Wei Shi
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/Rsubread |
| git_branch: RELEASE_3_13 |
| git_last_commit: 77deb77 |
| git_last_commit_date: 2021-07-14 21:45:41 -0400 (Wed, 14 Jul 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:20 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1639/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsubread 2.6.4 (landing page) Wei Shi
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Rsubread |
| Version: 2.6.4 |
| Command: rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_2.6.4.tar.gz |
| StartedAt: 2021-10-15 11:31:49 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 11:34:47 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 178.5 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rsubread_2.6.4.zip |
| PackageFileSize: 11.1 MiB |
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###
### Running command:
###
### rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_2.6.4.tar.gz
###
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install for i386
* installing *source* package 'Rsubread' ...
** using staged installation
@@@@@ The operating system is Windows.
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HelperFunctions.c -o HelperFunctions.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMbase-index.c -o LRMbase-index.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMchro-event.c -o LRMchro-event.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMfile-io.c -o LRMfile-io.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhashtable.c -o LRMhashtable.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhelper.c -o LRMhelper.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMseek-zlib.c -o LRMseek-zlib.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_wrapper.c -o R_wrapper.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RsimReads.c -o RsimReads.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SNPCalling.c -o SNPCalling.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c aligner.c -o aligner.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c atgcContent.c -o atgcContent.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c build-sam-index.c -o build-sam-index.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-bigtable.c -o core-bigtable.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-indel.c -o core-indel.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-aligner.c -o core-interface-aligner.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-subjunc.c -o core-interface-subjunc.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-junction.c -o core-junction.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core.c -o core.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detection-calls.c -o detection-calls.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCall.c -o detectionCall.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCallAnnotation.c -o detectionCallAnnotation.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-algorithms.c -o exon-algorithms.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align-indel.c -o exon-align-indel.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align.c -o exon-align.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flattenAnnotations.c -o flattenAnnotations.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fullscan.c -o fullscan.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fusion-align.c -o fusion-align.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gen_rand_reads.c -o gen_rand_reads.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-algorithms.c -o gene-algorithms.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-value-index.c -o gene-value-index.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hashtable.c -o hashtable.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c index-builder.c -o index-builder.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-blc.c -o input-blc.o
input-blc.c: In function 'cacheBCL_qualTest_BAMmode':
input-blc.c:1006:53: warning: variable 'lane_str' set but not used [-Wunused-but-set-variable]
char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL;
^~~~~~~~
input-blc.c:1006:31: warning: variable 'sample_barcode' set but not used [-Wunused-but-set-variable]
char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL;
^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-files.c -o input-files.o
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:5330:23: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
char * header_txt = malloc(max(1000000,pairer->BAM_l_text));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from input-files.c:24:
C:/rtools40/mingw32/i686-w64-mingw32/include/stdlib.h:457:17: note: in a call to allocation function 'malloc' declared here
void *__cdecl malloc(size_t _Size);
^~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interval_merge.c -o interval_merge.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c long-hashtable.c -o long-hashtable.o
long-hashtable.c: In function 'lnhash_create':
long-hashtable.c:46:46: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '8589934592' to '0' [-Woverflow]
the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c longread-mapping.c -o longread-mapping.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mergeVCF.c -o mergeVCF.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c processExons.c -o processExons.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c propmapped.c -o propmapped.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qualityScores.c -o qualityScores.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read-repair.c -o read-repair.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readSummary.c -o readSummary.o
readSummary.c: In function 'scRNA_find_gene_to_umi_mark_deletee':
readSummary.c:5955:43: warning: right shift count >= width of type [-Wshift-count-overflow]
int cellno = ( key_bc_umi_p1-NULL-1 ) >> 32;
^~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c removeDupReads.c -o removeDupReads.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam2bed.c -o sam2bed.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sambam-file.c -o sambam-file.o
sambam-file.c: In function 'SamBam_writer_sort_bins_to_BAM':
sambam-file.c:2381:24: warning: variable 'last_written_BAI_chro' set but not used [-Wunused-but-set-variable]
int old_chro_no = -1, last_written_BAI_chro = -1;;
^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c seek-zlib.c -o seek-zlib.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sorted-hashtable.c -o sorted-hashtable.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublog.c -o sublog.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tx-unique.c -o tx-unique.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o Rsubread.dll tmp.def HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/Rsubread.buildbin-libdir/00LOCK-Rsubread/00new/Rsubread/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rsubread'
finding HTML links ... done
RsubreadUsersGuide html
align html
atgcContent html
buildindex html
cellCounts html
detectionCall html
detectionCallAnnotation html
exactSNP html
featureCounts html
findCommonVariants html
flattenGTF html
getInBuiltAnnotation html
processExons html
promoterRegions html
propmapped html
qualityScores html
removeDupReads html
repair html
sam2bed html
simReads html
sublong html
txUnique html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'Rsubread' ...
