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (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
‘/Users/biocbuild/bbs-3.8-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.
CoGAPS.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CoGAPS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CoGAPS’ ...
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 clang++ accepts -g... yes
checking how to run the C++ preprocessor... clang++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether clang++ accepts -g... (cached) yes
checking for C++ compiler vendor... clang
checking for a sed that does not truncate output... /usr/bin/sed
checking for C++ compiler version... 4.0.0
checking for OpenMP flag of C++ compiler... unknown
building on clang compiler version 4.0.0
Using AVX instructions if available
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c Cogaps.cpp -o Cogaps.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c GapsParameters.cpp -o GapsParameters.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c GapsResult.cpp -o GapsResult.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsRunner.cpp:17:
In file included from include/boost/date_time/posix_time/posix_time.hpp:24:
In file included from include/boost/date_time/posix_time/time_formatters.hpp:12:
In file included from include/boost/date_time/gregorian/gregorian.hpp:31:
In file included from include/boost/date_time/gregorian/gregorian_io.hpp:16:
In file included from include/boost/date_time/date_facet.hpp:23:
In file included from include/boost/date_time/period_parser.hpp:14:
In file included from include/boost/date_time/string_parse_tree.hpp:13:
In file included from include/boost/lexical_cast.hpp:32:
In file included from include/boost/lexical_cast/try_lexical_convert.hpp:42:
In file included from include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from include/boost/container/container_fwd.hpp:61:
include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
#define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c GapsStatistics.cpp -o GapsStatistics.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c test-runner.cpp -o test-runner.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/HashSets.cpp -o data_structures/HashSets.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/Matrix.cpp -o data_structures/Matrix.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/Vector.cpp -o data_structures/Vector.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c file_parser/CsvParser.cpp -o file_parser/CsvParser.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c file_parser/FileParser.cpp -o file_parser/FileParser.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c file_parser/GctParser.cpp -o file_parser/GctParser.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c file_parser/TsvParser.cpp -o file_parser/TsvParser.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c gibbs_sampler/DenseStoragePolicy.cpp -o gibbs_sampler/DenseStoragePolicy.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c gibbs_sampler/SparseStoragePolicy.cpp -o gibbs_sampler/SparseStoragePolicy.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c math/Math.cpp -o math/Math.o
In file included from math/Math.cpp:4:
In file included from include/boost/math/distributions/exponential.hpp:10:
In file included from include/boost/math/constants/constants.hpp:13:
In file included from include/boost/math/tools/convert_from_string.hpp:15:
In file included from include/boost/lexical_cast.hpp:32:
In file included from include/boost/lexical_cast/try_lexical_convert.hpp:42:
In file included from include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from include/boost/container/container_fwd.hpp:61:
include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
#define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c math/MatrixMath.cpp -o math/MatrixMath.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c math/Random.cpp -o math/Random.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c math/VectorMath.cpp -o math/VectorMath.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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
* DONE (CoGAPS)
CoGAPS.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
[1] 0
This is CoGAPS version 3.2.40
Running genome-wide CoGAPS on 1363 genes and 9 samples
worker 1 is starting!
worker 2 is starting!
worker 1 is finished! Time: 00:00:00
worker 3 is starting!
worker 2 is finished! Time: 00:00:00
worker 4 is starting!
worker 3 is finished! Time: 00:00:00
worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 9 genes and 1363 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 9 genes and 1363 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 9 genes and 1363 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 9 genes and 1363 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 9 genes and 1363 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 9 genes and 1363 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
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 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 3.2.40
Running genome-wide CoGAPS on 1363 genes and 9 samples
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This is CoGAPS version 3.2.40
Running single-cell CoGAPS on 9 genes and 1363 samples
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This is CoGAPS version 3.2.40
Running single-cell CoGAPS on 9 genes and 1363 samples
worker 1 is starting!
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This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
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 3 is finished! Time: 00:00:00
worker 4 is finished! Time: 00:00:00
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worker 1 is starting!
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worker 4 is starting!
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 3.2.40
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!
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 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
Running Standard CoGAPS on 1363 genes and 9 samples
This is CoGAPS version 3.2.40
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 3.2.40
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)
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worker 5 is starting!
-- Calibration Phase --
-- Sampling Phase --
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worker 5 is finished! Time: 00:00:00
worker 2 is finished! Time: 00:00:00
worker 4 is starting!
worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.2.40
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 5 is starting!
-- Calibration Phase --
-- Sampling Phase --
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══ testthat results ═══════════════════════════════════════════════════════════
OK: 71 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
43.109 18.137 27.883
CoGAPS.Rcheck/CoGAPS-Ex.timings
| name | user | system | elapsed | |
| CoGAPS | 1.066 | 0.755 | 0.547 | |
| CogapsParams | 0.003 | 0.000 | 0.004 | |
| GWCoGAPS | 0.000 | 0.001 | 0.000 | |
| binaryA-methods | 0.034 | 0.006 | 0.043 | |
| buildReport | 0.000 | 0.000 | 0.001 | |
| calcZ-methods | 0.033 | 0.006 | 0.041 | |
| checkpointsEnabled | 0 | 0 | 0 | |
| getClusteredPatterns-methods | 0.027 | 0.006 | 0.033 | |
| getCorrelationToMeanPattern-methods | 0.029 | 0.007 | 0.036 | |
| getFeatureLoadings-methods | 0.065 | 0.026 | 0.096 | |
| getMeanChiSq-methods | 0.031 | 0.007 | 0.039 | |
| getOriginalParameters-methods | 0.032 | 0.007 | 0.038 | |
| getParam-methods | 0.001 | 0.000 | 0.002 | |
| getRetinaSubset | 2.963 | 1.142 | 4.137 | |
| getSampleFactors-methods | 0.030 | 0.005 | 0.035 | |
| getSubsets-methods | 0.030 | 0.005 | 0.035 | |
| getUnmatchedPatterns-methods | 0.027 | 0.004 | 0.031 | |
| getVersion-methods | 0.031 | 0.004 | 0.034 | |
| plotResiduals-methods | 0.032 | 0.006 | 0.038 | |
| reconstructGene-methods | 0.029 | 0.005 | 0.033 | |
| scCoGAPS | 0 | 0 | 0 | |
| setAnnotationWeights-methods | 0.002 | 0.000 | 0.003 | |
| setDistributedParams-methods | 0.003 | 0.000 | 0.003 | |
| setFixedPatterns-methods | 0.034 | 0.006 | 0.039 | |
| setParam-methods | 0.002 | 0.000 | 0.002 | |