BioC 3.6: BUILD BIN report for pqsfinder on veracruz1

Package: pqsfinder

Version: 1.5.13

Command: rm -rf pqsfinder.buildbin-libdir && mkdir pqsfinder.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh pqsfinder_1.5.13.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R pqsfinder.buildbin-libdir

StartedAt: 2017-08-16 11:04:53 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 11:06:22 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 88.7 seconds

RetCode: 0

Status:  OK

PackageFile: pqsfinder_1.5.13.tgz

PackageFileSize: 3.061 MiB

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf pqsfinder.buildbin-libdir && mkdir pqsfinder.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh pqsfinder_1.5.13.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R pqsfinder.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=pqsfinder.buildbin-libdir pqsfinder_1.5.13.tar.gz'
>>>>>>> 

* installing *source* package ‘pqsfinder’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/RcppCommon.h:179:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:516:61: warning: unused parameter 'object' [-Wunused-parameter]
        inline SEXP wrap_dispatch_unknown_iterable(const T& object, ::Rcpp::traits::false_type) {
                                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:906:48: warning: unused parameter 'obj' [-Wunused-parameter]
     inline SEXP module_wrap_dispatch(const T& obj, Rcpp::traits::void_wrap_tag) {
                                               ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:40:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/Vector.h:52:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:25:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Subsetter.h:146:68: warning: unused parameter 't' [-Wunused-parameter]
    void get_indices( traits::identity< traits::int2type<INTSXP> > t ) {
                                                                   ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Subsetter.h:156:69: warning: unused parameter 't' [-Wunused-parameter]
    void get_indices( traits::identity< traits::int2type<REALSXP> > t ) {
                                                                    ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Subsetter.h:168:68: warning: unused parameter 't' [-Wunused-parameter]
    void get_indices( traits::identity< traits::int2type<STRSXP> > t ) {
                                                                   ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Subsetter.h:183:68: warning: unused parameter 't' [-Wunused-parameter]
    void get_indices( traits::identity< traits::int2type<LGLSXP> > t ) {
                                                                   ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:40:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/Vector.h:52:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:516:82: warning: unused parameter 'names' [-Wunused-parameter]
    static void replace_element__dispatch( traits::false_type, iterator it, SEXP names, R_xlen_t index, const U& u){
                                                                                 ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:516:98: warning: unused parameter 'index' [-Wunused-parameter]
    static void replace_element__dispatch( traits::false_type, iterator it, SEXP names, R_xlen_t index, const U& u){
                                                                                                 ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:44:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/Promise.h:74:33: warning: unused parameter 'data' [-Wunused-parameter]
        inline void update(SEXP data){}
                                ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:52:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/StretchyList.h:51:26: warning: unused parameter 'x' [-Wunused-parameter]
        void update(SEXP x){}
                         ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:64:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/Module.h:134:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:46:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:56:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:69:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:83:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:98:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:114:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:131:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:64:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/Module.h:135:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:37:35: warning: unused parameter 'args' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                  ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:37:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:51:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:65:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:82:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:100:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:119:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:139:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:160:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:64:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/Module.h:340:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/class.h:451:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_Field.h:57:21: warning: unused parameter 'object' [-Wunused-parameter]
    void set(Class* object, SEXP value) { throw std::range_error("read only data member") ; }
                    ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_Field.h:57:34: warning: unused parameter 'value' [-Wunused-parameter]
    void set(Class* object, SEXP value) { throw std::range_error("read only data member") ; }
                                 ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:65:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/InternalFunction.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/InternalFunctionWithStdFunction.h:32:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/generated/InternalFunctionWithStdFunction_call.h:29:69: warning: unused parameter 'args' [-Wunused-parameter]
    RESULT_TYPE call(const std::function<RESULT_TYPE()> &fun, SEXP* args) {
                                                                    ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:72:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/operators/operators.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/operators/Comparator_With_One_Value.h:56:27: warning: unused parameter 'i' [-Wunused-parameter]
