############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL hapFabia ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library' * installing *source* package 'hapFabia' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.3.0' gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c interfaceR.c -o interfaceR.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c split_sparse_matrixB.c -o split_sparse_matrixB.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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] 50 | if (ch == EOF) | ^~ vcftoFABIAB.c:54:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 54 | while (idx > *linebufsz - 2) { | ^~~~~ vcftoFABIAB.c: In function 'vcftoFABIAB': vcftoFABIAB.c:394:19: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] 394 | strncat(format[j],Iformat,19); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:382:19: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation] 382 | strncat(info[j],Iinfo,190); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:372:19: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] 372 | strncat(filter[j],Ifilter,19); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:362:19: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation] 362 | strncat(qual[j],Iqual,19); | ^~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:352:19: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] 352 | strncat(minor[j],Iminor,190); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:342:19: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation] 342 | strncat(major[j],Imajor,190); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:332:19: warning: 'strncat' output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation] 332 | strncat(snpName[j],IsnpName,49); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vcftoFABIAB.c:250:21: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 250 | snpName[0] = calloc((long) 50*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from vcftoFABIAB.c:2: c:\rtools43\x86_64-w64-mingw32.static.posix\include\stdlib.h:535:17: note: in a call to allocation function 'calloc' declared here 535 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ vcftoFABIAB.c:258:20: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 258 | filter[0] = calloc((long) 20*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c:\rtools43\x86_64-w64-mingw32.static.posix\include\stdlib.h:535:17: note: in a call to allocation function 'calloc' declared here 535 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ vcftoFABIAB.c:266:18: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | qual[0] = calloc((long) 20*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c:\rtools43\x86_64-w64-mingw32.static.posix\include\stdlib.h:535:17: note: in a call to allocation function 'calloc' declared here 535 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ vcftoFABIAB.c:281:20: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 281 | format[0] = calloc((long) 20*snps, sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c:\rtools43\x86_64-w64-mingw32.static.posix\include\stdlib.h:535:17: note: in a call to allocation function 'calloc' declared here 535 | void *__cdecl calloc(size_t _NumOfElements,size_t _SizeOfElements); | ^~~~~~ gcc -shared -s -static-libgcc -o hapFabia.dll tmp.def interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-hapFabia/00new/hapFabia/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (hapFabia)