############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/hapFabia_1.36.0.tar.gz && rm -rf hapFabia.buildbin-libdir && mkdir hapFabia.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hapFabia.buildbin-libdir hapFabia_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL hapFabia_1.36.0.zip && rm hapFabia_1.36.0.tar.gz hapFabia_1.36.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 956k 100 956k 0 0 981k 0 --:--:-- --:--:-- --:--:-- 981k 100 956k 100 956k 0 0 981k 0 --:--:-- --:--:-- --:--:-- 981k install for i386 * installing *source* package 'hapFabia' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interfaceR.c -o interfaceR.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c split_sparse_matrixB.c -o split_sparse_matrixB.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcftoFABIAB.c -o vcftoFABIAB.o vcftoFABIAB.c: In function 'getdelimS': vcftoFABIAB.c:50:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (ch == EOF) ^~ vcftoFABIAB.c:54:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' while (idx > *linebufsz - 2) { ^~~~~ vcftoFABIAB.c: In function 'vcftoFABIAB': vcftoFABIAB.c:394:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] strncat(format[j],Iformat,19); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:382:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation] strncat(info[j],Iinfo,190); ^~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:372:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] strncat(filter[j],Ifilter,19); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:362:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] strncat(qual[j],Iqual,19); ^~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:352:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] strncat(minor[j],Iminor,190); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:342:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] strncat(major[j],Imajor,190); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:332:5: warning: 'strncat' output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation] strncat(snpName[j],IsnpName,49); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o hapFabia.dll tmp.def interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -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/hapFabia.buildbin-libdir/00LOCK-hapFabia/00new/hapFabia/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'hapFabia' finding HTML links ... done IBDsegment-class html REDIRECT:topic IBDsegment,numeric,numeric,character,numeric,numeric,numeric,numeric,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector-method -> IBDsegment-class.html [ FAIL ] IBDsegmentList-class html IBDsegmentList2excel html analyzeIBDsegments html chr1ASW1000G html compareIBDsegmentLists html extractIBDsegments html REDIRECT:topic extractIBDsegments,Factorization,list,data.frame,character,matrix,numeric,numeric,numeric,numeric,numeric,numeric,numeric,numeric-method -> extractIBDsegments.html [ FAIL ] findDenseRegions html hapFabia html hapFabiaVersion html hapRes html identifyDuplicates html iterateIntervals html makePipelineFile html matrixPlot html mergeIBDsegmentLists html mergedIBDsegmentList html plotIBDsegment html res html setAnnotation html setStatistics html sim html simu html simulateIBDsegments html simulateIBDsegmentsFabia html split_sparse_matrix html toolsFactorizationClass html vcftoFABIA 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 'hapFabia' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interfaceR.c -o interfaceR.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c split_sparse_matrixB.c -o split_sparse_matrixB.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcftoFABIAB.c -o vcftoFABIAB.o vcftoFABIAB.c: In function 'getdelimS': vcftoFABIAB.c:50:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (ch == EOF) ^~ vcftoFABIAB.c:54:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' while (idx > *linebufsz - 2) { ^~~~~ vcftoFABIAB.c: In function 'vcftoFABIAB': vcftoFABIAB.c:394:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] strncat(format[j],Iformat,19); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:382:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation] strncat(info[j],Iinfo,190); ^~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:372:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] strncat(filter[j],Ifilter,19); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:362:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] strncat(qual[j],Iqual,19); ^~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:352:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] strncat(minor[j],Iminor,190); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:342:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] strncat(major[j],Imajor,190); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:332:5: warning: 'strncat' output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation] strncat(snpName[j],IsnpName,49); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o hapFabia.dll tmp.def interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -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/hapFabia.buildbin-libdir/hapFabia/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'hapFabia' as hapFabia_1.36.0.zip * DONE (hapFabia) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'hapFabia' successfully unpacked and MD5 sums checked