Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P [Q] R  S  T  U  V  W  X  Y  Z 

BioC 3.4: BUILD BIN report for QuasR on morelia

This page was generated on 2017-04-15 16:24:30 -0400 (Sat, 15 Apr 2017).

Package 984/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuasR 1.14.0
Michael Stadler
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/QuasR
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: QuasR
Version: 1.14.0
Command: rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh QuasR_1.14.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R QuasR.buildbin-libdir
StartedAt: 2017-04-15 10:50:26 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 10:51:10 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 43.4 seconds
RetCode: 0
Status:  OK 
PackageFile: QuasR_1.14.0.tgz
PackageFileSize: 1.634 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh QuasR_1.14.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R QuasR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=QuasR.buildbin-libdir QuasR_1.14.0.tar.gz'
>>>>>>> 

* installing *source* package ‘QuasR’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_QuasR.cpp -o R_init_QuasR.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c cat_bam.c -o cat_bam.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c count_alignments.c -o count_alignments.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c count_alignments_subregions.c -o count_alignments_subregions.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c count_junctions.cpp -o count_junctions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c export_wig.c -o export_wig.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c extract_unmapped_reads.c -o extract_unmapped_reads.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c idxstats_bam.c -o idxstats_bam.o
idxstats_bam.c:30:1: warning: unused function 'kh_init_i' [-Wunused-function]
KHASH_MAP_INIT_INT(i, bam_binlist_t)
^
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include/samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
        KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/Rsamtools/include/samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
        SCOPE kh_##name##_t *kh_init_##name() {                                                         \
                             ^
<scratch space>:46:1: note: expanded from here
kh_init_i
^
idxstats_bam.c:30:1: warning: unused function 'kh_destroy_i' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include/samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
        KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.3/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/3.3/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>:51:1: note: expanded from here
kh_destroy_i
^
idxstats_bam.c:30:1: warning: unused function 'kh_clear_i' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include/samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
        KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.3/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/3.3/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>:54:1: note: expanded from here
kh_clear_i
^
idxstats_bam.c:30:1: warning: unused function 'kh_put_i' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include/samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
        KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.3/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/3.3/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>:63:1: note: expanded from here
kh_put_i
^
idxstats_bam.c:30:1: warning: unused function 'kh_del_i' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include/samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
        KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
        ^
/Library/Frameworks/R.framework/Versions/3.3/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/3.3/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>:68:1: note: expanded from here
kh_del_i
^
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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c merge_reorder_sam.cpp -o merge_reorder_sam.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c profile_alignments.c -o profile_alignments.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c quantify_methylation.cpp -o quantify_methylation.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c split_sam_chr.c -o split_sam_chr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c utilities.c -o utilities.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 QuasR.so R_init_QuasR.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o split_sam_chr.o utilities.o /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.3/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-3.4-bioc/meat/QuasR.buildbin-libdir/QuasR/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 (QuasR)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "QuasR.buildbin-libdir/QuasR/libs//QuasR.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "QuasR.buildbin-libdir/QuasR/libs//QuasR.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "QuasR.buildbin-libdir/QuasR/libs//QuasR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "QuasR.buildbin-libdir/QuasR/libs//QuasR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "QuasR.buildbin-libdir/QuasR/libs//QuasR.so"