############################################################################## ############################################################################## ### ### Running command: ### ### 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 ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 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(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(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(x, y, i, atm, 0, count, skip); ^~~ matter.cpp: In function 'double var(MatterIterator&, 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(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(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(x, y, i, atm, 0, count, skip); ^~~ matter.cpp: In function 'double var(MatterIterator&, 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