Wei Shi
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Rsubread |
| Branch: RELEASE_3_9 |
| Last Commit: 57d9049 |
| Last Changed Date: 2019-09-05 00:19:32 -0400 (Thu, 05 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:24:58 -0400 (Wed, 16 Oct 2019).
| Package 1425/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rsubread 1.34.7 Wei Shi
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | [ OK ] | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Rsubread |
| Version: 1.34.7 |
| Command: rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_1.34.7.tar.gz |
| StartedAt: 2019-10-16 10:07:35 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 10:09:46 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 130.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rsubread_1.34.7.zip |
| PackageFileSize: 10.96 MiB |
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###
### Running command:
###
### rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_1.34.7.tar.gz
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install for i386
* installing *source* package 'Rsubread' ...
** using staged installation
@@@@@ The operating system is Windows.
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c HelperFunctions.c -o HelperFunctions.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMbase-index.c -o LRMbase-index.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMchro-event.c -o LRMchro-event.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMfile-io.c -o LRMfile-io.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMhashtable.c -o LRMhashtable.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMhelper.c -o LRMhelper.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMseek-zlib.c -o LRMseek-zlib.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c R_wrapper.c -o R_wrapper.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c RsimReads.c -o RsimReads.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c SNPCalling.c -o SNPCalling.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c aligner.c -o aligner.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c atgcContent.c -o atgcContent.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c build-sam-index.c -o build-sam-index.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c core-bigtable.c -o core-bigtable.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c core-indel.c -o core-indel.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c core-interface-aligner.c -o core-interface-aligner.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c core-interface-subjunc.c -o core-interface-subjunc.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c core-junction.c -o core-junction.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c core.c -o core.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c detection-calls.c -o detection-calls.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c detectionCall.c -o detectionCall.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c detectionCallAnnotation.c -o detectionCallAnnotation.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c exon-algorithms.c -o exon-algorithms.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c exon-align-indel.c -o exon-align-indel.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c exon-align.c -o exon-align.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c flattenAnnotations.c -o flattenAnnotations.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c fullscan.c -o fullscan.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c fusion-align.c -o fusion-align.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c gen_rand_reads.c -o gen_rand_reads.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c gene-algorithms.c -o gene-algorithms.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c gene-value-index.c -o gene-value-index.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c hashtable.c -o hashtable.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c index-builder.c -o index-builder.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c input-blc.c -o input-blc.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c input-files.c -o input-files.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c interval_merge.c -o interval_merge.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c long-hashtable.c -o long-hashtable.o
long-hashtable.c: In function 'lnhash_create':
long-hashtable.c:46:46: warning: large integer implicitly truncated to unsigned type [-Woverflow]
the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c longread-mapping.c -o longread-mapping.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c mergeVCF.c -o mergeVCF.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c processExons.c -o processExons.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c propmapped.c -o propmapped.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c qualityScores.c -o qualityScores.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c read-repair.c -o read-repair.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c readSummary.c -o readSummary.o
readSummary.c: In function 'calc_total_frag_len':
readSummary.c:2063:113: warning: array subscript is above array bounds [-Warray-bounds]
CIGAR_intervals_R2[R2_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[insmov_i];
^
readSummary.c:2088:113: warning: array subscript is above array bounds [-Warray-bounds]
CIGAR_intervals_R1[R1_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R1[R1_i].insertion_start_pos[insmov_i];
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c removeDupReads.c -o removeDupReads.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c sam2bed.c -o sam2bed.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c sambam-file.c -o sambam-file.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c seek-zlib.c -o seek-zlib.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c sorted-hashtable.c -o sorted-hashtable.o
sorted-hashtable.c: In function 'gehash_go_q_CtoT':
sorted-hashtable.c:619:22: warning: array subscript is above array bounds [-Warray-bounds]
mutation_stack[j] = 0;
^
sorted-hashtable.c:640:22: warning: array subscript is above array bounds [-Warray-bounds]
error_pos_stack[j] = error_pos_stack[i] + (j-i);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c sublog.c -o sublog.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c tx-unique.c -o tx-unique.o
C:/Rtools/mingw_32/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-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c HelperFunctions.c -o HelperFunctions.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMbase-index.c -o LRMbase-index.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMchro-event.c -o LRMchro-event.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMfile-io.c -o LRMfile-io.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMhashtable.c -o LRMhashtable.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMhelper.c -o LRMhelper.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMseek-zlib.c -o LRMseek-zlib.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c R_wrapper.c -o R_wrapper.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c RsimReads.c -o RsimReads.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c SNPCalling.c -o SNPCalling.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c aligner.c -o aligner.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c atgcContent.c -o atgcContent.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c build-sam-index.c -o build-sam-index.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c core-bigtable.c -o core-bigtable.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c core-indel.c -o core-indel.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c core-interface-aligner.c -o core-interface-aligner.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c core-interface-subjunc.c -o core-interface-subjunc.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c core-junction.c -o core-junction.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c core.c -o core.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c detection-calls.c -o detection-calls.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c detectionCall.c -o detectionCall.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c detectionCallAnnotation.c -o detectionCallAnnotation.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c exon-algorithms.c -o exon-algorithms.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c exon-align-indel.c -o exon-align-indel.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c exon-align.c -o exon-align.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c flattenAnnotations.c -o flattenAnnotations.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c fullscan.c -o fullscan.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c fusion-align.c -o fusion-align.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c gen_rand_reads.c -o gen_rand_reads.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c gene-algorithms.c -o gene-algorithms.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c gene-value-index.c -o gene-value-index.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c hashtable.c -o hashtable.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c index-builder.c -o index-builder.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c input-blc.c -o input-blc.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c input-files.c -o input-files.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c interval_merge.c -o interval_merge.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c long-hashtable.c -o long-hashtable.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c longread-mapping.c -o longread-mapping.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c mergeVCF.c -o mergeVCF.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c processExons.c -o processExons.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c propmapped.c -o propmapped.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c qualityScores.c -o qualityScores.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c read-repair.c -o read-repair.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c readSummary.c -o readSummary.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c removeDupReads.c -o removeDupReads.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c sam2bed.c -o sam2bed.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c sambam-file.c -o sambam-file.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c seek-zlib.c -o seek-zlib.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c sorted-hashtable.c -o sorted-hashtable.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c sublog.c -o sublog.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c tx-unique.c -o tx-unique.o
C:/Rtools/mingw_64/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-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Rsubread.buildbin-libdir/Rsubread/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsubread' as Rsubread_1.34.7.zip
* DONE (Rsubread)