Multiple platform build/check report for BioC 3.14 - CHECK results for Rsubread on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

Package: Rsubread

Version: 2.8.2

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rsubread.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Rsubread_2.8.2.tar.gz

StartedAt: 2022-04-13 02:03:08 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 02:09:01 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 353.2 seconds

RetCode: 0

Status: OK

CheckDir: Rsubread.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rsubread.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Rsubread_2.8.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Rsubread.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.8.2'
* 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 35.4Mb
  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 use of PKG_*FLAGS in Makefiles ... 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-3.14-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-3.14-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 (user + system) or elapsed time > 5s
            user system elapsed
align      16.96   2.14   20.18
propmapped 16.60   1.78   18.40
sublong    13.49   1.55   20.20
buildindex  4.68   0.93    5.61
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
align      46.35   5.41   61.70
propmapped 40.60   5.07   63.16
sublong    37.74   5.23   42.56
buildindex 12.37   2.85   15.47
* 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-3.14-bioc/meat/Rsubread.Rcheck/00check.log'
for details.

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###
### 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
###
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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

CHECK results for Rsubread on tokay2

Summary

Command output

Installation output

Tests output

Example timings