Wei Shi
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Rsubread |
| Branch: RELEASE_3_9 |
| Last Commit: 57d9049 |
| Last Changed Date: 2019-09-05 00:19:32 -0400 (Thu, 05 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:24:57 -0400 (Wed, 16 Oct 2019).
| Package 1425/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rsubread 1.34.7 Wei Shi
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Rsubread |
| Version: 1.34.7 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rsubread.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rsubread_1.34.7.tar.gz |
| StartedAt: 2019-10-16 06:48:12 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:51:11 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 178.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rsubread.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rsubread.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rsubread_1.34.7.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rsubread.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rsubread/DESCRIPTION' ... OK
* this is package 'Rsubread' version '1.34.7'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Rsubread' can be installed ... OK
* checking installed package size ... NOTE
installed size is 35.3Mb
sub-directories of 1Mb or more:
annot 28.5Mb
libs 1.9Mb
qualf 3.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rsubread/libs/i386/Rsubread.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rsubread/libs/x64/Rsubread.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sublong 14.89 3.45 16.84
align 5.88 1.94 8.94
propmapped 4.93 1.92 7.50
buildindex 5.28 1.00 6.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sublong 12.89 3.89 15.11
propmapped 4.42 2.02 8.62
align 4.50 1.88 7.20
buildindex 4.23 1.20 5.44
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rsubread.Rcheck/00check.log'
for details.
Rsubread.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Rsubread_1.34.7.tar.gz && rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_1.34.7.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Rsubread_1.34.7.zip && rm Rsubread_1.34.7.tar.gz Rsubread_1.34.7.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
44 10.3M 44 4688k 0 0 45.6M 0 --:--:-- --:--:-- --:--:-- 48.1M
100 10.3M 100 10.3M 0 0 59.9M 0 --:--:-- --:--:-- --:--:-- 62.0M
install for i386
* installing *source* package 'Rsubread' ...
** using staged installation
@@@@@ The operating system is Windows.
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c HelperFunctions.c -o HelperFunctions.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMbase-index.c -o LRMbase-index.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMchro-event.c -o LRMchro-event.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMfile-io.c -o LRMfile-io.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMhashtable.c -o LRMhashtable.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMhelper.c -o LRMhelper.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMseek-zlib.c -o LRMseek-zlib.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c R_wrapper.c -o R_wrapper.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c RsimReads.c -o RsimReads.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c SNPCalling.c -o SNPCalling.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c aligner.c -o aligner.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c atgcContent.c -o atgcContent.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c build-sam-index.c -o build-sam-index.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c core-bigtable.c -o core-bigtable.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c core-indel.c -o core-indel.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c core-interface-aligner.c -o core-interface-aligner.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c core-interface-subjunc.c -o core-interface-subjunc.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c core-junction.c -o core-junction.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c core.c -o core.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c detection-calls.c -o detection-calls.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c detectionCall.c -o detectionCall.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c detectionCallAnnotation.c -o detectionCallAnnotation.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c exon-algorithms.c -o exon-algorithms.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c exon-align-indel.c -o exon-align-indel.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c exon-align.c -o exon-align.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c flattenAnnotations.c -o flattenAnnotations.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c fullscan.c -o fullscan.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c fusion-align.c -o fusion-align.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c gen_rand_reads.c -o gen_rand_reads.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c gene-algorithms.c -o gene-algorithms.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c gene-value-index.c -o gene-value-index.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c hashtable.c -o hashtable.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c index-builder.c -o index-builder.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c input-blc.c -o input-blc.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c input-files.c -o input-files.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c interval_merge.c -o interval_merge.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c long-hashtable.c -o long-hashtable.o
long-hashtable.c: In function 'lnhash_create':
long-hashtable.c:46:46: warning: large integer implicitly truncated to unsigned type [-Woverflow]
the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c longread-mapping.c -o longread-mapping.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c mergeVCF.c -o mergeVCF.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c processExons.c -o processExons.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c propmapped.c -o propmapped.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c qualityScores.c -o qualityScores.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c read-repair.c -o read-repair.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c readSummary.c -o readSummary.o
readSummary.c: In function 'calc_total_frag_len':
readSummary.c:2063:113: warning: array subscript is above array bounds [-Warray-bounds]
CIGAR_intervals_R2[R2_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[insmov_i];
^
readSummary.c:2088:113: warning: array subscript is above array bounds [-Warray-bounds]
CIGAR_intervals_R1[R1_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R1[R1_i].insertion_start_pos[insmov_i];
