matter 1.4.1
Kylie A. Bemis
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/matter |
| Branch: RELEASE_3_6 |
| Last Commit: ec72f93 |
| Last Changed Date: 2017-11-02 17:56:24 -0400 (Thu, 02 Nov 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf matter.buildbin-libdir && mkdir matter.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/matter_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=matter.buildbin-libdir --merge-multiarch matter_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL matter_1.4.1.zip && rm matter_1.4.1.tar.gz matter_1.4.1.zip
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install for i386
* installing *source* package 'matter' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=generic -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 = long int; size_t = unsigned int]':
matter.cpp:2903:25: 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 = long int; size_t = unsigned int]':
matter.cpp:2903:25: 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 = long int; size_t = unsigned int]':
matter.cpp:2903:25: 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:3538:17: warning: 's_new' may be used uninitialized in this function [-Wmaybe-uninitialized]
s_new = s_old + (*x - m_old) * (*x - m_new);
^
matter.cpp:3537:17: 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++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o matter.dll tmp.def init.o matter.o utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/matter.buildbin-libdir/matter/libs/i386
** R
** data
** preparing package for lazy loading
Creating a new generic function for 'apply' in package 'matter'
Creating a new generic function for 'scale' in package 'matter'
** help
*** installing help indices
converting help for package 'matter'
finding HTML links ... done
apply html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWStPvF/R.INSTALL90c7c9ed67/matter/man/apply.Rd:28: missing file link 'colMeans,matter_mat-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWStPvF/R.INSTALL90c7c9ed67/matter/man/apply.Rd:28: missing file link 'rowMeans,matter_mat-method'
bigglm html
delayed-ops html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWStPvF/R.INSTALL90c7c9ed67/matter/man/delayed-ops.rd:108: missing file link 'Arith'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWStPvF/R.INSTALL90c7c9ed67/matter/man/delayed-ops.rd:109: missing file link 'Compare'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWStPvF/R.INSTALL90c7c9ed67/matter/man/delayed-ops.rd:110: missing file link 'Math'
drle-class html
matter-class html
matter_arr-class html
matter_df-class html
matter_ex 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
scale html
summary-stats html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWStPvF/R.INSTALL90c7c9ed67/matter/man/summary-stats.Rd:79: missing file link 'colMeans'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWStPvF/R.INSTALL90c7c9ed67/matter/man/summary-stats.Rd:80: missing file link 'rowSums'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWStPvF/R.INSTALL90c7c9ed67/matter/man/summary-stats.Rd:81: missing file link 'rowMeans'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'matter' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=generic -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 int; size_t = long long unsigned int]':
matter.cpp:2903:25: 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 int; size_t = long long unsigned int]':
matter.cpp:2903:25: 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 int; size_t = long long unsigned int]':
matter.cpp:2903:25: 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:3538:17: warning: 's_new' may be used uninitialized in this function [-Wmaybe-uninitialized]
s_new = s_old + (*x - m_old) * (*x - m_new);
^
matter.cpp:3537:17: 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++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o matter.dll tmp.def init.o matter.o utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/matter.buildbin-libdir/matter/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'matter' as matter_1.4.1.zip
* DONE (matter)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'matter' successfully unpacked and MD5 sums checked
In R CMD INSTALL