Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:21:28 -0400 (Tue, 09 Apr 2019).
Package 116/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
BDMMAcorrect 1.1.1 ZHENWEI DAI
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: BDMMAcorrect |
Version: 1.1.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BDMMAcorrect.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BDMMAcorrect_1.1.1.tar.gz |
StartedAt: 2019-04-09 00:05:12 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 00:09:08 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 236.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BDMMAcorrect.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BDMMAcorrect.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BDMMAcorrect_1.1.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BDMMAcorrect.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BDMMAcorrect/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BDMMAcorrect’ version ‘1.1.1’ * package encoding: UTF-8 * checking package namespace information ... NOTE Namespace with empty importFrom: ‘RcppEigen’ * 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 ‘BDMMAcorrect’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘Test.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-3.9-bioc/meat/BDMMAcorrect.Rcheck/00check.log’ for details.
BDMMAcorrect.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BDMMAcorrect ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘BDMMAcorrect’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include" -I/usr/local/include -DARMA_DONT_USE_OPENMP -fPIC -Wall -g -O2 -c MCMC_algorithm.cpp -o MCMC_algorithm.o In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Core:535: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/QR:17: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseQR:35: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:35: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:39: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from MCMC_algorithm.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:40: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ 17 warnings generated. clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include" -I/usr/local/include -DARMA_DONT_USE_OPENMP -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Core:535: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/QR:17: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseQR:35: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:35: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:39: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/RcppEigenForward.h:40: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ 17 warnings generated. clang++ -std=gnu++11 -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 BDMMAcorrect.so MCMC_algorithm.o RcppExports.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 -Wall -g -O2 -msse2 -mfpmath=sse -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-BDMMAcorrect/00new/BDMMAcorrect/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 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 (BDMMAcorrect)
BDMMAcorrect.Rcheck/tests/Test.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" 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. > BiocGenerics:::testPackage("BDMMAcorrect") This is vegan 2.5-4 Attaching package: 'ellipse' The following object is masked from 'package:graphics': pairs Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply, rowsum #################### Start MCMC #################### Iteration = 50 Iteration = 100 Iteration = 150 Iteration = 200 RUNIT TEST PROTOCOL -- Tue Apr 9 00:08:58 2019 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : BDMMAcorrect RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 10.097 0.999 11.052
BDMMAcorrect.Rcheck/BDMMAcorrect-Ex.timings
name | user | system | elapsed | |
BDMMA | 0.006 | 0.005 | 0.011 | |
VBatch | 0.731 | 0.080 | 0.811 | |
fdr_cut | 0.003 | 0.003 | 0.006 | |
trace_plot | 0.003 | 0.002 | 0.005 | |