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### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/matter_1.20.0.tar.gz && rm -rf matter.buildbin-libdir && mkdir matter.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=matter.buildbin-libdir matter_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL matter_1.20.0.zip && rm matter_1.20.0.tar.gz matter_1.20.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
32 1105k 32 355k 0 0 1049k 0 0:00:01 --:--:-- 0:00:01 1049k
100 1105k 100 1105k 0 0 1550k 0 --:--:-- --:--:-- --:--:-- 1551k
install for i386
* installing *source* package 'matter' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c altrep.cpp -o altrep.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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) )
~~~~~~~~~~~~~~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
In file included from init.cpp:5:
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;
^~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:3409:25: 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:3409:25: 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:3409:25: 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;
~~~~^~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vectools.cpp -o vectools.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o matter.dll tmp.def altrep.o bsearch.o init.o matter.o utils.o vectools.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/matter.buildbin-libdir/00LOCK-matter/00new/matter/libs/i386
** 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
converting help for package 'matter'
finding HTML links ... done
apply html
finding level-2 HTML links ... done
biglm html
binvec html
bsearch html
checksum html
chunk_apply html
colStats html
combine-method html
combiner-method html
delayed-ops html
drle-class html
keys-method html
lapply html
locmax html
matter-class html
matter-datatypes html
matter-options html
matter-utils html
matter_arr-class html
matter_df-class html
matter_fc-class html
matter_list-class html
matter_mat-class html
matter_str-class html
matter_vec-class html
prcomp html
profmem html
rep_vt html
scale html
sparse_mat-class html
stream-stats html
struct html
summary-stats html
tolerance-method html
uuid html
virtual_mat-class html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'matter' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c altrep.cpp -o altrep.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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) )
~~~~~~~~~~~~~~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
In file included from init.cpp:5:
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;
^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:3409:25: 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:3409:25: 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:3409:25: 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;
~~~~^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vectools.cpp -o vectools.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o matter.dll tmp.def altrep.o bsearch.o init.o matter.o utils.o vectools.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/matter.buildbin-libdir/matter/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'matter' as matter_1.20.0.zip
* DONE (matter)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'matter' successfully unpacked and MD5 sums checked
