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BUILD BIN report for kebabs on machv2

This page was generated on 2020-10-17 11:58:46 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE kebabs PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 917/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kebabs 1.22.0
Ulrich Bodenhofer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/kebabs
Branch: RELEASE_3_11
Last Commit: 4b5d1a8
Last Changed Date: 2020-04-27 14:44:54 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: kebabs
Version: 1.22.0
Command: rm -rf kebabs.buildbin-libdir && mkdir kebabs.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh kebabs_1.22.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R kebabs.buildbin-libdir
StartedAt: 2020-10-17 07:20:47 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:22:49 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 122.0 seconds
RetCode: 0
Status:  OK 
PackageFile: kebabs_1.22.0.tgz
PackageFileSize: 3.751 MiB

Command output

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###
### Running command:
###
###   rm -rf kebabs.buildbin-libdir && mkdir kebabs.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh kebabs_1.22.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R kebabs.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=kebabs.buildbin-libdir kebabs_1.22.0.tar.gz'
>>>>>>> 

* 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 /Users/biocbuild/bbs-3.11-bioc/meat/kebabs.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING LINKS FOR kebabs.buildbin-libdir/kebabs/libs/kebabs.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "kebabs.buildbin-libdir/kebabs/libs/kebabs.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "kebabs.buildbin-libdir/kebabs/libs/kebabs.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "kebabs.buildbin-libdir/kebabs/libs/kebabs.so"