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BioC 3.5: BUILD BIN report for seqbias on toluca2

This page was generated on 2017-04-23 14:35:32 -0400 (Sun, 23 Apr 2017).

Package 1196/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqbias 1.23.0
Daniel Jones
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK [ OK ]
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: seqbias
Version: 1.23.0
Command: rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh seqbias_1.23.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R seqbias.buildbin-libdir
StartedAt: 2017-04-23 12:43:36 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 12:44:08 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 31.2 seconds
RetCode: 0
Status:  OK 
PackageFile: seqbias_1.23.0.tgz
PackageFileSize: 886.4 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh seqbias_1.23.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R seqbias.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=seqbias.buildbin-libdir seqbias_1.23.0.tar.gz'
>>>>>>> 

* installing *source* package ‘seqbias’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c common.c -o common.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c miscmath.c -o miscmath.o
miscmath.c:21:12: warning: 'finite' is deprecated: first deprecated in OS X 10.9 [-Wdeprecated-declarations]
    return finite(a) && 0.0 <= a && a <= 1.0;
           ^
/usr/include/math.h:718:12: note: 'finite' has been explicitly marked deprecated here
extern int finite(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA);
           ^
miscmath.c:47:9: warning: 'finite' is deprecated: first deprecated in OS X 10.9 [-Wdeprecated-declarations]
    if (finite(u)) return x + log1p(-exp(u));
        ^
/usr/include/math.h:718:12: note: 'finite' has been explicitly marked deprecated here
extern int finite(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA);
           ^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c pos_table.c -o pos_table.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c samtools_extra.c -o samtools_extra.o
samtools_extra.c:36:1: warning: unused function 'kh_init_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, faidx1_t)
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
        SCOPE kh_##name##_t *kh_init_##name() {                                                         \
                             ^
<scratch space>:196:1: note: expanded from here
kh_init_s
^
samtools_extra.c:36:1: warning: unused function 'kh_destroy_s' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_destroy_##name(kh_##name##_t *h)                                          \
                   ^
<scratch space>:201:1: note: expanded from here
kh_destroy_s
^
samtools_extra.c:36:1: warning: unused function 'kh_clear_s' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_clear_##name(kh_##name##_t *h)                                            \
                   ^
<scratch space>:204:1: note: expanded from here
kh_clear_s
^
samtools_extra.c:36:1: warning: unused function 'kh_put_s' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
        SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
                      ^
<scratch space>:213:1: note: expanded from here
kh_put_s
^
samtools_extra.c:36:1: warning: unused function 'kh_del_s' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
        KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
        KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
        SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)                           \
                   ^
<scratch space>:218:1: note: expanded from here
kh_del_s
^
5 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c kmer_matrix.cpp -o kmer_matrix.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c logger.cpp -o logger.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c motif.cpp -o motif.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c seqbias.cpp -o seqbias.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c sequencing_bias.cpp -o sequencing_bias.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c twobitseq.cpp -o twobitseq.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/node.cpp -o yaml-cpp/node.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/null.cpp -o yaml-cpp/null.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:2:
yaml-cpp/collectionstack.h:28:48: warning: unused parameter 'type' [-Wunused-parameter]
                void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
                                                             ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -Wextra -I. -fPIC  -Wall -mtune=core2 -g -O2  -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
clang++ -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 seqbias.so common.o miscmath.o pos_table.o samtools_extra.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o yaml-cpp/aliasmanager.o yaml-cpp/conversion.o yaml-cpp/directives.o yaml-cpp/emitfromevents.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/nodebuilder.o yaml-cpp/node.o yaml-cpp/nodeownership.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/regex.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/simplekey.o yaml-cpp/singledocparser.o yaml-cpp/stream.o yaml-cpp/tag.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-3.5-bioc/meat/seqbias.buildbin-libdir/seqbias/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (seqbias)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "seqbias.buildbin-libdir/seqbias/libs//seqbias.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "seqbias.buildbin-libdir/seqbias/libs//seqbias.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "seqbias.buildbin-libdir/seqbias/libs//seqbias.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "seqbias.buildbin-libdir/seqbias/libs//seqbias.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "seqbias.buildbin-libdir/seqbias/libs//seqbias.so"