"Blame Jeroen" build/check report for BioC 3.11 - CHECK report for Rsubread on tokay2

Package: Rsubread

Version: 2.1.2

Command: C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:Rsubread.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings Rsubread_2.1.2.tar.gz

StartedAt: 2020-04-13 22:55:06 -0400 (Mon, 13 Apr 2020)

EndedAt: 2020-04-13 23:03:36 -0400 (Mon, 13 Apr 2020)

EllapsedTime: 509.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: Rsubread.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:Rsubread.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings Rsubread_2.1.2.tar.gz
###
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* using log directory 'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/Rsubread.Rcheck'
* using R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116)
* 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 '2.1.2'
* 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 ... WARNING
Found the following significant warnings:
  detection-calls.c:52:2: warning: 'strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
  detection-calls.c:53:2: warning: 'strncpy' specified bound 200 equals destination size [-Wstringop-truncation]
  gene-algorithms.c:2583:4: warning: 'strncpy' output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
  gene-algorithms.c:2575:4: warning: 'strncat' output may be truncated copying 99 bytes from a string of length 99 [-Wstringop-truncation]
  gene-algorithms.c:2576:4: warning: 'strncpy' output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
  readSummary.c:4506:31: warning: '.AmbSum' directive writing 7 bytes into a region of size between 3 and 1010 [-Wformat-overflow=]
  readSummary.c:4527:31: warning: '.no0Genes' directive writing 9 bytes into a region of size between 3 and 1010 [-Wformat-overflow=]
  sambam-file.c:560:6: warning: 'strncpy' specified bound 100 equals destination size [-Wstringop-truncation]
See 'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/Rsubread.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 35.2Mb
  sub-directories of 1Mb or more:
    annot  28.5Mb
    libs    1.8Mb
    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/bioctesting/bbs-3.11-bioc-testing/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)

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      45.89  40.03   86.22
propmapped 38.31  31.35  139.06
sublong    11.93   1.62   13.09
buildindex  6.48   1.61   16.96
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
align      17.30  32.53   50.82
propmapped 17.63  31.63   85.04
sublong    12.28   1.84   24.17
buildindex  3.84   1.19    6.37
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/Rsubread.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/Rsubread_2.1.2.tar.gz && rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_2.1.2.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL Rsubread_2.1.2.zip && rm Rsubread_2.1.2.tar.gz Rsubread_2.1.2.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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 77 10.3M   77 8192k    0     0  41.2M      0 --:--:-- --:--:-- --:--:-- 42.5M
100 10.3M  100 10.3M    0     0  47.7M      0 --:--:-- --:--:-- --:--:-- 49.0M

