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BioC 3.3: CHECK report for Biostrings on moscato2

This page was generated on 2016-10-13 12:47:20 -0700 (Thu, 13 Oct 2016).

Package 118/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.40.2
H. Pagès
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/Biostrings
Last Changed Rev: 118256 / Revision: 122332
Last Changed Date: 2016-06-07 10:35:06 -0700 (Tue, 07 Jun 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Biostrings
Version: 2.40.2
Command: rm -rf Biostrings.buildbin-libdir Biostrings.Rcheck && mkdir Biostrings.buildbin-libdir Biostrings.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Biostrings.buildbin-libdir Biostrings_2.40.2.tar.gz >Biostrings.Rcheck\00install.out 2>&1 && cp Biostrings.Rcheck\00install.out Biostrings-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=Biostrings.buildbin-libdir --install="check:Biostrings-install.out" --force-multiarch --no-vignettes --timings Biostrings_2.40.2.tar.gz
StartedAt: 2016-10-13 01:29:24 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:54:37 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 1513.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Biostrings.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Biostrings.buildbin-libdir Biostrings.Rcheck && mkdir Biostrings.buildbin-libdir Biostrings.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Biostrings.buildbin-libdir Biostrings_2.40.2.tar.gz >Biostrings.Rcheck\00install.out 2>&1 && cp Biostrings.Rcheck\00install.out Biostrings-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=Biostrings.buildbin-libdir --install="check:Biostrings-install.out" --force-multiarch --no-vignettes --timings Biostrings_2.40.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/Biostrings.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.40.2'
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'Biostrings' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata  11.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'BiocGenerics' 'IRanges' 'XVector'
A package should be listed in only one of these fields.
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::testPackage' 'IRanges:::.showAtomicList'
  'IRanges:::new_Views' 'IRanges:::showRangesList'
  'S4Vectors:::anyMissingOrOutside' 'XVector:::finalize_filexp'
  'XVector:::new_XVectorList_from_list_of_XVector'
  'XVector:::open_input_files' 'XVector:::open_output_file'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
writePairwiseAlignments: no visible global function definition for
  'packageVersion'
encoding,XStringQuality: no visible global function definition for
  'setNames'
Undefined global functions or variables:
  packageVersion setNames
Consider adding
  importFrom("stats", "setNames")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'twoWayAlphabetFrequency'
Undocumented S4 methods:
  generic 'match' and siglist 'Vector,XStringSet'
  generic 'match' and siglist 'XStringSet,Vector'
  generic 'match' and siglist 'XStringSet,vector'
  generic 'match' and siglist 'vector,XStringSet'
  generic 'pcompare' and siglist 'Vector,XStringSet'
  generic 'pcompare' and siglist 'XStringSet,Vector'
  generic 'pcompare' and siglist 'XStringSet,vector'
  generic 'pcompare' and siglist 'vector,XStringSet'
  generic 'relistToClass' and siglist 'XString'
  generic 'relistToClass' and siglist 'XStringSet'
  generic 'showAsCell' and siglist 'XStringSetList'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XStringSet'
  generic 'unstrsplit' and siglist 'XStringSet'
  generic 'unstrsplit' and siglist 'XStringSetList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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 'E:/biocbld/bbs-3.3-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/i386/Biostrings.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
matchPDict-exact   415.35   1.02  416.44
matchPDict-inexact  56.29   0.39   56.69
findPalindromes     42.11   0.57   43.19
stringDist          12.68   0.02   12.70
XStringSet-class    12.37   0.18   14.98
XStringSet-io        9.87   0.24   10.44
matchPattern         9.47   0.11    9.58
PDict-class          4.68   0.03    5.12
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
matchPDict-exact   395.26   1.43  396.80
matchPDict-inexact  62.04   0.36   62.41
findPalindromes     45.26   0.73   45.99
XStringSet-class    12.99   0.36   13.36
XStringSet-io        9.17   0.21   13.04
matchPattern         8.89   0.03    8.95
stringDist           7.72   0.00    7.72
PDict-class          5.15   0.09    5.24
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.R'
 OK
* 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, 6 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/Biostrings.Rcheck/00check.log'
for details.

Biostrings.Rcheck/00install.out:


