DeMixT 1.4.0
Shaolong Cao, Peng Yang
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/DeMixT |
| Branch: RELEASE_3_11 |
| Last Commit: 79d97ec |
| Last Changed Date: 2020-04-27 15:25:08 -0400 (Mon, 27 Apr 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 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 | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/DeMixT_1.4.0.tar.gz && rm -rf DeMixT.buildbin-libdir && mkdir DeMixT.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DeMixT.buildbin-libdir DeMixT_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DeMixT_1.4.0.zip && rm DeMixT_1.4.0.tar.gz DeMixT_1.4.0.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
100 2745k 100 2745k 0 0 32.4M 0 --:--:-- --:--:-- --:--:-- 35.7M
install for i386
* installing *source* package 'DeMixT' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DeMixT.c -o DeMixT.o
DeMixT.c: In function 'Tdemix':
DeMixT.c:267:28: warning: implicit declaration of function 'Rprintf'; did you mean 'wprintf'? [-Wimplicit-function-declaration]
if (nHavepi != 1) Rprintf("Iteration %d: updating parameters\n", i+1);
^~~~~~~
wprintf
DeMixT.c:36:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable]
double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
^~~~~~~~~
DeMixT.c:36:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable]
double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
^~~~~~~~~
DeMixT.c:36:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable]
double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
^~~~~~~~
DeMixT.c:36:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable]
double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
^~~~~~~~
DeMixT.c: In function 'gettumor':
DeMixT.c:589:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c:589:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c: In function 'getpi':
DeMixT.c:1278:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c:1278:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c: In function 'getspikeinpi':
DeMixT.c:1305:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c:1305:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c: In function 'getpiT':
DeMixT.c:1320:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c:1320:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c: In function 'Tdemix':
DeMixT.c:193:11: warning: 'Tavgtmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0));
^
DeMixT.c:92:8: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
FD = calloc(nS ,sizeof(double *));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from DeMixT.c:8:
C:/rtools40/mingw32/i686-w64-mingw32/include/stdlib.h:455:17: note: in a call to allocation function 'calloc' declared here
void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements);
^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Profile_2D.cpp -o Profile_2D.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o DeMixT.dll tmp.def DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/DeMixT.buildbin-libdir/00LOCK-DeMixT/00new/DeMixT/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DeMixT'
finding HTML links ... done
DeMixT html
DeMixT_GS html
DeMixT_S1 html
DeMixT_S2 html
Optimum_KernelC html
simulate_2comp html
simulate_3comp html
test.data.2comp html
test.data.3comp 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 'DeMixT' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DeMixT.c -o DeMixT.o
DeMixT.c: In function 'Tdemix':
DeMixT.c:267:28: warning: implicit declaration of function 'Rprintf'; did you mean 'wprintf'? [-Wimplicit-function-declaration]
if (nHavepi != 1) Rprintf("Iteration %d: updating parameters\n", i+1);
^~~~~~~
wprintf
DeMixT.c:36:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable]
double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
^~~~~~~~~
DeMixT.c:36:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable]
double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
^~~~~~~~~
DeMixT.c:36:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable]
double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
^~~~~~~~
DeMixT.c:36:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable]
double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
^~~~~~~~
DeMixT.c: In function 'gettumor':
DeMixT.c:589:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c:589:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c: In function 'getpi':
DeMixT.c:1278:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c:1278:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c: In function 'getspikeinpi':
DeMixT.c:1305:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c:1305:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c: In function 'getpiT':
DeMixT.c:1320:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c:1320:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^~~~~~~
DeMixT.c: In function 'Tdemix':
DeMixT.c:193:11: warning: 'Tavgtmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0));
^
DeMixT.c:92:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
FD = calloc(nS ,sizeof(double *));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from DeMixT.c:8:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/stdlib.h:455:17: note: in a call to allocation function 'calloc' declared here
void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements);
^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Profile_2D.cpp -o Profile_2D.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c registerDynamicSymbol.c -o registerDynamicSymbol.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o DeMixT.dll tmp.def DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/DeMixT.buildbin-libdir/DeMixT/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeMixT' as DeMixT_1.4.0.zip
* DONE (DeMixT)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DeMixT' successfully unpacked and MD5 sums checked