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BioC 3.6: BUILD BIN report for qrqc on veracruz1

This page was generated on 2017-08-16 13:41:39 -0400 (Wed, 16 Aug 2017).

Package 1056/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qrqc 1.31.0
Vince Buffalo
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/qrqc
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: qrqc
Version: 1.31.0
Command: rm -rf qrqc.buildbin-libdir && mkdir qrqc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh qrqc_1.31.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R qrqc.buildbin-libdir
StartedAt: 2017-08-16 11:07:30 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 11:08:03 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 32.7 seconds
RetCode: 0
Status:  OK 
PackageFile: qrqc_1.31.0.tgz
PackageFileSize: 520 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf qrqc.buildbin-libdir && mkdir qrqc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh qrqc_1.31.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R qrqc.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=qrqc.buildbin-libdir qrqc_1.31.0.tar.gz'
>>>>>>> 

* installing *source* package ‘qrqc’ ...
** 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   -fPIC  -Wall -g -O2  -c R_init_io.c -o R_init_io.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   -fPIC  -Wall -g -O2  -c io.c -o io.o
io.c:34:1: warning: unused function 'kseq_destroy' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/kseq.h:223:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/include/samtools/kseq.h:158:13: note: expanded from macro '__KSEQ_BASIC'
        SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
                   ^
io.c:37:1: warning: unused function 'kh_clear_str' [-Wunused-function]
KHASH_MAP_INIT_STR(str, double)
^
/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>:94:1: note: expanded from here
kh_clear_str
^
io.c:37:1: warning: unused function 'kh_del_str' [-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>:108:1: note: expanded from here
kh_del_str
^
3 warnings generated.
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 qrqc.so R_init_io.o io.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-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Users/biocbuild/bbs-3.6-bioc/meat/qrqc.buildbin-libdir/qrqc/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 (qrqc)


>>>>>>> 
>>>>>>> FIXING LINKS FOR qrqc.buildbin-libdir/qrqc/libs//qrqc.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" "qrqc.buildbin-libdir/qrqc/libs//qrqc.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "qrqc.buildbin-libdir/qrqc/libs//qrqc.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" "qrqc.buildbin-libdir/qrqc/libs//qrqc.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "qrqc.buildbin-libdir/qrqc/libs//qrqc.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "qrqc.buildbin-libdir/qrqc/libs//qrqc.so"