        inline int rhs_is_na(int i) const { return rhs ; }
                                 ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/operators/Comparator_With_One_Value.h:95:27: warning: unused parameter 'i' [-Wunused-parameter]
        inline int rhs_is_na(int i) const { return rhs ; }
                                 ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:72:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/functions.h:36:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/is_na.h:58:41: warning: unused parameter 'i' [-Wunused-parameter]
        inline int operator[]( R_xlen_t i ) const {
                                        ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:72:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/functions.h:85:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/cbind.h:154:44: warning: unused parameter 'i' [-Wunused-parameter]
    inline stored_type operator[](R_xlen_t i) const {
                                           ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/cbind.h:158:44: warning: unused parameter 'i' [-Wunused-parameter]
    inline stored_type operator()(R_xlen_t i, R_xlen_t j) const {
                                           ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/cbind.h:158:56: warning: unused parameter 'j' [-Wunused-parameter]
    inline stored_type operator()(R_xlen_t i, R_xlen_t j) const {
                                                       ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/cbind.h:446:23: warning: unused parameter 't' [-Wunused-parameter]
MakeBindable(const T& t) {
                      ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/cbind.h:455:23: warning: unused parameter 't' [-Wunused-parameter]
MakeBindable(const T& t) {
                      ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:72:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/matrix/matrix_functions.h:26:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/matrix/row.h:39:36: warning: unused parameter 'j' [-Wunused-parameter]
        inline int operator()( int i, int j ) const {
                                          ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:72:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/matrix/matrix_functions.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/matrix/col.h:39:29: warning: unused parameter 'i' [-Wunused-parameter]
        inline int operator()( int i, int j ) const {
                                   ^
39 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c pqsfinder.cpp -o pqsfinder.o
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/RcppCommon.h:179:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:516:61: warning: unused parameter 'object' [-Wunused-parameter]
        inline SEXP wrap_dispatch_unknown_iterable(const T& object, ::Rcpp::traits::false_type) {
                                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:906:48: warning: unused parameter 'obj' [-Wunused-parameter]
     inline SEXP module_wrap_dispatch(const T& obj, Rcpp::traits::void_wrap_tag) {
                                               ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:40:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/Vector.h:52:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:25:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Subsetter.h:146:68: warning: unused parameter 't' [-Wunused-parameter]
    void get_indices( traits::identity< traits::int2type<INTSXP> > t ) {
                                                                   ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Subsetter.h:156:69: warning: unused parameter 't' [-Wunused-parameter]
    void get_indices( traits::identity< traits::int2type<REALSXP> > t ) {
                                                                    ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Subsetter.h:168:68: warning: unused parameter 't' [-Wunused-parameter]
    void get_indices( traits::identity< traits::int2type<STRSXP> > t ) {
                                                                   ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Subsetter.h:183:68: warning: unused parameter 't' [-Wunused-parameter]
    void get_indices( traits::identity< traits::int2type<LGLSXP> > t ) {
                                                                   ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:40:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/Vector.h:52:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:516:82: warning: unused parameter 'names' [-Wunused-parameter]
    static void replace_element__dispatch( traits::false_type, iterator it, SEXP names, R_xlen_t index, const U& u){
                                                                                 ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/vector/Vector.h:516:98: warning: unused parameter 'index' [-Wunused-parameter]
    static void replace_element__dispatch( traits::false_type, iterator it, SEXP names, R_xlen_t index, const U& u){
                                                                                                 ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:44:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/Promise.h:74:33: warning: unused parameter 'data' [-Wunused-parameter]
        inline void update(SEXP data){}
                                ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:52:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/StretchyList.h:51:26: warning: unused parameter 'x' [-Wunused-parameter]
        void update(SEXP x){}
                         ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:64:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/Module.h:134:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:46:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:56:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:69:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:83:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:98:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:114:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:131:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:64:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/Module.h:135:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:37:35: warning: unused parameter 'args' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                  ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:37:45: warning: unused parameter 'nargs' [-Wunused-parameter]
