Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:58:59 -0400 (Wed, 17 Oct 2018).
Package 1387/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
slalom 1.2.0 Davis McCarthy
| 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: slalom |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:slalom.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings slalom_1.2.0.tar.gz |
StartedAt: 2018-10-17 00:08:31 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 00:13:15 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 283.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: slalom.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:slalom.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings slalom_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/slalom.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 ‘slalom/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘slalom’ 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 ‘slalom’ can be installed ... OK * checking installed package size ... NOTE installed size is 22.3Mb sub-directories of 1Mb or more: data 3.5Mb extdata 18.3Mb * 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 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 * 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-3.7-bioc/meat/slalom.Rcheck/00check.log’ for details.
slalom.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL slalom ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘slalom’ ... ** libs clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/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 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c slalom-classes.cpp -o slalom-classes.o In file included from slalom-classes.cpp:20: In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/digamma.hpp:20: 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 { ^ slalom-classes.cpp:223:20: warning: unused variable 'meanerr' [-Wunused-variable] double meanerr = arma::mean(error); ^ slalom-classes.cpp:202:12: warning: unused variable 'meanerr' [-Wunused-variable] double meanerr = arma::mean(error); ^ 3 warnings generated. 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 slalom.so RcppExports.o slalom-classes.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/slalom/libs ** R ** data *** moving datasets to lazyload DB ** 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 (slalom)
slalom.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. > # test package > library(testthat) > library(slalom) > > test_check("slalom") 14 annotated factors retained; 16 annotated factors dropped. 196 genes retained for analysis. 14 annotated factors retained; 16 annotated factors dropped. 196 genes retained for analysis. 14 annotated factors retained; 16 annotated factors dropped. 196 genes retained for analysis. Error in x$.self$finalize() : attempt to apply non-function 14 annotated factors retained; 16 annotated factors dropped. 196 genes retained for analysis. 20 annotated factors retained; 3 annotated factors dropped. 500 genes retained for analysis. iteration 0 Switched off factor 20 Switched off factor 17 Switched off factor 15 iteration 100 Switched off factor 10 Switched off factor 11 iteration 200 iteration 300 iteration 400 iteration 500 Model not converged after 500 iterations. 20 annotated factors retained; 3 annotated factors dropped. 500 genes retained for analysis. pre-training model for faster convergence iteration 0 Model not converged after 50 iterations. iteration 0 Model not converged after 50 iterations. iteration 0 Switched off factor 20 Switched off factor 17 Switched off factor 15 iteration 100 Switched off factor 10 Switched off factor 11 iteration 200 iteration 300 iteration 400 iteration 500 Model not converged after 500 iterations. 20 annotated factors retained; 3 annotated factors dropped. 500 genes retained for analysis. pre-training model for faster convergence iteration 0 Model not converged after 50 iterations. iteration 0 Model not converged after 50 iterations. iteration 0 Switched off factor 20 Switched off factor 17 Switched off factor 15 iteration 100 Switched off factor 10 Switched off factor 11 iteration 200 iteration 300 iteration 400 iteration 500 iteration 600 iteration 700 iteration 800 iteration 900 iteration 1000 iteration 1100 iteration 1200 iteration 1300 iteration 1400 iteration 1500 iteration 1600 iteration 1700 Model converged after 1750 iterations. 20 annotated factors retained; 3 annotated factors dropped. 500 genes retained for analysis. pre-training model for faster convergence iteration 0 Model not converged after 50 iterations. iteration 0 Model not converged after 50 iterations. iteration 0 Switched off factor 20 Switched off factor 10 Switched off factor 17 Switched off factor 16 iteration 100 Switched off factor 15 Switched off factor 11 iteration 200 iteration 300 iteration 400 iteration 500 iteration 600 iteration 700 iteration 800 iteration 900 iteration 1000 iteration 1100 iteration 1200 iteration 1300 iteration 1400 iteration 1500 iteration 1600 iteration 1700 iteration 1800 iteration 1900 iteration 2000 iteration 2100 iteration 2200 iteration 2300 iteration 2400 iteration 2500 iteration 2600 iteration 2700 iteration 2800 Model converged after 2850 iterations. 25 annotated factors retained; 75 annotated factors dropped. 355 genes retained for analysis. pre-training model for faster convergence iteration 0 Model not converged after 50 iterations. iteration 0 Model not converged after 50 iterations. iteration 0 Switched off factor 11 Switched off factor 29 Switched off factor 25 Switched off factor 12 Switched off factor 24 Switched off factor 14 Switched off factor 15 Switched off factor 28 Switched off factor 26 Switched off factor 7 Switched off factor 18 Switched off factor 23 Switched off factor 17 Switched off factor 13 Switched off factor 27 Switched off factor 22 Switched off factor 21 Switched off factor 20 Switched off factor 9 Switched off factor 5 Switched off factor 16 Switched off factor 8 Switched off factor 6 Switched off factor 10 Switched off factor 19 iteration 100 Switched off factor 3 iteration 200 iteration 300 iteration 400 iteration 500 iteration 600 iteration 700 iteration 800 iteration 900 iteration 1000 iteration 1100 iteration 1200 iteration 1300 iteration 1400 iteration 1500 iteration 1600 iteration 1700 Model converged after 1750 iterations. ══ testthat results ═══════════════════════════════════════════════════════════ OK: 38 SKIPPED: 1 FAILED: 0 > > proc.time() user system elapsed 69.038 1.072 70.709
slalom.Rcheck/slalom-Ex.timings
name | user | system | elapsed | |
addResultsToSingleCellExperiment | 3.355 | 0.092 | 3.480 | |
initSlalom | 0.777 | 0.034 | 0.819 | |
newSlalomModel | 0.374 | 0.025 | 0.402 | |
plotLoadings | 3.000 | 0.034 | 3.057 | |
plotRelevance | 3.617 | 0.103 | 3.748 | |
plotTerms | 2.797 | 0.070 | 2.882 | |
topTerms | 3.058 | 0.061 | 3.145 | |
trainSlalom | 2.629 | 0.077 | 2.732 | |
updateSlalom | 0.276 | 0.040 | 0.319 | |