Package: qrqc

Version: 1.38.0

Command: rm -rf qrqc.buildbin-libdir && mkdir qrqc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh qrqc_1.38.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R qrqc.buildbin-libdir

StartedAt: 2019-10-16 09:11:59 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 09:13:04 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 65.1 seconds

RetCode: 0

Status:  OK

PackageFile: qrqc_1.38.0.tgz

PackageFileSize: 667.5 KiB

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### Running command:
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###   rm -rf qrqc.buildbin-libdir && mkdir qrqc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh qrqc_1.38.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R qrqc.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=qrqc.buildbin-libdir qrqc_1.38.0.tar.gz'
>>>>>>> 

* installing *source* package ‘qrqc’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c io.c -o io.o
io.c:348:14: warning: incompatible pointer types initializing 'gzFile *' (aka 'struct gzFile_s **') with an expression of type 'gzFile' (aka 'struct gzFile_s *') [-Wincompatible-pointer-types]
  FILE_TYPE *fp = FILE_OPEN(CHAR(STRING_ELT(filename, 0)), "r");
             ^    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c:351:21: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  block = kseq_init(fp);
                    ^~
                    *
io.c:35:1: note: passing argument to parameter 'fd' here
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include/htslib/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/3.6/Resources/library/Rhtslib/include/htslib/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include/htslib/kseq.h:170:33: note: expanded from macro '__KSEQ_BASIC'
        SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
                                       ^
io.c:453:21: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  block = kseq_init(fp);
                    ^~
                    *
io.c:35:1: note: passing argument to parameter 'fd' here
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include/htslib/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/3.6/Resources/library/Rhtslib/include/htslib/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include/htslib/kseq.h:170:33: note: expanded from macro '__KSEQ_BASIC'
        SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
                                       ^
io.c:454:14: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  FILE_CLOSE(fp);
             ^~
             *
io.c:34:32: note: expanded from macro 'FILE_CLOSE'
#define FILE_CLOSE(x) (gzclose(x))
                               ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:1521:43: note: passing argument to parameter 'file' here
ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                                          ^
io.c:35:1: warning: unused function 'kseq_destroy' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include/htslib/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/3.6/Resources/library/Rhtslib/include/htslib/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include/htslib/kseq.h:176:13: note: expanded from macro '__KSEQ_BASIC'
        SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
                   ^
5 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/3.6/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/qrqc.buildbin-libdir/00LOCK-qrqc/00new/qrqc/libs
** R
** 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 (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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/Resources/lib/libquadmath.0.dylib" "qrqc.buildbin-libdir/qrqc/libs//qrqc.so"