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INSTALL report for Rsubread on tokay2

This page was generated on 2020-10-17 11:57:42 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Rsubread PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1543/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 2.2.6
Wei Shi , Yang Liao and Gordon K Smyth
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Rsubread
Branch: RELEASE_3_11
Last Commit: 4e999a3
Last Changed Date: 2020-08-02 18:51:16 -0400 (Sun, 02 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rsubread
Version: 2.2.6
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Rsubread_2.2.6.tar.gz && rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_2.2.6.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Rsubread_2.2.6.zip && rm Rsubread_2.2.6.tar.gz Rsubread_2.2.6.zip
StartedAt: 2020-10-16 17:03:54 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 17:06:31 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 156.7 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Rsubread_2.2.6.tar.gz && rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_2.2.6.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Rsubread_2.2.6.zip && rm Rsubread_2.2.6.tar.gz Rsubread_2.2.6.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 10.3M  100 10.3M    0     0  66.3M      0 --:--:-- --:--:-- --:--:-- 69.6M

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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-blc.c -o input-blc.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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:5267:23: 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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readSummary.c -o readSummary.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sambam-file.c -o sambam-file.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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
   'Rsubread.Rnw' 
** 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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-blc.c -o input-blc.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sambam-file.c -o sambam-file.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/Rsubread.buildbin-libdir/Rsubread/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsubread' as Rsubread_2.2.6.zip
* DONE (Rsubread)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Rsubread' successfully unpacked and MD5 sums checked