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c removeDupReads.c -o removeDupReads.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c sam2bed.c -o sam2bed.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c sambam-file.c -o sambam-file.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c seek-zlib.c -o seek-zlib.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c sorted-hashtable.c -o sorted-hashtable.o
sorted-hashtable.c: In function 'gehash_go_q_CtoT':
sorted-hashtable.c:619:22: warning: array subscript is above array bounds [-Warray-bounds]
mutation_stack[j] = 0;
^
sorted-hashtable.c:640:22: warning: array subscript is above array bounds [-Warray-bounds]
error_pos_stack[j] = error_pos_stack[i] + (j-i);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c sublog.c -o sublog.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -mtune=generic -c tx-unique.c -o tx-unique.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Rsubread.dll tmp.def HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Rsubread.buildbin-libdir/00LOCK-Rsubread/00new/Rsubread/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rsubread'
finding HTML links ... done
RsubreadUsersGuide html
align html
atgcContent html
buildindex html
cellCounts html
detectionCall html
detectionCallAnnotation html
exactSNP html
featureCounts html
findCommonVariants html
flattenGTF html
getInBuiltAnnotation html
processExons html
promoterRegions html
propmapped html
qualityScores html
removeDupReads html
repair html
sam2bed html
simReads html
sublong html
txUnique html
** building package indices
** installing vignettes
'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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c HelperFunctions.c -o HelperFunctions.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMbase-index.c -o LRMbase-index.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMchro-event.c -o LRMchro-event.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMfile-io.c -o LRMfile-io.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMhashtable.c -o LRMhashtable.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMhelper.c -o LRMhelper.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMseek-zlib.c -o LRMseek-zlib.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c R_wrapper.c -o R_wrapper.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c RsimReads.c -o RsimReads.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c SNPCalling.c -o SNPCalling.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c aligner.c -o aligner.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c atgcContent.c -o atgcContent.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c build-sam-index.c -o build-sam-index.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c core-bigtable.c -o core-bigtable.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c core-indel.c -o core-indel.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c core-interface-aligner.c -o core-interface-aligner.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c core-interface-subjunc.c -o core-interface-subjunc.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c core-junction.c -o core-junction.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c core.c -o core.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c detection-calls.c -o detection-calls.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c detectionCall.c -o detectionCall.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c detectionCallAnnotation.c -o detectionCallAnnotation.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c exon-algorithms.c -o exon-algorithms.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c exon-align-indel.c -o exon-align-indel.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c exon-align.c -o exon-align.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c flattenAnnotations.c -o flattenAnnotations.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c fullscan.c -o fullscan.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c fusion-align.c -o fusion-align.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c gen_rand_reads.c -o gen_rand_reads.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c gene-algorithms.c -o gene-algorithms.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c gene-value-index.c -o gene-value-index.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c hashtable.c -o hashtable.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c index-builder.c -o index-builder.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c input-blc.c -o input-blc.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c input-files.c -o input-files.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c interval_merge.c -o interval_merge.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c long-hashtable.c -o long-hashtable.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c longread-mapping.c -o longread-mapping.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c mergeVCF.c -o mergeVCF.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c processExons.c -o processExons.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c propmapped.c -o propmapped.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c qualityScores.c -o qualityScores.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c read-repair.c -o read-repair.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c readSummary.c -o readSummary.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c removeDupReads.c -o removeDupReads.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c sam2bed.c -o sam2bed.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c sambam-file.c -o sambam-file.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c seek-zlib.c -o seek-zlib.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c sorted-hashtable.c -o sorted-hashtable.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c sublog.c -o sublog.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.34.7\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mtune=generic -c tx-unique.c -o tx-unique.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Rsubread.dll tmp.def HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Rsubread.buildbin-libdir/Rsubread/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsubread' as Rsubread_1.34.7.zip
* DONE (Rsubread)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Rsubread' successfully unpacked and MD5 sums checked
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Rsubread.Rcheck/examples_i386/Rsubread-Ex.timings
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Rsubread.Rcheck/examples_x64/Rsubread-Ex.timings
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