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###
### 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_1.22.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/kebabs.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.22.0’
* 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-3.11-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 (user + system) or elapsed time > 5s
                        user system elapsed
performModelSelection 13.512  2.111  15.667
performGridSearch      6.842  1.013   7.864
* 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-3.11-bioc/meat/kebabs.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL kebabs
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ByteStringVector.c -o ByteStringVector.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ExplicitRepC.cpp -o ExplicitRepC.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c KernelUtils.cpp -o KernelUtils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c PredictionC.cpp -o PredictionC.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c PredictionProfileC.cpp -o PredictionProfileC.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_kebabs.cpp -o R_init_kebabs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rsvm.c -o Rsvm.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c SparseMatrixHash.cpp -o SparseMatrixHash.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c SymmetricPairC.cpp -o SymmetricPairC.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Utils.cpp -o Utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c svm.cpp -o svm.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o 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/4.0/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)