Package: kebabs

Version: 1.20.0

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_1.20.0.tar.gz

StartedAt: 2020-04-15 03:20:46 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:24:26 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 220.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: kebabs.Rcheck

Warnings: 1

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### Running command:
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###   /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_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/kebabs.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.20.0’
* 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++17 [-Wdeprecated-register]
  MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Users/biocbuild/bbs-3.10-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 12.632  2.879  15.638
performGridSearch      6.017  1.224   7.285
* 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-3.10-bioc/meat/kebabs.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL kebabs
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* 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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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++17 [-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	0.058	0.002	0.060
CrossValidationResultAccessors	0.003	0.000	0.003
KBModelAccessors	0.001	0.000	0.002
KernelMatrixAccessors	0.001	0.000	0.001
LinearKernel	3.739	0.062	3.831
ModelSelectionResultAccessors	0.000	0.000	0.001
PredictionProfileAccessors	0.002	0.000	0.001
ROCDataAccessors	0.001	0.000	0.001
SVMAccess	0.427	0.009	0.439
annotationSpecificKernel	0.132	0.004	0.137
computeROCandAUC	2.440	0.405	2.863
evaluatePrediction	0.802	0.125	0.934
explicitRepresentation	0.181	0.003	0.184
featureWeights	0.334	0.050	0.385
gappyPairKernel	0.007	0.000	0.009
genRandBioSeqs	0.068	0.000	0.069
getPredProfMixture-methods	2.663	0.265	2.947
getPredictionProfile-methods	0.742	0.042	0.790
heatmap-methods	0.492	0.025	0.522
kbsvm-methods	0.283	0.033	0.317
kebabsCollectInfo	0.058	0.004	0.063
kebabsOverview	0.350	0.031	0.383
mismatchKernel	0.009	0.000	0.009
motifKernel	0.008	0.000	0.009
performCrossValidation-methods	0.318	0.054	0.373
performGridSearch	6.017	1.224	7.285
performModelSelection	12.632	2.879	15.638
plot-methods	0.502	0.096	0.600
positionDependentKernel	0.014	0.002	0.016
predict-methods	0.321	0.049	0.371
sequenceKernel	0.047	0.002	0.049
show-methods	0.032	0.008	0.040
spectrumKernel	0.006	0.000	0.007
symmetricPairKernel	0.111	0.011	0.122