Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2021-12-13 13:06:03 -0500 (Mon, 13 Dec 2021).
To the developers/maintainers of the networkBMA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/networkBMA.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1292/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
networkBMA 2.34.0 (landing page) Ka Yee Yeung
| nebbiolo2 | Linux (Ubuntu 20.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: networkBMA |
Version: 2.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:networkBMA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings networkBMA_2.34.0.tar.gz |
StartedAt: 2021-12-12 17:07:30 -0500 (Sun, 12 Dec 2021) |
EndedAt: 2021-12-12 17:09:16 -0500 (Sun, 12 Dec 2021) |
EllapsedTime: 106.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: networkBMA.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:networkBMA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings networkBMA_2.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/networkBMA.Rcheck’ * using R version 4.1.2 (2021-11-01) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘networkBMA/DESCRIPTION’ ... OK * this is package ‘networkBMA’ version ‘2.34.0’ * 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 ‘networkBMA’ can be installed ... WARNING Found the following significant warnings: ./fastBMA.hpp:662:45: warning: field 'nModels' will be initialized after field 'hashValue' [-Wreorder] Found the following additional notes/warnings: ./fastBMA.hpp:282:2: warning: control may reach end of non-void function [-Wreturn-type] See ‘/Users/biocbuild/bbs-3.14-bioc/meat/networkBMA.Rcheck/00install.out’ for details. * 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 ... NOTE Found the following apparent S3 methods exported but not registered: summary.networkBMA See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * 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 ... NOTE Package has both ‘src/Makevars.in’ and ‘src/Makevars’. Installation with --no-configure' is unlikely to work. If you intended ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ‘cleanup’ script. * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... NOTE PKG_CFLAGS set in ‘src/Makevars’ without any corresponding files PKG_CFLAGS set in ‘src/Makevars.in’ without any corresponding files PKG_CFLAGS set in ‘src/Makevars.win’ without any corresponding files * checking compiled code ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ScanBMAcontrol 6.723 0.078 6.807 gControl 6.748 0.035 6.789 * 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: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/networkBMA.Rcheck/00check.log’ for details.
networkBMA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL networkBMA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘networkBMA’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MurmurHash3.cpp -o MurmurHash3.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:35: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:39: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:40: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ 18 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ScanBMA_full.cpp -o ScanBMA_full.o In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:35: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:39: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from ScanBMA_full.