############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/iBMQ_1.34.0.tar.gz && rm -rf iBMQ.buildbin-libdir && mkdir iBMQ.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iBMQ.buildbin-libdir iBMQ_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL iBMQ_1.34.0.zip && rm iBMQ_1.34.0.tar.gz iBMQ_1.34.0.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 5 3798k 5 222k 0 0 656k 0 0:00:05 --:--:-- 0:00:05 656k 45 3798k 45 1746k 0 0 1306k 0 0:00:02 0:00:01 0:00:01 1306k 100 3798k 100 3798k 0 0 1735k 0 0:00:02 0:00:02 --:--:-- 1736k install for i386 * installing *source* package 'iBMQ' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ARS.c -o ARS.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RngStream.c -o RngStream.o RngStream.c: In function 'RngStream_CreateStream': RngStream.c:321:7: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy (g->name, name, len + 1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RngStream.c:319:13: note: length computed here len = strlen (name); ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c iBMQ_common.c -o iBMQ_common.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c main_parallel_sparse.c -o main_parallel_sparse.o main_parallel_sparse.c: In function 'iBMQ_main': main_parallel_sparse.c:289:3: warning: 'Cfile' may be used uninitialized in this function [-Wmaybe-uninitialized] fclose(Cfile); ^~~~~~~~~~~~~ main_parallel_sparse.c:288:3: warning: 'Sig2file' may be used uninitialized in this function [-Wmaybe-uninitialized] fclose(Sig2file); ^~~~~~~~~~~~~~~~ main_parallel_sparse.c:287:3: warning: 'Mufile' may be used uninitialized in this function [-Wmaybe-uninitialized] fclose(Mufile); ^~~~~~~~~~~~~~ main_parallel_sparse.c:285:3: warning: 'Bfile' may be used uninitialized in this function [-Wmaybe-uninitialized] fclose(Bfile); ^~~~~~~~~~~~~ main_parallel_sparse.c:284:3: warning: 'Afile' may be used uninitialized in this function [-Wmaybe-uninitialized] fclose(Afile); ^~~~~~~~~~~~~ main_parallel_sparse.c:286:3: warning: 'Pfile' may be used uninitialized in this function [-Wmaybe-uninitialized] fclose(Pfile); ^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c main_parallel_sparse_constC.c -o main_parallel_sparse_constC.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c norm_gamma_generation.c -o norm_gamma_generation.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/i386/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sparse.c -o sparse.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o iBMQ.dll tmp.def ARS.o RngStream.o iBMQ_common.o main_parallel_sparse.o main_parallel_sparse_constC.o norm_gamma_generation.o sparse.o -L/i386/lib -lgsl -lgslcblas -lm -fopenmp -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/iBMQ.buildbin-libdir/00LOCK-iBMQ/00new/iBMQ/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'iBMQ' finding HTML links ... done PPA.liver html calculateThreshold html eqtlClassifier html eqtlFinder html eqtlMcmc html gene html genepos html genotype.liver html hotspotFinder html iBMQ-package html map.liver html phenotype.liver html probe.liver html snp html snppos 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 'iBMQ' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ARS.c -o ARS.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RngStream.c -o RngStream.o RngStream.c: In function 'RngStream_CreateStream': RngStream.c:321:7: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy (g->name, name, len + 1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RngStream.c:319:13: note: length computed here len = strlen (name); ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c iBMQ_common.c -o iBMQ_common.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c main_parallel_sparse.c -o main_parallel_sparse.o main_parallel_sparse.c: In function 'iBMQ_main': main_parallel_sparse.c:289:3: warning: 'Cfile' may be used uninitialized in this function [-Wmaybe-uninitialized] fclose(Cfile); ^~~~~~~~~~~~~ main_parallel_sparse.c:288:3: warning: 'Sig2file' may be used uninitialized in this function [-Wmaybe-uninitialized] fclose(Sig2file); ^~~~~~~~~~~~~~~~ main_parallel_sparse.c:287:3: warning: 'Mufile' may be used uninitialized in this function [-Wmaybe-uninitialized] fclose(Mufile); ^~~~~~~~~~~~~~ main_parallel_sparse.c:285:3: warning: 'Bfile' may be used uninitialized in this function [-Wmaybe-uninitialized] fclose(Bfile); ^~~~~~~~~~~~~ main_parallel_sparse.c:284:3: warning: 'Afile' may be used uninitialized in this function [-Wmaybe-uninitialized] fclose(Afile); ^~~~~~~~~~~~~ main_parallel_sparse.c:286:3: warning: 'Pfile' may be used uninitialized in this function [-Wmaybe-uninitialized] fclose(Pfile); ^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c main_parallel_sparse_constC.c -o main_parallel_sparse_constC.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c norm_gamma_generation.c -o norm_gamma_generation.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sparse.c -o sparse.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o iBMQ.dll tmp.def ARS.o RngStream.o iBMQ_common.o main_parallel_sparse.o main_parallel_sparse_constC.o norm_gamma_generation.o sparse.o -L/x64/lib -lgsl -lgslcblas -lm -fopenmp -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/iBMQ.buildbin-libdir/iBMQ/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'iBMQ' as iBMQ_1.34.0.zip * DONE (iBMQ) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'iBMQ' successfully unpacked and MD5 sums checked