install for i386

* installing *source* package 'Rsubread' ...
** using staged installation
@@@@@ The operating system is Windows.
** libs
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HelperFunctions.c -o HelperFunctions.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMbase-index.c -o LRMbase-index.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMchro-event.c -o LRMchro-event.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMfile-io.c -o LRMfile-io.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhashtable.c -o LRMhashtable.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhelper.c -o LRMhelper.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMseek-zlib.c -o LRMseek-zlib.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_wrapper.c -o R_wrapper.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RsimReads.c -o RsimReads.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SNPCalling.c -o SNPCalling.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c aligner.c -o aligner.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c atgcContent.c -o atgcContent.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c build-sam-index.c -o build-sam-index.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-bigtable.c -o core-bigtable.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-indel.c -o core-indel.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-aligner.c -o core-interface-aligner.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-subjunc.c -o core-interface-subjunc.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-junction.c -o core-junction.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core.c -o core.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detection-calls.c -o detection-calls.o
detection-calls.c: In function 'DTCdo_add_feature':
detection-calls.c:52:2: warning: 'strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
  strncpy(new_exon -> gene_name, gene_name, FEATURE_NAME_LENGTH);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
detection-calls.c:53:2: warning: 'strncpy' specified bound 200 equals destination size [-Wstringop-truncation]
  strncpy(new_exon -> chro_name, chro_name, MAX_CHROMOSOME_NAME_LEN);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCall.c -o detectionCall.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCallAnnotation.c -o detectionCallAnnotation.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-algorithms.c -o exon-algorithms.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align-indel.c -o exon-align-indel.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align.c -o exon-align.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flattenAnnotations.c -o flattenAnnotations.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fullscan.c -o fullscan.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fusion-align.c -o fusion-align.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gen_rand_reads.c -o gen_rand_reads.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c: In function 'bad_reverse_cigar':
gene-algorithms.c:2583:4: warning: 'strncpy' output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
    strncpy(ncg, ncg2, 99);
    ^~~~~~~~~~~~~~~~~~~~~~
gene-algorithms.c:2575:4: warning: 'strncat' output may be truncated copying 99 bytes from a string of length 99 [-Wstringop-truncation]
    strncat(ncg2, ncg, 99);
    ^~~~~~~~~~~~~~~~~~~~~~
gene-algorithms.c:2576:4: warning: 'strncpy' output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
    strncpy(ncg, ncg2, 99);
    ^~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-value-index.c -o gene-value-index.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hashtable.c -o hashtable.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c index-builder.c -o index-builder.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-blc.c -o input-blc.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -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:5267:23: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
   char * header_txt = malloc(max(1000000,pairer->BAM_l_text));
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from input-files.c:24:
C:/rtools40/mingw32/i686-w64-mingw32/include/stdlib.h:457:17: note: in a call to allocation function 'malloc' declared here
   void *__cdecl malloc(size_t _Size);
                 ^~~~~~
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interval_merge.c -o interval_merge.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -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);
                                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c longread-mapping.c -o longread-mapping.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mergeVCF.c -o mergeVCF.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c processExons.c -o processExons.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c propmapped.c -o propmapped.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qualityScores.c -o qualityScores.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read-repair.c -o read-repair.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readSummary.c -o readSummary.o
readSummary.c: In function 'scRNA_merged_write_sparse_matrix':
readSummary.c:4412:23: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'void *' [-Wformat=]
     fprintf(ofp_bcs,"%s\n", ArrayListGet(global_context -> scRNA_cell_barcodes_array, bc_no));
                      ~^     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                      %p
readSummary.c:4412:23: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'void *' [-Wformat=]
     fprintf(ofp_bcs,"%s\n", ArrayListGet(global_context -> scRNA_cell_barcodes_array, bc_no));
                      ~^     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                      %p