    virtual Class* get_new( SEXP* args, int nargs ){
                                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:51:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:65:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:82:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:100:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:119:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:139:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_generated_Factory.h:160:43: warning: unused parameter 'nargs' [-Wunused-parameter]
  virtual Class* get_new( SEXP* args, int nargs ){
                                          ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:64:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/Module.h:340:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/class.h:451:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_Field.h:57:21: warning: unused parameter 'object' [-Wunused-parameter]
    void set(Class* object, SEXP value) { throw std::range_error("read only data member") ; }
                    ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/module/Module_Field.h:57:34: warning: unused parameter 'value' [-Wunused-parameter]
    void set(Class* object, SEXP value) { throw std::range_error("read only data member") ; }
                                 ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:65:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/InternalFunction.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/InternalFunctionWithStdFunction.h:32:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/generated/InternalFunctionWithStdFunction_call.h:29:69: warning: unused parameter 'args' [-Wunused-parameter]
    RESULT_TYPE call(const std::function<RESULT_TYPE()> &fun, SEXP* args) {
                                                                    ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:72:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/operators/operators.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/operators/Comparator_With_One_Value.h:56:27: warning: unused parameter 'i' [-Wunused-parameter]
        inline int rhs_is_na(int i) const { return rhs ; }
                                 ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/operators/Comparator_With_One_Value.h:95:27: warning: unused parameter 'i' [-Wunused-parameter]
        inline int rhs_is_na(int i) const { return rhs ; }
                                 ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:72:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/functions.h:36:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/is_na.h:58:41: warning: unused parameter 'i' [-Wunused-parameter]
        inline int operator[]( R_xlen_t i ) const {
                                        ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:72:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/functions.h:85:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/cbind.h:154:44: warning: unused parameter 'i' [-Wunused-parameter]
    inline stored_type operator[](R_xlen_t i) const {
                                           ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/cbind.h:158:44: warning: unused parameter 'i' [-Wunused-parameter]
    inline stored_type operator()(R_xlen_t i, R_xlen_t j) const {
                                           ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/cbind.h:158:56: warning: unused parameter 'j' [-Wunused-parameter]
    inline stored_type operator()(R_xlen_t i, R_xlen_t j) const {
                                                       ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/cbind.h:446:23: warning: unused parameter 't' [-Wunused-parameter]
MakeBindable(const T& t) {
                      ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/functions/cbind.h:455:23: warning: unused parameter 't' [-Wunused-parameter]
MakeBindable(const T& t) {
                      ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:72:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/matrix/matrix_functions.h:26:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/matrix/row.h:39:36: warning: unused parameter 'j' [-Wunused-parameter]
        inline int operator()( int i, int j ) const {
                                          ^
In file included from pqsfinder.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:72:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/matrix/matrix_functions.h:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/sugar/matrix/col.h:39:29: warning: unused parameter 'i' [-Wunused-parameter]
        inline int operator()( int i, int j ) const {
                                   ^
39 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/cregex.cpp -o boost_regex/cregex.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/icu.cpp -o boost_regex/icu.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/instances.cpp -o boost_regex/instances.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/regex.cpp -o boost_regex/regex.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -Wall -Wextra -fPIC  -Wall -g -O2 -c boost_regex/winstances.cpp -o boost_regex/winstances.o
mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib"
ar rs "/Users/biocbuild/bbs-3.6-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a" boost_regex/c_regex_traits.o boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/instances.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/regex_raw_buffer.o boost_regex/regex_traits_defaults.o boost_regex/static_mutex.o boost_regex/usinstances.o boost_regex/w32_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o
ar: creating archive /Users/biocbuild/bbs-3.6-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.6-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a(icu.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.6-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a(regex_debug.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.6-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a(usinstances.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.6-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a(w32_regex_traits.o) has no symbols
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 pqsfinder.so RcppExports.o pqsfinder.o /Users/biocbuild/bbs-3.6-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/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 (pqsfinder)


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