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/RcppEigenForward.h:40: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ 18 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I./include -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fastBMAR.cpp -o fastBMAR.o In file included from fastBMAR.cpp:3: ./fastBMA.hpp:123:30: warning: operator '>>' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses] return (array[index/8] >> 7-(index & 0x7)) & 0x1; ~~ ~^~~~~~~~~~~~~~ ./fastBMA.hpp:123:30: note: place parentheses around the '-' expression to silence this warning return (array[index/8] >> 7-(index & 0x7)) & 0x1; ^ ( ) ./fastBMA.hpp:126:44: warning: operator '<<' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses] array[index/8] = array[index/8] | 1 << 7-(index & 0x7); ~~ ~^~~~~~~~~~~~~~ ./fastBMA.hpp:126:44: note: place parentheses around the '-' expression to silence this warning array[index/8] = array[index/8] | 1 << 7-(index & 0x7); ^ ( ) ./fastBMA.hpp:187:62: warning: operator '<<' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses] retValue |= ((uint64_t) array[i]) << elementSize-bitsRead-tBits; ~~ ~~~~~~~~~~~~~~~~~~~~^~~~~~ ./fastBMA.hpp:187:62: note: place parentheses around the '-' expression to silence this warning retValue |= ((uint64_t) array[i]) << elementSize-bitsRead-tBits; ^ ( ) ./fastBMA.hpp:225:77: warning: operator '>>' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses] array[startIndex]=(array[startIndex] & mask) | (T)(value >> elementSize - (tBits-bitOffset)); ~~ ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ./fastBMA.hpp:225:77: note: place parentheses around the '-' expression to silence this warning array[startIndex]=(array[startIndex] & mask) | (T)(value >> elementSize - (tBits-bitOffset)); ^ ( ) ./fastBMA.hpp:229:51: warning: operator '>>' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses] array[i]=(T) (value >> elementSize-bitsWritten-tBits); ~~ ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ ./fastBMA.hpp:229:51: note: place parentheses around the '-' expression to silence this warning array[i]=(T) (value >> elementSize-bitsWritten-tBits); ^ ( ) ./fastBMA.hpp:235:29: warning: operator '>>' has lower precedence than '-'; '-' will be evaluated first [-Wshift-op-parentheses] mask= ones >> elementSize-bitsWritten; ~~ ~~~~~~~~~~~^~~~~~~~~~~~ ./fastBMA.hpp:235:29: note: place parentheses around the '-' expression to silence this warning mask= ones >> elementSize-bitsWritten; ^ ( ) ./fastBMA.hpp:395:12: warning: unused variable 'n' [-Wunused-variable] const int n=size*(size+1)/2; ^ ./fastBMA.hpp:625:12: warning: unused variable 'modelBits' [-Wunused-variable] uint8_t modelBits=gModelBits; ^ ./fastBMA.hpp:626:12: warning: unused variable 'nModels' [-Wunused-variable] uint8_t nModels=0; ^ ./fastBMA.hpp:721:18: warning: '&' within '|' [-Wbitwise-op-parentheses] return(hash & 0xFFFFFFF0 | size); ~~~~~^~~~~~~~~~~~ ~ ./fastBMA.hpp:721:18: note: place parentheses around the '&' expression to silence this warning return(hash & 0xFFFFFFF0 | size); ^ ( ) ./fastBMA.hpp:723:24: warning: '&' within '|' [-Wbitwise-op-parentheses] return(k.hashValue & 0xFFFFFFF0 | size); ~~~~~~~~~~~~^~~~~~~~~~~~ ~ ./fastBMA.hpp:723:24: note: place parentheses around the '&' expression to silence this warning return(k.hashValue & 0xFFFFFFF0 | size); ^ ( ) ./fastBMA.hpp:762:24: warning: '&' within '|' [-Wbitwise-op-parentheses] return(k.hashValue & 0xFFFFFFF0 | size); ~~~~~~~~~~~~^~~~~~~~~~~~ ~ ./fastBMA.hpp:762:24: note: place parentheses around the '&' expression to silence this warning return(k.hashValue & 0xFFFFFFF0 | size); ^ ( ) ./fastBMA.hpp:1406:10: warning: unused variable 'g0' [-Wunused-variable] double g0=g; ^ ./fastBMA.hpp:1401:6: warning: unused variable 'nIterations' [-Wunused-variable] int nIterations=0; ^ ./fastBMA.hpp:1402:7: warning: unused variable 'doneOptimizing' [-Wunused-variable] bool doneOptimizing=0; ^ ./fastBMA.hpp:1922:14: warning: unused variable 'izero' [-Wunused-variable] int ione=1,izero=0; ^ fastBMAR.cpp:33:7: warning: unused variable 'colNum' [-Wunused-variable] int colNum = x.ncol(); ^ In file included from fastBMAR.cpp:3: ./fastBMA.hpp:1701:7: warning: expression result unused [-Wunused-value] *dest++; ^~~~~~~ ./bmaNoMPI.hpp:102:2: note: in instantiation of function template specialization 'initRegressParms<double>' requested here initRegressParms<T>(A,ATA,data,nGenes,nRows,nSamples,nTimes,nVars,nThreads,timeSeries); ^ fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here findEdges( ^ In file included from fastBMAR.cpp:3: ./fastBMA.hpp:1408:10: warning: unused variable 'r2' [-Wunused-variable] Result r2 = boost::math::tools::brent_find_minima(BMAoptimizeFunction<T>(ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR), (T) 1, (T)nRows, optimizeBits, max_iter); ^ ./fastBMA.hpp:1757:13: note: in instantiation of function template specialization 'fastScanBMA_g<double>' requested here int nEdges=fastScanBMA_g(ATA,ATb,btb,sst,ignoreIndex,priors,rankOnly,postProbs,parents,nRows, nGenes,nVars, twoLogOR,g,optimizeBits,maxOptimizeCycles); ^ ./bmaNoMPI.hpp:127:14: note: in instantiation of function template specialization 'findRegulators<double>' requested here int nEdges=findRegulators(g,optimizeBits,maxOptimizeCycles,uniform_prob,twoLogOR,nVars,nThreads,rankOnly,evalSubset[k],data,rProbs,parentsSlice[th] ,weightsSlice[th],A,ATA, Aldr,ATAldr, nGenes,nRows,nSamples,nTimes); ^ fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here findEdges( ^ In file included from fastBMAR.cpp:3: ./fastBMA.hpp:1661:5: warning: unused variable 'rvalue' [-Wunused-variable] T rvalue=0; ^ ./fastBMA.hpp:1414:3: note: in instantiation of function template specialization 'chooseBestModels<double>' requested here chooseBestModels(g,ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR); ^ ./fastBMA.hpp:1757:13: note: in instantiation of function template specialization 'fastScanBMA_g<double>' requested here int nEdges=fastScanBMA_g(ATA,ATb,btb,sst,ignoreIndex,priors,rankOnly,postProbs,parents,nRows, nGenes,nVars, twoLogOR,g,optimizeBits,maxOptimizeCycles); ^ ./bmaNoMPI.hpp:127:14: note: in instantiation of function template specialization 'findRegulators<double>' requested here int nEdges=findRegulators(g,optimizeBits,maxOptimizeCycles,uniform_prob,twoLogOR,nVars,nThreads,rankOnly,evalSubset[k],data,rProbs,parentsSlice[th] ,weightsSlice[th],A,ATA, Aldr,ATAldr, nGenes,nRows,nSamples,nTimes); ^ fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here findEdges( ^ In file included from fastBMAR.cpp:3: ./fastBMA.hpp:662:45: warning: field 'nModels' will be initialized after field 'hashValue' [-Wreorder] CompactModelIndices( ModelIndices &mind): nModels(mind.nModels),hashValue(mind.hashValue){ ^ ./fastBMA.hpp:782:17: note: in instantiation of member function 'CompactModelIndices<unsigned long long>::CompactModelIndices' requested here modelIndices=CompactModelIndices<uint64_t>(mInd); ^ ./fastBMA.hpp:1430:23: note: in instantiation of member function 'ModelSet<double>::ModelSet' requested here activeModels.insert(ModelSet<T>(modelIndices, 0, 0, 0)); ^ ./fastBMA.hpp:1414:3: note: in instantiation of function template specialization 'chooseBestModels<double>' requested here chooseBestModels(g,ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR); ^ ./fastBMA.hpp:1757:13: note: in instantiation of function template specialization 'fastScanBMA_g<double>' requested here int nEdges=fastScanBMA_g(ATA,ATb,btb,sst,ignoreIndex,priors,rankOnly,postProbs,parents,nRows, nGenes,nVars, twoLogOR,g,optimizeBits,maxOptimizeCycles); ^ ./bmaNoMPI.hpp:127:14: note: in instantiation of function template specialization 'findRegulators<double>' requested here int nEdges=findRegulators(g,optimizeBits,maxOptimizeCycles,uniform_prob,twoLogOR,nVars,nThreads,rankOnly,evalSubset[k],data,rProbs,parentsSlice[th] ,weightsSlice[th],A,ATA, Aldr,ATAldr, nGenes,nRows,nSamples,nTimes); ^ fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here findEdges( ^ In file included from fastBMAR.cpp:3: ./fastBMA.hpp:282:2: warning: control may reach end of non-void function [-Wreturn-type] } ^ ./fastBMA.hpp:657:28: note: in instantiation of member function 'BitIndex<unsigned long long>::compare' requested here bool retvalue=bitIndex.compare(b.list,modelBits,nModels); ^ ./fastBMA.hpp:829:84: note: in instantiation of member function 'CompactModelIndices<unsigned long long>::operator==' requested here bool operator<(const ModelSet& b) const { return (bic < b.bic) && ! (modelIndices == b.modelIndices); } ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/__functional_base:55:21: note: in instantiation of member function 'ModelSet<double>::operator<' requested here {return __x < __y;} ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/__tree:2017:17: note: in instantiation of member function 'std::__1::less<ModelSet<double> >::operator()' requested here if (value_comp()(__v, __nd->__value_)) ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/__tree:2141:36: note: in instantiation of function template specialization 'std::__1::__tree<ModelSet<double>, std::__1::less<ModelSet<double> >, std::__1::allocator<ModelSet<double> > >::__find_equal<ModelSet<double> >' requested here __node_base_pointer& __child = __find_equal(__parent, __k); ^ /Library/Developer/CommandLineTools/usr/include/c++/v1/__tree:1276:16: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) return __emplace_unique_key_args(_NodeTypes::__get_key(__v), _VSTD::move(__v)); ^ ./fastBMA.hpp:1430:16: note: in instantiation of member function 'std::__1::set<ModelSet<double>, std::__1::less<ModelSet<double> >, std::__1::allocator<ModelSet<double> > >::insert' requested here activeModels.insert(ModelSet<T>(modelIndices, 0, 0, 0)); ^ ./fastBMA.hpp:1414:3: note: in instantiation of function template specialization 'chooseBestModels<double>' requested here chooseBestModels(g,ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR); ^ ./fastBMA.hpp:1757:13: note: in instantiation of function template specialization 'fastScanBMA_g<double>' requested here int nEdges=fastScanBMA_g(ATA,ATb,btb,sst,ignoreIndex,priors,rankOnly,postProbs,parents,nRows, nGenes,nVars, twoLogOR,g,optimizeBits,maxOptimizeCycles); ^ ./bmaNoMPI.hpp:127:14: note: in instantiation of function template specialization 'findRegulators<double>' requested here int nEdges=findRegulators(g,optimizeBits,maxOptimizeCycles,uniform_prob,twoLogOR,nVars,nThreads,rankOnly,evalSubset[k],data,rProbs,parentsSlice[th] ,weightsSlice[th],A,ATA, Aldr,ATAldr, nGenes,nRows,nSamples,nTimes); ^ fastBMAR.cpp:127:2: note: in instantiation of function template specialization 'findEdges<double>' requested here findEdges( ^ 22 warnings generated. clang++ -mmacosx-version-min=10.13 -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 networkBMA.so MurmurHash3.o RcppExports.o ScanBMA_full.o fastBMAR.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-darwin18/8.2.0 -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/4.1/Resources/library/00LOCK-networkBMA/00new/networkBMA/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (networkBMA)
networkBMA.Rcheck/networkBMA-Ex.timings
name | user | system | elapsed | |
ScanBMA | 0.133 | 0.013 | 0.148 | |
ScanBMAcontrol | 6.723 | 0.078 | 6.807 | |
contabs | 1.909 | 0.039 | 1.949 | |
contabs.netwBMA | 0 | 0 | 0 | |
contabs.prelim | 0.000 | 0.001 | 0.001 | |
fastBMAcontrol | 0.081 | 0.003 | 0.084 | |
fastgControl | 0.079 | 0.002 | 0.082 | |
gControl | 6.748 | 0.035 | 6.789 | |
iBMAcontrolLM | 0.637 | 0.004 | 0.642 | |
iterateBMAlm | 1.101 | 0.009 | 1.113 | |
networkBMA | 0.440 | 0.006 | 0.448 | |
roc | 0.975 | 0.015 | 0.990 | |
scores | 1.186 | 0.013 | 1.200 | |
summary.networkBMA | 0.394 | 0.005 | 0.398 | |
varord | 0.199 | 0.003 | 0.202 | |
vignette | 4.878 | 0.053 | 4.934 | |
writeEdges | 0.865 | 0.005 | 0.871 | |