Package: kebabs

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:kebabs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings kebabs_1.18.0.tar.gz

StartedAt: 2019-10-16 04:01:13 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:05:53 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 280.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: kebabs.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:kebabs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings kebabs_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/kebabs.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘kebabs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘kebabs’ version ‘1.18.0’
* 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 ‘kebabs’ can be installed ... WARNING
Found the following significant warnings:
  GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
  MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
  MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
  SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/kebabs.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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
kebabsDemo: no visible binding for global variable ‘enhancerFB’
kebabsDemo: no visible binding for global variable ‘yFB’
kebabsDemo: no visible binding for global variable ‘ccseq’
kebabsDemo: no visible binding for global variable ‘yCC’
Undefined global functions or variables:
  ccseq enhancerFB yCC yFB
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
performModelSelection      15.721  5.967  21.962
performGridSearch           7.845  2.683  10.532
getPredProfMixture-methods  4.823  0.530   5.355
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/kebabs.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c ByteStringVector.c -o ByteStringVector.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c ExplicitRepC.cpp -o ExplicitRepC.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c GappyPairC.cpp -o GappyPairC.o
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
KSORT_INIT(gappy, uint64_t, ks_lt_generic)
^
./ksort.h:242:45: note: expanded from macro 'KSORT_INIT'
                if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
                                            ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:246:41: note: expanded from macro 'KSORT_INIT'
            if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
                                        ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:247:41: note: expanded from macro 'KSORT_INIT'
            if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
                                        ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:248:40: note: expanded from macro 'KSORT_INIT'
            if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low);    \
                                       ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:249:13: note: expanded from macro 'KSORT_INIT'
            KSORT_SWAP(type_t, *mid, *(low+1));                            \
            ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:255:17: note: expanded from macro 'KSORT_INIT'
                KSORT_SWAP(type_t, *ll, *hh);                            \
                ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:257:13: note: expanded from macro 'KSORT_INIT'
            KSORT_SWAP(type_t, *low, *hh);                                \
            ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
7 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c KernelUtils.cpp -o KernelUtils.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c MismatchC.cpp -o MismatchC.o
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
KSORT_INIT(mism, uint64_t, ks_lt_generic)
^
./ksort.h:242:45: note: expanded from macro 'KSORT_INIT'
                if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
                                            ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:246:41: note: expanded from macro 'KSORT_INIT'
            if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
                                        ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:247:41: note: expanded from macro 'KSORT_INIT'
            if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
                                        ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:248:40: note: expanded from macro 'KSORT_INIT'
            if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low);    \
                                       ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:249:13: note: expanded from macro 'KSORT_INIT'
            KSORT_SWAP(type_t, *mid, *(low+1));                            \
            ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:255:17: note: expanded from macro 'KSORT_INIT'
                KSORT_SWAP(type_t, *ll, *hh);                            \
                ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:257:13: note: expanded from macro 'KSORT_INIT'
            KSORT_SWAP(type_t, *low, *hh);                                \
            ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c MotifC.cpp -o MotifC.o
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
KSORT_INIT(str, ksstr_t, ks_lt_str)
^
./ksort.h:242:45: note: expanded from macro 'KSORT_INIT'
                if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
                                            ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:246:41: note: expanded from macro 'KSORT_INIT'
            if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
                                        ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:247:41: note: expanded from macro 'KSORT_INIT'
            if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
                                        ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:248:40: note: expanded from macro 'KSORT_INIT'
            if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low);    \
                                       ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:249:13: note: expanded from macro 'KSORT_INIT'
            KSORT_SWAP(type_t, *mid, *(low+1));                            \
            ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:255:17: note: expanded from macro 'KSORT_INIT'
                KSORT_SWAP(type_t, *ll, *hh);                            \
                ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:257:13: note: expanded from macro 'KSORT_INIT'
            KSORT_SWAP(type_t, *low, *hh);                                \
            ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c PredictionC.cpp -o PredictionC.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c PredictionProfileC.cpp -o PredictionProfileC.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c R_init_kebabs.cpp -o R_init_kebabs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Rsvm.c -o Rsvm.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c SparseMatrixHash.cpp -o SparseMatrixHash.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c SpectrumC.cpp -o SpectrumC.o
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
KSORT_INIT(spec, uint64_t, ks_lt_generic)
^
./ksort.h:242:45: note: expanded from macro 'KSORT_INIT'
                if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
                                            ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:246:41: note: expanded from macro 'KSORT_INIT'
            if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
                                        ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:247:41: note: expanded from macro 'KSORT_INIT'
            if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
                                        ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:248:40: note: expanded from macro 'KSORT_INIT'
            if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low);    \
                                       ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:249:13: note: expanded from macro 'KSORT_INIT'
            KSORT_SWAP(type_t, *mid, *(low+1));                            \
            ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:255:17: note: expanded from macro 'KSORT_INIT'
                KSORT_SWAP(type_t, *ll, *hh);                            \
                ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:257:13: note: expanded from macro 'KSORT_INIT'
            KSORT_SWAP(type_t, *low, *hh);                                \
            ^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
                                   ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c SymmetricPairC.cpp -o SymmetricPairC.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Utils.cpp -o Utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c svm.cpp -o svm.o
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 kebabs.so Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o Rsvm.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o svm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-kebabs/00new/kebabs/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 (kebabs)

name	user	system	elapsed
BioVector	0.054	0.002	0.056
CrossValidationResultAccessors	0.002	0.000	0.002
KBModelAccessors	0.001	0.000	0.001
KernelMatrixAccessors	0.001	0.000	0.001
LinearKernel	4.009	0.091	4.104
ModelSelectionResultAccessors	0.001	0.001	0.003
PredictionProfileAccessors	0.002	0.001	0.002
ROCDataAccessors	0.002	0.001	0.002
SVMAccess	0.591	0.027	0.618
annotationSpecificKernel	0.171	0.011	0.182
computeROCandAUC	3.182	0.961	4.475
evaluatePrediction	1.089	0.228	1.317
explicitRepresentation	0.322	0.010	0.332
featureWeights	0.445	0.088	0.534
gappyPairKernel	0.011	0.001	0.014
genRandBioSeqs	0.091	0.001	0.092
getPredProfMixture-methods	4.823	0.530	5.355
getPredictionProfile-methods	1.272	0.091	1.363
heatmap-methods	0.644	0.038	0.683
kbsvm-methods	0.332	0.060	0.392
kebabsCollectInfo	0.055	0.007	0.061
kebabsOverview	0.450	0.076	0.526
mismatchKernel	0.013	0.002	0.016
motifKernel	0.011	0.002	0.014
performCrossValidation-methods	0.409	0.115	0.524
performGridSearch	7.845	2.683	10.532
performModelSelection	15.721	5.967	21.962
plot-methods	0.704	0.239	0.950
positionDependentKernel	0.019	0.004	0.024
predict-methods	0.476	0.115	0.677
sequenceKernel	0.051	0.003	0.054
show-methods	0.034	0.009	0.043
spectrumKernel	0.011	0.002	0.012
symmetricPairKernel	0.168	0.024	0.195