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CHECK report for martini on merida2

This page was generated on 2019-04-09 13:36:34 -0400 (Tue, 09 Apr 2019).

Package 902/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
martini 1.3.1
Hector Climente-Gonzalez
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/martini
Branch: master
Last Commit: 5710ce0
Last Changed Date: 2019-02-07 14:19:36 -0400 (Thu, 07 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: martini
Version: 1.3.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:martini.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings martini_1.3.1.tar.gz
StartedAt: 2019-04-09 01:57:06 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:59:13 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 126.9 seconds
RetCode: 0
Status:  OK 
CheckDir: martini.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:martini.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings martini_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/martini.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘martini/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘martini’ version ‘1.3.1’
* 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 ‘martini’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_GI_network: no visible binding for global variable ‘gene1’
get_GI_network: no visible binding for global variable ‘gene2’
get_GM_network: no visible binding for global variable ‘gene’
test_cones_modules : <anonymous> : <anonymous>: no visible binding for
  global variable ‘snp’
Undefined global functions or variables:
  gene gene1 gene2 snp
* 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
Examples with CPU or elapsed time > 5s
         user system elapsed
get_ppi 0.419  0.033   8.754
* 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-3.9-bioc/meat/martini.Rcheck/00check.log’
for details.

Installation output

martini.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL martini
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘martini’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rgin/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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:4:
In file included from ./../inst/include/martini.h:7:
In file included from ./../inst/include/martini_RcppExports.h:7:
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
                             ^
RcppExports.cpp:29:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
    int nprot = 0;                                                                               \
        ^
RcppExports.cpp:29:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
    static SEXP stop_sym = Rf_install("stop");                                                   \
                ^
19 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rgin/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c evo.cpp -o evo.o
In file included from evo.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 evo.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 evo.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 evo.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 evo.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 evo.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 evo.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 evo.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 evo.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 evo.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 evo.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 evo.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 evo.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 evo.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 evo.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 evo.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 evo.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
                             ^
In file included from evo.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rgin/include/gin/feature_selection/shake.h:8:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rgin/include/gin/io/grid_views.h:8:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rgin/include/gin/model_selection/grid_cv.h:10:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rgin/include/gin/regression/CRegression.h:191:8: warning: 'CLinearMixedRegression::fit' hides overloaded virtual functions [-Woverloaded-virtual]
                void fit(VectorXd const&, MatrixXd const&, MatrixXd const&) throw (CRegressionException);
                     ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rgin/include/gin/regression/CRegression.h:53:16: note: hidden overloaded virtual function 'CRegression::fit' declared here: different number of parameters (1 vs 3)
                virtual void fit(bool const&) throw (CRegressionException) {};
                             ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rgin/include/gin/regression/CRegression.h:54:16: note: hidden overloaded virtual function 'CRegression::fit' declared here: different number of parameters (2 vs 3)
                virtual void fit(VectorXd const&, MatrixXd const&) throw (CRegressionException) {};
                             ^
18 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rgin/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c run_scones.cpp -o run_scones.o
In file included from run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 run_scones.cpp:7:
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 martini.so RcppExports.o evo.o run_scones.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rgin/usrlib//libgin.a /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rgin/usrlib//libmaxflow.a /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rgin/usrlib//libcephes.a -lz -pthread -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/martini/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 (martini)

Tests output

martini.Rcheck/tests/testthat.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(martini)
> library(igraph)

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> 
> test_check("martini")
Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.003926 sec

