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###
### Running command:
###
###   rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --build --library=Rsubread.buildbin-libdir Rsubread_2.12.3.tar.gz
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* installing *source* package 'Rsubread' ...
** using staged installation
@@@@@ The operating system is Windows.
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture

gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c HelperFunctions.c -o HelperFunctions.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMbase-index.c -o LRMbase-index.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMchro-event.c -o LRMchro-event.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMfile-io.c -o LRMfile-io.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMhashtable.c -o LRMhashtable.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMhelper.c -o LRMhelper.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_wrapper.c -o R_wrapper.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RsimReads.c -o RsimReads.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c SNPCalling.c -o SNPCalling.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c aligner.c -o aligner.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c atgcContent.c -o atgcContent.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c build-sam-index.c -o build-sam-index.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c cell-counts.c -o cell-counts.o
cell-counts.c: In function 'cellCounts_find_hits_for_mapped_section':
cell-counts.c:1606:5: warning: 'search_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
 1606 |   if(search_start>0xffffff00) return;
      |     ^
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-bigtable.c -o core-bigtable.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-indel.c -o core-indel.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-interface-aligner.c -o core-interface-aligner.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-junction.c -o core-junction.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core.c -o core.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c detection-calls.c -o detection-calls.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c detectionCall.c -o detectionCall.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c exon-algorithms.c -o exon-algorithms.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c exon-align-indel.c -o exon-align-indel.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c exon-align.c -o exon-align.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c flattenAnnotations.c -o flattenAnnotations.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fullscan.c -o fullscan.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fusion-align.c -o fusion-align.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gen_rand_reads.c -o gen_rand_reads.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gene-algorithms.c -o gene-algorithms.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gene-value-index.c -o gene-value-index.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hashtable.c -o hashtable.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c index-builder.c -o index-builder.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c input-blc.c -o input-blc.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c input-files.c -o input-files.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c interval_merge.c -o interval_merge.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c long-hashtable.c -o long-hashtable.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c longread-mapping.c -o longread-mapping.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mergeVCF.c -o mergeVCF.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c processExons.c -o processExons.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c propmapped.c -o propmapped.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c qualityScores.c -o qualityScores.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c read-repair.c -o read-repair.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c readSummary.c -o readSummary.o
readSummary.c: In function 'vote_and_add_count':
readSummary.c:4938:31: warning: 'longest_overlap_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
 4938 |      if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0;
      |         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c removeDupReads.c -o removeDupReads.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sam2bed.c -o sam2bed.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sambam-file.c -o sambam-file.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c seek-zlib.c -o seek-zlib.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sorted-hashtable.c -o sorted-hashtable.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sublog.c -o sublog.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c tx-unique.c -o tx-unique.o
gcc -shared -s -static-libgcc -o Rsubread.dll tmp.def HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/Rsubread.buildbin-libdir/00LOCK-Rsubread/00new/Rsubread/libs/x64
** R
** 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
* MD5 sums
packaged installation of 'Rsubread' as Rsubread_2.12.3.zip
* DONE (Rsubread)