kebabs 1.17.0
Ulrich Bodenhofer
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/kebabs |
| Branch: master |
| Last Commit: 7f7820d |
| Last Changed Date: 2018-10-30 11:54:33 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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###
### Running command:
###
### rm -rf kebabs.buildbin-libdir && mkdir kebabs.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh kebabs_1.17.0.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_1.17.0.tar.gz'
>>>>>>>
* 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" -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" -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" -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" -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" -I/usr/local/include -fPIC -Wall -g -O2 -c GappyPairC.cpp -o GappyPairC.o
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
KSORT_INIT(gappy, uint64_t, ks_lt_generic)
^
./ksort.h:242:45: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:246:41: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:247:41: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:248:40: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:249:13: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *mid, *(low+1)); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:255:17: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *ll, *hh); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
GappyPairC.cpp:49:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:257:13: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *low, *hh); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
7 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -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" -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" -I/usr/local/include -fPIC -Wall -g -O2 -c MismatchC.cpp -o MismatchC.o
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
KSORT_INIT(mism, uint64_t, ks_lt_generic)
^
./ksort.h:242:45: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:246:41: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:247:41: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:248:40: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:249:13: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *mid, *(low+1)); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:255:17: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *ll, *hh); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
MismatchC.cpp:47:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:257:13: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *low, *hh); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c MotifC.cpp -o MotifC.o
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
KSORT_INIT(str, ksstr_t, ks_lt_str)
^
./ksort.h:242:45: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:246:41: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:247:41: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:248:40: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:249:13: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *mid, *(low+1)); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:255:17: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *ll, *hh); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
MotifC.cpp:53:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:257:13: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *low, *hh); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -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" -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" -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" -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" -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" -I/usr/local/include -fPIC -Wall -g -O2 -c SpectrumC.cpp -o SpectrumC.o
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
KSORT_INIT(spec, uint64_t, ks_lt_generic)
^
./ksort.h:242:45: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:246:41: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:247:41: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:248:40: note: expanded from macro 'KSORT_INIT'
if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:249:13: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *mid, *(low+1)); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:255:17: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *ll, *hh); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
SpectrumC.cpp:55:1: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
./ksort.h:257:13: note: expanded from macro 'KSORT_INIT'
KSORT_SWAP(type_t, *low, *hh); \
^
./ksort.h:76:36: note: expanded from macro 'KSORT_SWAP'
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/include" -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" -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" -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" -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 /Users/biocbuild/bbs-3.9-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/3.6/Resources/lib/libgcc_s.1.dylib" "kebabs.buildbin-libdir/kebabs/libs//kebabs.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "kebabs.buildbin-libdir/kebabs/libs//kebabs.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "kebabs.buildbin-libdir/kebabs/libs//kebabs.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "kebabs.buildbin-libdir/kebabs/libs//kebabs.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "kebabs.buildbin-libdir/kebabs/libs//kebabs.so"