############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_2.6.4.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'Rsubread' ... ** using staged installation @@@@@ The operating system is Windows. ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HelperFunctions.c -o HelperFunctions.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMbase-index.c -o LRMbase-index.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMchro-event.c -o LRMchro-event.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMfile-io.c -o LRMfile-io.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhashtable.c -o LRMhashtable.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhelper.c -o LRMhelper.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMseek-zlib.c -o LRMseek-zlib.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_wrapper.c -o R_wrapper.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RsimReads.c -o RsimReads.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SNPCalling.c -o SNPCalling.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c aligner.c -o aligner.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c atgcContent.c -o atgcContent.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c build-sam-index.c -o build-sam-index.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-bigtable.c -o core-bigtable.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-indel.c -o core-indel.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-aligner.c -o core-interface-aligner.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-subjunc.c -o core-interface-subjunc.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-junction.c -o core-junction.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core.c -o core.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detection-calls.c -o detection-calls.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCall.c -o detectionCall.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCallAnnotation.c -o detectionCallAnnotation.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-algorithms.c -o exon-algorithms.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align-indel.c -o exon-align-indel.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align.c -o exon-align.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flattenAnnotations.c -o flattenAnnotations.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fullscan.c -o fullscan.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fusion-align.c -o fusion-align.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gen_rand_reads.c -o gen_rand_reads.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-algorithms.c -o gene-algorithms.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-value-index.c -o gene-value-index.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hashtable.c -o hashtable.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c index-builder.c -o index-builder.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-blc.c -o input-blc.o input-blc.c: In function 'cacheBCL_qualTest_BAMmode': input-blc.c:1006:53: warning: variable 'lane_str' set but not used [-Wunused-but-set-variable] char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL; ^~~~~~~~ input-blc.c:1006:31: warning: variable 'sample_barcode' set but not used [-Wunused-but-set-variable] char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL; ^~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-files.c -o input-files.o input-files.c: In function 'SAM_nosort_run_once': input-files.c:5330:23: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] char * header_txt = malloc(max(1000000,pairer->BAM_l_text)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from input-files.c:24: C:/rtools40/mingw32/i686-w64-mingw32/include/stdlib.h:457:17: note: in a call to allocation function 'malloc' declared here void *__cdecl malloc(size_t _Size); ^~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interval_merge.c -o interval_merge.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c long-hashtable.c -o long-hashtable.o long-hashtable.c: In function 'lnhash_create': long-hashtable.c:46:46: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '8589934592' to '0' [-Woverflow] the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c longread-mapping.c -o longread-mapping.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mergeVCF.c -o mergeVCF.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c processExons.c -o processExons.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c propmapped.c -o propmapped.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qualityScores.c -o qualityScores.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read-repair.c -o read-repair.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readSummary.c -o readSummary.o readSummary.c: In function 'scRNA_find_gene_to_umi_mark_deletee': readSummary.c:5955:43: warning: right shift count >= width of type [-Wshift-count-overflow] int cellno = ( key_bc_umi_p1-NULL-1 ) >> 32; ^~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c removeDupReads.c -o removeDupReads.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam2bed.c -o sam2bed.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sambam-file.c -o sambam-file.o sambam-file.c: In function 'SamBam_writer_sort_bins_to_BAM': sambam-file.c:2381:24: warning: variable 'last_written_BAI_chro' set but not used [-Wunused-but-set-variable] int old_chro_no = -1, last_written_BAI_chro = -1;; ^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c seek-zlib.c -o seek-zlib.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sorted-hashtable.c -o sorted-hashtable.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublog.c -o sublog.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tx-unique.c -o tx-unique.o C:/rtools40/mingw32/bin/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 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:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/Rsubread.buildbin-libdir/00LOCK-Rsubread/00new/Rsubread/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'Rsubread' finding HTML links ... done RsubreadUsersGuide html align html atgcContent html buildindex html cellCounts html detectionCall html detectionCallAnnotation html exactSNP html featureCounts html findCommonVariants html flattenGTF html getInBuiltAnnotation html processExons html promoterRegions html propmapped html qualityScores html removeDupReads html repair html sam2bed html simReads html sublong html txUnique 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 'Rsubread' ... @@@@@ The operating system is Windows. ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HelperFunctions.c -o HelperFunctions.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMbase-index.c -o LRMbase-index.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMchro-event.c -o LRMchro-event.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMfile-io.c -o LRMfile-io.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhashtable.c -o LRMhashtable.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhelper.c -o LRMhelper.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMseek-zlib.c -o LRMseek-zlib.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_wrapper.c -o R_wrapper.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RsimReads.c -o RsimReads.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SNPCalling.c -o SNPCalling.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c aligner.c -o aligner.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c atgcContent.c -o atgcContent.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c build-sam-index.c -o build-sam-index.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-bigtable.c -o core-bigtable.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-indel.c -o core-indel.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-aligner.c -o core-interface-aligner.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-subjunc.c -o core-interface-subjunc.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-junction.c -o core-junction.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core.c -o core.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detection-calls.c -o detection-calls.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCall.c -o detectionCall.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCallAnnotation.c -o detectionCallAnnotation.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-algorithms.c -o exon-algorithms.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align-indel.c -o exon-align-indel.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align.c -o exon-align.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flattenAnnotations.c -o flattenAnnotations.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fullscan.c -o fullscan.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fusion-align.c -o fusion-align.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gen_rand_reads.c -o gen_rand_reads.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-algorithms.c -o gene-algorithms.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-value-index.c -o gene-value-index.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hashtable.c -o hashtable.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c index-builder.c -o index-builder.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-blc.c -o input-blc.o input-blc.c: In function 'cacheBCL_qualTest_BAMmode': input-blc.c:1006:53: warning: variable 'lane_str' set but not used [-Wunused-but-set-variable] char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL; ^~~~~~~~ input-blc.c:1006:31: warning: variable 'sample_barcode' set but not used [-Wunused-but-set-variable] char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL; ^~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-files.c -o input-files.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interval_merge.c -o interval_merge.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c long-hashtable.c -o long-hashtable.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c longread-mapping.c -o longread-mapping.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mergeVCF.c -o mergeVCF.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c processExons.c -o processExons.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c propmapped.c -o propmapped.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qualityScores.c -o qualityScores.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read-repair.c -o read-repair.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readSummary.c -o readSummary.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c removeDupReads.c -o removeDupReads.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam2bed.c -o sam2bed.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sambam-file.c -o sambam-file.o sambam-file.c: In function 'SamBam_writer_sort_bins_to_BAM': sambam-file.c:2381:24: warning: variable 'last_written_BAI_chro' set but not used [-Wunused-but-set-variable] int old_chro_no = -1, last_written_BAI_chro = -1;; ^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c seek-zlib.c -o seek-zlib.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sorted-hashtable.c -o sorted-hashtable.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublog.c -o sublog.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tx-unique.c -o tx-unique.o C:/rtools40/mingw64/bin/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 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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/Rsubread.buildbin-libdir/Rsubread/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'Rsubread' as Rsubread_2.6.4.zip * DONE (Rsubread)