Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:48:43 -0400 (Wed, 17 Oct 2018).
Package 287/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CoGAPS 3.0.2 Elana J. Fertig
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: CoGAPS |
Version: 3.0.2 |
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_3.0.2.tar.gz |
StartedAt: 2018-10-16 20:37:03 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 20:38:57 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 113.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CoGAPS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_3.0.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CoGAPS.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘3.0.2’ * 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 ... 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 ... NOTE GWCoGapsFromCheckpoint: no visible binding for global variable ‘i’ GWCoGapsFromCheckpoint: no visible binding for global variable ‘sampleS’ cellMatchR: no visible binding for global variable ‘cluster.method’ patternMatcher : <anonymous>: no visible binding for global variable ‘Samples’ patternMatcher : <anonymous>: no visible binding for global variable ‘value’ patternMatcher : <anonymous>: no visible binding for global variable ‘BySet’ runFinalPhase: no visible binding for global variable ‘i’ runFinalPhase: no visible binding for global variable ‘sampleS’ runInitialPhase: no visible binding for global variable ‘i’ runInitialPhase: no visible binding for global variable ‘sampleS’ scCoGapsFromCheckpoint: no visible binding for global variable ‘i’ scCoGapsFromCheckpoint: no visible binding for global variable ‘sampleS’ sc_runFinalPhase: no visible binding for global variable ‘i’ sc_runFinalPhase: no visible binding for global variable ‘sampleS’ sc_runInitialPhase: no visible binding for global variable ‘i’ sc_runInitialPhase: no visible binding for global variable ‘sampleS’ Undefined global functions or variables: BySet Samples cluster.method i sampleS value * 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 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 ‘_rand’, possibly from ‘rand’ (C) Found ‘_srand’, possibly from ‘srand’ (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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed plotDiag 53.096 5.329 58.921 * 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-3.7-bioc/meat/CoGAPS.Rcheck/00check.log’ for details.
CoGAPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CoGAPS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘CoGAPS’ ... ** libs clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Algorithms.cpp -o Algorithms.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c AtomicSupport.cpp -o AtomicSupport.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Cogaps.cpp -o Cogaps.o In file included from Cogaps.cpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/posix_time/posix_time.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/posix_time/time_formatters.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/gregorian/gregorian.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/gregorian/gregorian_io.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/date_facet.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/period_parser.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/date_time/string_parse_tree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/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 ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/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 { ^ In file included from Cogaps.cpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/archive/text_oarchive.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/archive/basic_text_oarchive.hpp:29: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/archive/detail/common_oarchive.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/archive/detail/interface_oarchive.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/archive/detail/oserializer.hpp:40: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/serialization/extended_type_info_typeid.hpp:27: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/serialization/static_warning.hpp:67: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/mpl/print.hpp:52:19: warning: in-class initialization of non-static data member is a C++11 extension [-Wc++11-extensions] const int m_x = 1 / (sizeof(T) - sizeof(T)); ^ 2 warnings generated. clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c GibbsSampler.cpp -o GibbsSampler.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Matrix.cpp -o Matrix.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Random.cpp -o Random.o In file included from Random.cpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/distributions/normal.hpp:19: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/erf.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/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 ^ /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/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 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -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 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -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 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_tests/testAlgorithms.cpp -o cpp_tests/testAlgorithms.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_tests/testAtomicSupport.cpp -o cpp_tests/testAtomicSupport.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_tests/testGibbsSampler.cpp -o cpp_tests/testGibbsSampler.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_tests/testMatrix.cpp -o cpp_tests/testMatrix.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_tests/testRandom.cpp -o cpp_tests/testRandom.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_tests/testSerialization.cpp -o cpp_tests/testSerialization.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 Algorithms.o AtomicSupport.o Cogaps.o GibbsSampler.o Matrix.o Random.o RcppExports.o test-runner.o cpp_tests/testAlgorithms.o cpp_tests/testAtomicSupport.o cpp_tests/testGibbsSampler.o cpp_tests/testMatrix.o cpp_tests/testRandom.o cpp_tests/testSerialization.o -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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 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) Loading required package: Rcpp Attaching package: 'CoGAPS' The following object is masked from 'package:stats': residuals > > test_check("CoGAPS") ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ is a Catch v1.10.0 host application. Run with -? for options ------------------------------------------------------------------------------- Test GibbsSampler.h GibbsSampler Statistics ------------------------------------------------------------------------------- cpp_tests/testGibbsSampler.cpp:57 ............................................................................... cpp_tests/testGibbsSampler.cpp:105: FAILED: REQUIRE( sampler.meanChiSq() == Approx(8371.568).epsilon(0.001) ) with expansion: 11813.07031f == Approx( 8371.568 ) =============================================================================== test cases: 7 | 6 passed | 1 failed assertions: 94506 | 94505 passed | 1 failed ══ testthat results ═══════════════════════════════════════════════════════════ OK: 0 SKIPPED: 2 FAILED: 0 > > proc.time() user system elapsed 1.656 0.144 1.790
CoGAPS.Rcheck/CoGAPS-Ex.timings
name | user | system | elapsed | |
CoGAPS | 0.535 | 0.003 | 0.542 | |
GWCoGAPS | 0.267 | 0.177 | 0.300 | |
GWCoGapsFromCheckpoint | 0.680 | 0.448 | 0.643 | |
binaryA | 0.058 | 0.011 | 0.071 | |
calcCoGAPSStat | 0.058 | 0.017 | 0.076 | |
calcGeneGSStat | 0.040 | 0.007 | 0.047 | |
calcZ | 0.005 | 0.002 | 0.007 | |
computeGeneGSProb | 0.101 | 0.016 | 0.117 | |
createGWCoGAPSSets | 0.006 | 0.001 | 0.007 | |
createscCoGAPSSets | 0.006 | 0.001 | 0.007 | |
displayBuildReport | 0.001 | 0.000 | 0.001 | |
gapsMapRun | 0.422 | 0.002 | 0.425 | |
gapsRun | 0.479 | 0.002 | 0.495 | |
plotAtoms | 0.008 | 0.002 | 0.010 | |
plotDiag | 53.096 | 5.329 | 58.921 | |
plotGAPS | 0.015 | 0.006 | 0.022 | |
plotP | 0.006 | 0.001 | 0.008 | |
reconstructGene | 0.008 | 0.003 | 0.011 | |
residuals | 0.033 | 0.003 | 0.037 | |