readSummary.c: In function 'scRNA_merged_45K_to_90K_sum_WRT':
readSummary.c:4493:21: warning: pointer targets in initialization of 'char *' from 'unsigned char *' differ in signedness [-Wpointer-sign]
  char * gene_name = global_context -> gene_name_array[ kyGeneID - NULL-1 ];
                     ^~~~~~~~~~~~~~
readSummary.c:4489:11: warning: unused variable 'sample_no' [-Wunused-variable]
  srInt_64 sample_no = me -> counter1;
           ^~~~~~~~~
readSummary.c: In function 'scRNA_merged_45K_to_90K_sum':
readSummary.c:4502:11: warning: unused variable 'x1' [-Wunused-variable]
  srInt_64 x1;
           ^~
readSummary.c: In function 'scRNA_merged_write_nozero_geneids_WRT':
readSummary.c:4521:22: warning: pointer targets in initialization of 'char *' from 'unsigned char *' differ in signedness [-Wpointer-sign]
  char* gene_symbol = global_context -> gene_name_array [k-NULL-1];
                      ^~~~~~~~~~~~~~
readSummary.c: In function 'scRNA_merged_write_nozero_geneids':
readSummary.c:4529:11: warning: unused variable 'x1' [-Wunused-variable]
  srInt_64 x1;
           ^~
readSummary.c: In function 'scRNA_merged_45K_to_90K_sum':
readSummary.c:4506:31: warning: '.AmbSum' directive writing 7 bytes into a region of size between 3 and 1010 [-Wformat-overflow=]
  sprintf(ofname,"%s.scRNA.%03d.AmbSum",global_context->input_file_name, sample_no+1);
                               ^~~~~~~
readSummary.c:4506:2: note: 'sprintf' output between 18 and 1025 bytes into a destination of size 1020
  sprintf(ofname,"%s.scRNA.%03d.AmbSum",global_context->input_file_name, sample_no+1);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'scRNA_merged_write_nozero_geneids':
readSummary.c:4527:31: warning: '.no0Genes' directive writing 9 bytes into a region of size between 3 and 1010 [-Wformat-overflow=]
  sprintf(ofname,"%s.scRNA.%03d.no0Genes",global_context->input_file_name, samplenno+1);
                               ^~~~~~~~~
readSummary.c:4527:2: note: 'sprintf' output between 20 and 1027 bytes into a destination of size 1020
  sprintf(ofname,"%s.scRNA.%03d.no0Genes",global_context->input_file_name, samplenno+1);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c removeDupReads.c -o removeDupReads.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam2bed.c -o sam2bed.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -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 'PBam_chunk_headers':
sambam-file.c:560:6: warning: 'strncpy' specified bound 100 equals destination size [-Wstringop-truncation]
      strncpy(new_event->chro_name, chro_name, BAM_MAX_CHROMOSOME_NAME_LEN);
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c seek-zlib.c -o seek-zlib.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sorted-hashtable.c -o sorted-hashtable.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublog.c -o sublog.o
/mingw32/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tx-unique.c -o tx-unique.o
/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/BIOCTE~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/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
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HelperFunctions.c -o HelperFunctions.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMbase-index.c -o LRMbase-index.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMchro-event.c -o LRMchro-event.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMfile-io.c -o LRMfile-io.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhashtable.c -o LRMhashtable.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhelper.c -o LRMhelper.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMseek-zlib.c -o LRMseek-zlib.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_wrapper.c -o R_wrapper.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RsimReads.c -o RsimReads.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SNPCalling.c -o SNPCalling.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c aligner.c -o aligner.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c atgcContent.c -o atgcContent.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c build-sam-index.c -o build-sam-index.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-bigtable.c -o core-bigtable.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-indel.c -o core-indel.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-aligner.c -o core-interface-aligner.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-subjunc.c -o core-interface-subjunc.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-junction.c -o core-junction.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core.c -o core.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detection-calls.c -o detection-calls.o
detection-calls.c: In function 'DTCdo_add_feature':
detection-calls.c:52:2: warning: 'strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
  strncpy(new_exon -> gene_name, gene_name, FEATURE_NAME_LENGTH);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
detection-calls.c:53:2: warning: 'strncpy' specified bound 200 equals destination size [-Wstringop-truncation]
  strncpy(new_exon -> chro_name, chro_name, MAX_CHROMOSOME_NAME_LEN);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCall.c -o detectionCall.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCallAnnotation.c -o detectionCallAnnotation.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-algorithms.c -o exon-algorithms.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align-indel.c -o exon-align-indel.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align.c -o exon-align.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flattenAnnotations.c -o flattenAnnotations.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fullscan.c -o fullscan.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fusion-align.c -o fusion-align.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gen_rand_reads.c -o gen_rand_reads.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c: In function 'bad_reverse_cigar':
