matter 1.12.0
Kylie A. Bemis
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/matter |
| Branch: RELEASE_3_10 |
| Last Commit: dc00133 |
| Last Changed Date: 2019-10-29 13:10:10 -0400 (Tue, 29 Oct 2019) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/matter_1.12.0.tar.gz && rm -rf matter.buildbin-libdir && mkdir matter.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=matter.buildbin-libdir matter_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL matter_1.12.0.zip && rm matter_1.12.0.tar.gz matter_1.12.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 1103k 100 1103k 0 0 19.6M 0 --:--:-- --:--:-- --:--:-- 21.1M
install for i386
* installing *source* package 'matter' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c altrep.cpp -o altrep.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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*; size_t = unsigned int; SEXP = SEXPREC*]':
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; size_t = unsigned int; SEXP = SEXPREC*]':
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:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c init.cpp -o init.o
In file included from init.cpp:5:0:
altrep.h:16:25: warning: 'MatterAlt_raw' defined but not used [-Wunused-variable]
static R_altrep_class_t MatterAlt_raw;
^
altrep.h:17:25: warning: 'MatterAlt_logical' defined but not used [-Wunused-variable]
static R_altrep_class_t MatterAlt_logical;
^
altrep.h:18:25: warning: 'MatterAlt_integer' defined but not used [-Wunused-variable]
static R_altrep_class_t MatterAlt_integer;
^
altrep.h:19:25: warning: 'MatterAlt_real' defined but not used [-Wunused-variable]
static R_altrep_class_t MatterAlt_real;
^
altrep.h:20:25: warning: 'MatterAlt_string' defined but not used [-Wunused-variable]
static R_altrep_class_t MatterAlt_string;
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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 = int; index_t = int; size_t = unsigned 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; index_t = int; size_t = unsigned int]':
matter.cpp:3409:25: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
matter.cpp: In member function 'void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = double; index_t = int; size_t = unsigned int]':
matter.cpp:3409:25: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
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:4143:17: warning: 'm_new' may be used uninitialized in this function [-Wmaybe-uninitialized]
m_new = m_old + (*x - m_old) / n;
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c vectools.cpp -o vectools.o
C:/Rtools/mingw_32/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-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-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:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c altrep.cpp -o altrep.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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*; size_t = long long unsigned int; SEXP = SEXPREC*]':
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; size_t = long long unsigned int; SEXP = SEXPREC*]':
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:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c init.cpp -o init.o
In file included from init.cpp:5:0:
altrep.h:16:25: warning: 'MatterAlt_raw' defined but not used [-Wunused-variable]
static R_altrep_class_t MatterAlt_raw;
^
altrep.h:17:25: warning: 'MatterAlt_logical' defined but not used [-Wunused-variable]
static R_altrep_class_t MatterAlt_logical;
^
altrep.h:18:25: warning: 'MatterAlt_integer' defined but not used [-Wunused-variable]
static R_altrep_class_t MatterAlt_integer;
^
altrep.h:19:25: warning: 'MatterAlt_real' defined but not used [-Wunused-variable]
static R_altrep_class_t MatterAlt_real;
^
altrep.h:20:25: warning: 'MatterAlt_string' defined but not used [-Wunused-variable]
static R_altrep_class_t MatterAlt_string;
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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; index_t = long long int; size_t = long long unsigned 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 = int; index_t = long long int; size_t = long long unsigned int]':
matter.cpp:3409:25: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
matter.cpp: In member function 'void Ops::do_ops(T*, Atoms*, index_t, index_t, size_t) [with T = unsigned char; index_t = long long int; size_t = long long unsigned int]':
matter.cpp:3409:25: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized]
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:4143:17: warning: 'm_new' may be used uninitialized in this function [-Wmaybe-uninitialized]
m_new = m_old + (*x - m_old) / n;
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c vectools.cpp -o vectools.o
C:/Rtools/mingw_64/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-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/matter.buildbin-libdir/matter/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'matter' as matter_1.12.0.zip
* DONE (matter)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'matter' successfully unpacked and MD5 sums checked