##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL matter
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘matter’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c altrep.cpp -o altrep.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c bsearch.cpp -o bsearch.o
bsearch.cpp: In function ‘size_t binary_search(T, SEXP, size_t, size_t, double, int, int, bool) [with T = const char*]’:
bsearch.cpp:51:36: warning: ‘result’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   else if ( mid == right && result > 0 )
                             ~~~~~~~^~~
bsearch.cpp: In function ‘size_t binary_search(T, SEXP, size_t, size_t, double, int, int, bool) [with T = double]’:
bsearch.cpp:136:27: warning: ‘diff’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   else if ( (mid == right && diff > 0) && (nearest || dright < tol) )
             ~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
In file included from init.cpp:5:0:
altrep.h:20:25: warning: ‘MatterAlt_string’ defined but not used [-Wunused-variable]
 static R_altrep_class_t MatterAlt_string;
                         ^~~~~~~~~~~~~~~~
altrep.h:19:25: warning: ‘MatterAlt_real’ defined but not used [-Wunused-variable]
 static R_altrep_class_t MatterAlt_real;
                         ^~~~~~~~~~~~~~
altrep.h:18:25: warning: ‘MatterAlt_integer’ defined but not used [-Wunused-variable]
 static R_altrep_class_t MatterAlt_integer;
                         ^~~~~~~~~~~~~~~~~
altrep.h:17:25: warning: ‘MatterAlt_logical’ defined but not used [-Wunused-variable]
 static R_altrep_class_t MatterAlt_logical;
                         ^~~~~~~~~~~~~~~~~
altrep.h:16:25: warning: ‘MatterAlt_raw’ defined but not used [-Wunused-variable]
 static R_altrep_class_t MatterAlt_raw;
                         ^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c matter.cpp -o matter.o
matter.cpp: In member function ‘void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = double]’:
matter.cpp:3409:33: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                         add<T,T>(x, y, i, atm, 0, count, skip);
                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
matter.cpp: In member function ‘void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = int]’:
matter.cpp:3409:33: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                         add<T,T>(x, y, i, atm, 0, count, skip);
                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
matter.cpp: In member function ‘void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = unsigned char]’:
matter.cpp:3409:33: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                         add<T,T>(x, y, i, atm, 0, count, skip);
                         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
matter.cpp: In function ‘double var(MatterIterator<T>&, bool) [with T = double]’:
matter.cpp:4144:17: warning: ‘s_new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 s_new = s_old + (*x - m_old) * (*x - m_new);
                 ^~~~~
matter.cpp:4143:37: warning: ‘m_new’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 m_new = m_old + (*x - m_old) / n;
                                 ~~~~^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c vectools.cpp -o vectools.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o matter.so altrep.o bsearch.o init.o matter.o utils.o vectools.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-matter/00new/matter/libs
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘apply’ in package ‘matter’
Creating a new generic function for ‘scale’ in package ‘matter’
Creating a new generic function for ‘biglm’ in package ‘matter’
** 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 (matter)