Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:10 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the matter package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/matter.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1046/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
matter 1.18.0 (landing page) Kylie A. Bemis
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: matter |
Version: 1.18.0 |
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/matter_1.18.0.tar.gz && rm -rf matter.buildbin-libdir && mkdir matter.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=matter.buildbin-libdir matter_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL matter_1.18.0.zip && rm matter_1.18.0.tar.gz matter_1.18.0.zip |
StartedAt: 2021-10-14 07:26:03 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 07:29:05 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 182.3 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/matter_1.18.0.tar.gz && rm -rf matter.buildbin-libdir && mkdir matter.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=matter.buildbin-libdir matter_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL matter_1.18.0.zip && rm matter_1.18.0.tar.gz matter_1.18.0.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 37 1107k 37 412k 0 0 1371k 0 --:--:-- --:--:-- --:--:-- 1370k 100 1107k 100 1107k 0 0 2949k 0 --:--:-- --:--:-- --:--:-- 2952k 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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/matter.buildbin-libdir/matter/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'matter' as matter_1.18.0.zip * DONE (matter) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'matter' successfully unpacked and MD5 sums checked