Searching ConES with eta = 3 and lambda = 2.5

Finished in 9.7e-05 sec

Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.002305 sec

Searching ConES with eta = 1 and lambda = 2

Finished in 9.8e-05 sec

Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.022976 sec

Searching ConES with eta = 1e-06 and lambda = 1e-07

Finished in 0.000108 sec

Grid of consistency scores (etas x lambdas):
     99   99   99   99   99   99   99   99   99   99
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
Selected parameters:
eta = 99 
lambda = 99 
Grid of consistency scores (etas x lambdas):
                       99 52.7071225004667 28.0610178008001 14.9395505324702
99                   -Inf             -Inf             -Inf             -Inf
52.7071225004667 90.00000         90.00000         90.00000         90.00000
28.0610178008001 90.00000         90.00000         90.00000         90.00000
14.9395505324702 90.00000         90.00000         90.00000         90.00000
7.95374464663453 90.00000         90.00000         90.00000         90.00000
4.23453528714745 90.00000         90.00000         90.00000         90.00000
2.2544461627498  90.00000         90.00000         90.00000         90.00000
1.20025626334102 88.69231         88.69231         88.69231         88.69231
0.63901064549361     -Inf             -Inf             -Inf             -Inf
0.34020618556701     -Inf             -Inf             -Inf             -Inf
                 7.95374464663453 4.23453528714745 2.2544461627498
99                           -Inf             -Inf            -Inf
52.7071225004667         90.00000         90.00000        90.00000
28.0610178008001         90.00000         90.00000        90.00000
14.9395505324702         90.00000         90.00000        90.00000
7.95374464663453         90.00000         90.00000        90.00000
4.23453528714745         90.00000         90.00000        90.00000
2.2544461627498          90.00000         90.00000        90.00000
1.20025626334102         88.69231         88.69231        88.69231
0.63901064549361             -Inf             -Inf            -Inf
0.34020618556701             -Inf             -Inf            -Inf
                 1.20025626334102 0.63901064549361 0.34020618556701
99                           -Inf             -Inf             -Inf
52.7071225004667         90.00000         90.00000         90.00000
28.0610178008001         90.00000         90.00000         90.00000
14.9395505324702         90.00000         90.00000         90.00000
7.95374464663453         90.00000         90.00000         90.00000
4.23453528714745         90.00000         90.00000         90.00000
2.2544461627498          90.00000         90.00000         90.00000
1.20025626334102         88.69231         88.69231         88.69231
0.63901064549361             -Inf             -Inf             -Inf
0.34020618556701             -Inf             -Inf             -Inf
Selected parameters:
eta = 52.70712 
lambda = 99 
Grid of consistency scores (etas x lambdas):
     99   99   99   99   99   99   99   99   99   99
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
Selected parameters:
eta = 99 
lambda = 99 
Grid of consistency scores (etas x lambdas):
     0
0 -Inf
Selected parameters:
eta = 0 
lambda = 0 
Grid of consistency scores (etas x lambdas):
                         0 0.222222222222222 0.444444444444445
0                     -Inf              -Inf              -Inf
0.222222222222222     -Inf              -Inf              -Inf
0.444444444444445     -Inf              -Inf              -Inf
0.666666666666667     -Inf              -Inf              -Inf
0.888888888888889     -Inf              -Inf              -Inf
1.11111111111111  88.69231          88.69231          88.69231
1.33333333333333  88.69231          88.69231          88.69231
1.55555555555556  88.69231          88.69231          88.69231
1.77777777777778  88.69231          88.69231          88.69231
2                 88.69231          88.69231          88.69231
                  0.666666666666667 0.888888888888889 1.11111111111111
0                              -Inf              -Inf             -Inf
0.222222222222222              -Inf              -Inf             -Inf
0.444444444444445              -Inf              -Inf             -Inf
0.666666666666667              -Inf              -Inf             -Inf
0.888888888888889              -Inf              -Inf             -Inf
1.11111111111111           88.69231          88.69231         88.69231
1.33333333333333           88.69231          88.69231         88.69231
1.55555555555556           88.69231          88.69231         88.69231
1.77777777777778           88.69231          88.69231         88.69231
2                          88.69231          88.69231         88.69231
                  1.33333333333333 1.55555555555556 1.77777777777778        2
0                             -Inf             -Inf             -Inf     -Inf
0.222222222222222             -Inf             -Inf             -Inf     -Inf
0.444444444444445             -Inf             -Inf             -Inf     -Inf
0.666666666666667             -Inf             -Inf             -Inf     -Inf
0.888888888888889             -Inf             -Inf             -Inf     -Inf
1.11111111111111          88.69231         88.69231         88.69231 88.69231
1.33333333333333          88.69231         88.69231         88.69231 88.69231
1.55555555555556          88.69231         88.69231         88.69231 88.69231
1.77777777777778          88.69231         88.69231         88.69231 88.69231
2                         88.69231         88.69231         88.69231 88.69231
Selected parameters:
eta = 1.111111 
lambda = 0 
Grid of bic scores (etas x lambdas):
                          0 0.222222222222222 0.444444444444445
0                      -Inf              -Inf              -Inf
0.222222222222222      -Inf              -Inf              -Inf
0.444444444444445      -Inf              -Inf              -Inf
0.666666666666667      -Inf              -Inf              -Inf
0.888888888888889      -Inf              -Inf              -Inf
1.11111111111111  -1395.976         -1395.976         -1395.976
1.33333333333333  -1395.976         -1395.976         -1395.976
1.55555555555556  -1395.976         -1395.976         -1395.976
1.77777777777778  -1395.976         -1395.976         -1395.976
2                 -1395.976         -1395.976         -1395.976
                  0.666666666666667 0.888888888888889 1.11111111111111
0                              -Inf              -Inf             -Inf
0.222222222222222              -Inf              -Inf             -Inf
0.444444444444445              -Inf              -Inf             -Inf
0.666666666666667              -Inf              -Inf             -Inf
0.888888888888889              -Inf              -Inf             -Inf
1.11111111111111          -1395.976         -1395.976        -1395.976
1.33333333333333          -1395.976         -1395.976        -1395.976
1.55555555555556          -1395.976         -1395.976        -1395.976
1.77777777777778          -1395.976         -1395.976        -1395.976
2                         -1395.976         -1395.976        -1395.976
                  1.33333333333333 1.55555555555556 1.77777777777778         2
0                             -Inf             -Inf             -Inf      -Inf
0.222222222222222             -Inf             -Inf             -Inf      -Inf
0.444444444444445             -Inf             -Inf             -Inf      -Inf
0.666666666666667             -Inf             -Inf             -Inf      -Inf
0.888888888888889             -Inf             -Inf             -Inf      -Inf
1.11111111111111         -1395.976        -1395.976        -1395.976 -1395.976
1.33333333333333         -1395.976        -1395.976        -1395.976 -1395.976
1.55555555555556         -1395.976        -1395.976        -1395.976 -1395.976
1.77777777777778         -1395.976        -1395.976        -1395.976 -1395.976
2                        -1395.976        -1395.976        -1395.976 -1395.976
Selected parameters:
eta = 1.111111 
lambda = 0 
Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.019157 sec

