Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2022-04-13 12:07:16 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

INSTALL results for Rsubread on tokay2


To the developers/maintainers of the Rsubread package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsubread.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1664/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 2.8.2  (landing page)
Wei Shi , Yang Liao and Gordon K Smyth
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/Rsubread
git_branch: RELEASE_3_14
git_last_commit: 9fde88e
git_last_commit_date: 2022-03-16 23:02:15 -0400 (Wed, 16 Mar 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rsubread
Version: 2.8.2
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Rsubread_2.8.2.tar.gz && rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_2.8.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Rsubread_2.8.2.zip && rm Rsubread_2.8.2.tar.gz Rsubread_2.8.2.zip
StartedAt: 2022-04-12 04:01:27 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 04:05:50 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 263.7 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Rsubread_2.8.2.tar.gz && rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_2.8.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Rsubread_2.8.2.zip && rm Rsubread_2.8.2.tar.gz Rsubread_2.8.2.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 10.3M    0  1136    0     0  13854      0  0:13:05 --:--:--  0:13:05 13853
  8 10.3M    8  887k    0     0   818k      0  0:00:12  0:00:01  0:00:11  818k
 25 10.3M   25 2686k    0     0  1284k      0  0:00:08  0:00:02  0:00:06 1284k
 51 10.3M   51 5422k    0     0  1753k      0  0:00:06  0:00:03  0:00:03 1753k
 85 10.3M   85 9089k    0     0  2219k      0  0:00:04  0:00:04 --:--:-- 2219k
100 10.3M  100 10.3M    0     0  2395k      0  0:00:04  0:00:04 --:--:-- 2440k

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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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:5355:23: 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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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:5761:43: 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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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:2379:24: 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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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:2379:24: 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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/Rsubread.buildbin-libdir/Rsubread/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsubread' as Rsubread_2.8.2.zip
* DONE (Rsubread)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Rsubread' successfully unpacked and MD5 sums checked