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BUILD BIN report for scPipe on merida2

This page was generated on 2018-10-17 08:59:01 -0400 (Wed, 17 Oct 2018).

Package 1332/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scPipe 1.2.1
Luyi Tian
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/scPipe
Branch: RELEASE_3_7
Last Commit: 19a1726
Last Changed Date: 2018-05-31 19:42:56 -0400 (Thu, 31 May 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: scPipe
Version: 1.2.1
Command: rm -rf scPipe.buildbin-libdir && mkdir scPipe.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scPipe_1.2.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scPipe.buildbin-libdir
StartedAt: 2018-10-17 02:06:54 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:08:18 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 83.7 seconds
RetCode: 0
Status:  OK 
PackageFile: scPipe_1.2.1.tgz
PackageFileSize: 1.385 MiB

Command output

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###
### Running command:
###
###   rm -rf scPipe.buildbin-libdir && mkdir scPipe.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scPipe_1.2.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scPipe.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=scPipe.buildbin-libdir scPipe_1.2.1.tar.gz'
>>>>>>> 

* installing *source* package ‘scPipe’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Gene.cpp -o Gene.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Interval.cpp -o Interval.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c cellbarcode.cpp -o cellbarcode.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c detect_barcode.cpp -o detect_barcode.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c parsebam.cpp -o parsebam.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c parsecount.cpp -o parsecount.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
In file included from rcpp_scPipe_func.cpp:3:
./trimbarcode.h:11:1: warning: unused function 'kseq_init' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:170:16: note: expanded from macro '__KSEQ_BASIC'
        SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
                      ^
In file included from rcpp_scPipe_func.cpp:3:
./trimbarcode.h:11:1: warning: unused function 'kseq_destroy' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:176:13: note: expanded from macro '__KSEQ_BASIC'
        SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
                   ^
In file included from rcpp_scPipe_func.cpp:3:
./trimbarcode.h:11:1: warning: unused function 'kseq_read' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:242:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_READ(SCOPE)
        ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include/kseq.h:190:12: note: expanded from macro '__KSEQ_READ'
        SCOPE int kseq_read(kseq_t *seq) \
                  ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c transcriptmapping.cpp -o transcriptmapping.o
transcriptmapping.cpp:605:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
    sam_hdr_write(of, header);
    ^˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜
transcriptmapping.cpp:569:10: warning: unused function 'report_every_3_mins' [-Wunused-function]
    void report_every_3_mins(atomic<unsigned long long> &cnt, atomic<bool> &running) {
         ^
In file included from transcriptmapping.cpp:2:
./transcriptmapping.h:138:15: warning: private field 'SOURCE' is not used [-Wunused-private-field]
    const int SOURCE = 1;
              ^
./transcriptmapping.h:142:15: warning: private field 'SCORE' is not used [-Wunused-private-field]
    const int SCORE = 5;
              ^
./transcriptmapping.h:144:15: warning: private field 'PHASE' is not used [-Wunused-private-field]
    const int PHASE = 7;
              ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c trimbarcode.cpp -o trimbarcode.o
trimbarcode.cpp:92:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
    sam_hdr_write(fp, hdr);
    ^˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c utils.cpp -o utils.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 scPipe.so Gene.o Interval.o RcppExports.o cellbarcode.o detect_barcode.o parsebam.o parsecount.o rcpp_scPipe_func.o transcriptmapping.o trimbarcode.o utils.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.7-bioc/meat/scPipe.buildbin-libdir/scPipe/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
* DONE (scPipe)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "scPipe.buildbin-libdir/scPipe/libs//scPipe.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "scPipe.buildbin-libdir/scPipe/libs//scPipe.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "scPipe.buildbin-libdir/scPipe/libs//scPipe.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "scPipe.buildbin-libdir/scPipe/libs//scPipe.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "scPipe.buildbin-libdir/scPipe/libs//scPipe.so"