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### Running command:
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### 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
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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)