Searching ConES with eta = 1e-06 and lambda = 1e-07

Finished in 9e-05 sec

eta = 1e-06 
lambda = 1e-07 
Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.001939 sec

Searching ConES with eta = 1 and lambda = 2

Finished in 8.2e-05 sec

eta = 1 
lambda = 2 
Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.019696 sec

Searching ConES with eta = 1e-06 and lambda = 1e-07

Finished in 6.5e-05 sec

eta = 1e-06 
lambda = 1e-07 
Grid of consistency scores (etas x lambdas):
     99   99   99   99   99   99   99   99   99   99
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
Selected parameters:
eta = 99 
lambda = 99 
Grid of consistency scores (etas x lambdas):
     99   99   99   99   99   99   99   99   99   99
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
Selected parameters:
eta = 99 
lambda = 99 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 234 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 19.177   0.968  40.132

Example timings

martini.Rcheck/martini-Ex.timings

nameusersystemelapsed
check_installed0.0000.0000.001
encode_gwas0.0130.0090.024
get_GI_network0.0740.0030.076
get_GM_network0.0290.0010.029
get_GS_network0.0080.0000.008
get_evo_settings0.0010.0010.001
get_ppi0.4190.0338.754
get_snp_modules0.2630.0170.283
is_coherent0.0040.0010.005
ldweight_edges0.0880.0030.091
minigwas0.0230.0060.029
minippi0.0020.0010.003
minisnpMapping0.0040.0010.005
parse_scones_settings0.0010.0010.002
scones0.0570.0020.060
scones.cv0.3330.0120.351
search_cones0.1450.0060.153
simulate_causal_snps0.0640.0010.066
simulate_phenotype0.0720.0040.075
subnet0.0620.0020.063
subvert0.0330.0010.034
test_cones_modules0.3290.0060.337