gene-algorithms.c:2583:4: warning: 'strncpy' output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
    strncpy(ncg, ncg2, 99);
    ^~~~~~~~~~~~~~~~~~~~~~
gene-algorithms.c:2575:4: warning: 'strncat' output may be truncated copying 99 bytes from a string of length 99 [-Wstringop-truncation]
    strncat(ncg2, ncg, 99);
    ^~~~~~~~~~~~~~~~~~~~~~
gene-algorithms.c:2576:4: warning: 'strncpy' output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
    strncpy(ncg, ncg2, 99);
    ^~~~~~~~~~~~~~~~~~~~~~
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-value-index.c -o gene-value-index.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hashtable.c -o hashtable.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c index-builder.c -o index-builder.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-blc.c -o input-blc.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-files.c -o input-files.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interval_merge.c -o interval_merge.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c long-hashtable.c -o long-hashtable.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c longread-mapping.c -o longread-mapping.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mergeVCF.c -o mergeVCF.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c processExons.c -o processExons.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c propmapped.c -o propmapped.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qualityScores.c -o qualityScores.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read-repair.c -o read-repair.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readSummary.c -o readSummary.o
readSummary.c: In function 'scRNA_merged_write_sparse_matrix':
readSummary.c:4412:23: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'void *' [-Wformat=]
     fprintf(ofp_bcs,"%s\n", ArrayListGet(global_context -> scRNA_cell_barcodes_array, bc_no));
                      ~^     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                      %p
readSummary.c:4412:23: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'void *' [-Wformat=]
     fprintf(ofp_bcs,"%s\n", ArrayListGet(global_context -> scRNA_cell_barcodes_array, bc_no));
                      ~^     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                      %p
readSummary.c: In function 'scRNA_merged_45K_to_90K_sum_WRT':
readSummary.c:4493:21: warning: pointer targets in initialization of 'char *' from 'unsigned char *' differ in signedness [-Wpointer-sign]
  char * gene_name = global_context -> gene_name_array[ kyGeneID - NULL-1 ];
                     ^~~~~~~~~~~~~~
readSummary.c:4489:11: warning: unused variable 'sample_no' [-Wunused-variable]
  srInt_64 sample_no = me -> counter1;
           ^~~~~~~~~
readSummary.c: In function 'scRNA_merged_45K_to_90K_sum':
readSummary.c:4502:11: warning: unused variable 'x1' [-Wunused-variable]
  srInt_64 x1;
           ^~
readSummary.c: In function 'scRNA_merged_write_nozero_geneids_WRT':
readSummary.c:4521:22: warning: pointer targets in initialization of 'char *' from 'unsigned char *' differ in signedness [-Wpointer-sign]
  char* gene_symbol = global_context -> gene_name_array [k-NULL-1];
                      ^~~~~~~~~~~~~~
readSummary.c: In function 'scRNA_merged_write_nozero_geneids':
readSummary.c:4529:11: warning: unused variable 'x1' [-Wunused-variable]
  srInt_64 x1;
           ^~
readSummary.c: In function 'scRNA_merged_45K_to_90K_sum':
readSummary.c:4506:31: warning: '.AmbSum' directive writing 7 bytes into a region of size between 3 and 1010 [-Wformat-overflow=]
  sprintf(ofname,"%s.scRNA.%03d.AmbSum",global_context->input_file_name, sample_no+1);
                               ^~~~~~~
readSummary.c:4506:2: note: 'sprintf' output between 18 and 1025 bytes into a destination of size 1020
  sprintf(ofname,"%s.scRNA.%03d.AmbSum",global_context->input_file_name, sample_no+1);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'scRNA_merged_write_nozero_geneids':
readSummary.c:4527:31: warning: '.no0Genes' directive writing 9 bytes into a region of size between 3 and 1010 [-Wformat-overflow=]
  sprintf(ofname,"%s.scRNA.%03d.no0Genes",global_context->input_file_name, samplenno+1);
                               ^~~~~~~~~
readSummary.c:4527:2: note: 'sprintf' output between 20 and 1027 bytes into a destination of size 1020
  sprintf(ofname,"%s.scRNA.%03d.no0Genes",global_context->input_file_name, samplenno+1);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c removeDupReads.c -o removeDupReads.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam2bed.c -o sam2bed.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -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 'PBam_chunk_headers':
sambam-file.c:560:6: warning: 'strncpy' specified bound 100 equals destination size [-Wstringop-truncation]
      strncpy(new_event->chro_name, chro_name, BAM_MAX_CHROMOSOME_NAME_LEN);
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c seek-zlib.c -o seek-zlib.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sorted-hashtable.c -o sorted-hashtable.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublog.c -o sublog.o
/mingw64/bin/gcc  -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tx-unique.c -o tx-unique.o
/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/BIOCTE~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/Rsubread.buildbin-libdir/Rsubread/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsubread' as Rsubread_2.1.2.zip
* DONE (Rsubread)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'Rsubread' successfully unpacked and MD5 sums checked

CHECK report for Rsubread on tokay2

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