@@@@@ The operating system is Windows.
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HelperFunctions.c -o HelperFunctions.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMbase-index.c -o LRMbase-index.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMchro-event.c -o LRMchro-event.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMfile-io.c -o LRMfile-io.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhashtable.c -o LRMhashtable.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhelper.c -o LRMhelper.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMseek-zlib.c -o LRMseek-zlib.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_wrapper.c -o R_wrapper.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RsimReads.c -o RsimReads.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SNPCalling.c -o SNPCalling.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c aligner.c -o aligner.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c atgcContent.c -o atgcContent.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c build-sam-index.c -o build-sam-index.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-bigtable.c -o core-bigtable.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-indel.c -o core-indel.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-aligner.c -o core-interface-aligner.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-subjunc.c -o core-interface-subjunc.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-junction.c -o core-junction.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core.c -o core.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detection-calls.c -o detection-calls.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCall.c -o detectionCall.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCallAnnotation.c -o detectionCallAnnotation.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-algorithms.c -o exon-algorithms.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align-indel.c -o exon-align-indel.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align.c -o exon-align.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flattenAnnotations.c -o flattenAnnotations.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fullscan.c -o fullscan.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fusion-align.c -o fusion-align.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gen_rand_reads.c -o gen_rand_reads.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-algorithms.c -o gene-algorithms.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-value-index.c -o gene-value-index.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hashtable.c -o hashtable.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c index-builder.c -o index-builder.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-blc.c -o input-blc.o
input-blc.c: In function 'cacheBCL_qualTest_BAMmode':
input-blc.c:1006:53: warning: variable 'lane_str' set but not used [-Wunused-but-set-variable]
char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL;
^~~~~~~~
input-blc.c:1006:31: warning: variable 'sample_barcode' set but not used [-Wunused-but-set-variable]
char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL;
^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-files.c -o input-files.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interval_merge.c -o interval_merge.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c long-hashtable.c -o long-hashtable.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c longread-mapping.c -o longread-mapping.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mergeVCF.c -o mergeVCF.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c processExons.c -o processExons.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c propmapped.c -o propmapped.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qualityScores.c -o qualityScores.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read-repair.c -o read-repair.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readSummary.c -o readSummary.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c removeDupReads.c -o removeDupReads.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam2bed.c -o sam2bed.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sambam-file.c -o sambam-file.o
sambam-file.c: In function 'SamBam_writer_sort_bins_to_BAM':
sambam-file.c:2381:24: warning: variable 'last_written_BAI_chro' set but not used [-Wunused-but-set-variable]
int old_chro_no = -1, last_written_BAI_chro = -1;;
^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c seek-zlib.c -o seek-zlib.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sorted-hashtable.c -o sorted-hashtable.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublog.c -o sublog.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tx-unique.c -o tx-unique.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o Rsubread.dll tmp.def HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/Rsubread.buildbin-libdir/Rsubread/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsubread' as Rsubread_2.6.4.zip
* DONE (Rsubread)