install for i386

* installing *source* package 'Biostrings' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c BAB_class.c -o BAB_class.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: 'BitMatrix_print' defined but not used [-Wunused-function]
 static void BitMatrix_print(BitMatrix *bitmat)
             ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:179:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
  IntAE *poffsets, *poffsets_order;
                    ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_Biostrings.c -o R_init_Biostrings.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c RoSeqs_utils.c -o RoSeqs_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c SparseList_utils.c -o SparseList_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XStringSetList_class.c -o XStringSetList_class.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:109:3: warning: 'lkup_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
   ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function 'parse_FASTQ_file':
XStringSet_io.c:799:7: warning: 'load_rec' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (load_rec && loader->load_qual != NULL)
       ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XString_class.c -o XString_class.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:155:22: warning: 'sc' may be used uninitialized in this function [-Wmaybe-uninitialized]
  INTEGER(ans_elt)[0] = score;
                      ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
align_utils.c:254:14: warning: 'indelWidthSubject' may be used uninitialized in this function [-Wmaybe-uninitialized]
     jPattern += indelWidthSubject;
              ^
align_utils.c:235:42: warning: 'indelStartSubject' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
                                          ^
align_utils.c:243:30: warning: 'indelWidthPattern' may be used uninitialized in this function [-Wmaybe-uninitialized]
       mappedStringPtr[index] = gapCodeValue;
                              ^
align_utils.c:236:50: warning: 'indelStartPattern' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
                                                  ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c find_palindromes.c -o find_palindromes.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c gtestsim.c -o gtestsim.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c inject_code.c -o inject_code.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function 'XStringSet_two_way_letter_frequency':
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
   int x_width, y_width, x_length, *ans_mat, i, x_pos;
                                                ^
letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
   SEXP ans, ans_dimnames;
             ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c lowlevel_matching.c -o lowlevel_matching.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_BOC.c -o match_BOC.o
match_BOC.c: In function 'split4_offsets':
match_BOC.c:193:79: warning: unused variable 'j' [-Wunused-variable]
  int tmp_codes[4], *tmp_offsets[4], tmp_noffsets[4], order[4], i, offset, ii, j;
                                                                               ^
match_BOC.c: In function 'BOC_exact_search':
match_BOC.c:292:3: warning: label 'continue0' defined but not used [-Wunused-label]
   continue0: ;
   ^
match_BOC.c:239:68: warning: unused variable 'noffsets' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                    ^
match_BOC.c:239:59: warning: unused variable 'offsets' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                           ^
match_BOC.c:239:55: warning: unused variable 'j' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                       ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function 'split4_offsets':
match_BOC2.c:167:79: warning: unused variable 'j' [-Wunused-variable]
  int tmp_codes[4], *tmp_offsets[4], tmp_noffsets[4], order[4], i, offset, ii, j;
                                                                               ^
match_BOC2.c: In function 'BOC2_exact_search':
match_BOC2.c:255:3: warning: label 'continue0' defined but not used [-Wunused-label]
   continue0: ;
   ^
match_BOC2.c:212:68: warning: unused variable 'noffsets' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                    ^
match_BOC2.c:212:59: warning: unused variable 'offsets' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                           ^
match_BOC2.c:212:55: warning: unused variable 'j' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                       ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_PWM.c -o match_PWM.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pattern.c -o match_pattern.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: 'test_match_pattern_indels' defined but not used [-Wunused-function]
 static void test_match_pattern_indels(const char *p, const char *s,
             ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:419:12: warning: 'ans_col' may be used uninitialized in this function [-Wmaybe-uninitialized]
    ans_col += tb_length;
            ^
match_pdict.c:392:58: note: 'ans_col' was declared here
  int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
                                                          ^
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:470:13: warning: 'ans_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
     ans_elt += P_length;
             ^
match_pdict.c:441:57: note: 'ans_elt' was declared here
  int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
                                                         ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function 'split_and_move_pointers':
match_pdict_ACtree2.c:1031:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^
match_pdict_ACtree2.c: In function 'merge_pointers':
match_pdict_ACtree2.c:1076:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^
match_pdict_ACtree2.c: At top level:
match_pdict_ACtree2.c:139:13: warning: 'debug_node_counting_functions' defined but not used [-Wunused-function]
 static void debug_node_counting_functions(int maxdepth)
             ^
match_pdict_ACtree2.c:602:21: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used [-Wunused-function]
 static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
                     ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from match_pdict_Twobit.c:10:
match_pdict_Twobit.c: In function 'build_Twobit':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:661:20: warning: 'twobit_sign2pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
match_pdict_Twobit.c:110:12: note: 'twobit_sign2pos' was declared here
  SEXP ans, twobit_sign2pos;
            ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:652:49: warning: unused variable 'ncol' [-Wunused-variable]
  int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
                                                 ^
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:712:6: warning: unused variable 'nelt' [-Wunused-variable]
  int nelt, nkey0, nkey1, nkey2, i, key;
      ^
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:819:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                            ^
match_pdict_utils.c:819:27: warning: unused variable 'total_NFC' [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                           ^
match_pdict_utils.c:818:33: warning: unused variable 'NFC' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                 ^
match_pdict_utils.c:818:26: warning: unused variable 'nloci' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                          ^
match_pdict_utils.c:818:20: warning: unused variable 'ndup' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                    ^
match_pdict_utils.c: At top level:
match_pdict_utils.c:260:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function]
 static void match_headtail_by_loc(const HeadTail *headtail,
             ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c match_reporting.c -o match_reporting.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matchprobes.c -o matchprobes.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pmatchPattern.c -o pmatchPattern.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c replaceAt.c -o replaceAt.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c replace_letter_at.c -o replace_letter_at.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c strutils.c -o strutils.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c translate.c -o translate.o
translate.c: In function 'DNAStringSet_translate':
translate.c:126:29: warning: 'if_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
                             ^
translate.c:126:14: warning: 'if_non_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
              ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c unstrsplit_methods.c -o unstrsplit_methods.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature':
utils.c:157:2: warning: 'twobit_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return twobit_sign;
  ^
utils.c: In function '_get_twobit_signature_at':
utils.c:164:12: warning: 'twobit_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, twobit_sign;
            ^
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c xscat.c -o xscat.o
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function 'XString_xscat':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:661:20: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
xscat.c:18:13: note: 'ans_length' was declared here
  int nargs, ans_length, tag_offset, j;
             ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:661:20: warning: 'ans_classname' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
xscat.c:20:14: note: 'ans_classname' was declared here
  const char *ans_classname;
              ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function 'XStringSet_xscat':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:661:20: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
xscat.c:66:32: note: 'ans_length' was declared here
  int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
                                ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:661:20: warning: 'ans_element_type' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
xscat.c:68:14: note: 'ans_element_type' was declared here
  const char *ans_element_type;
              ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Biostrings.dll tmp.def BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'ls' from package 'base' in package 'Biostrings'
Creating a new generic function for 'offset' in package 'Biostrings'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Biostrings' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c BAB_class.c -o BAB_class.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: 'BitMatrix_print' defined but not used [-Wunused-function]
 static void BitMatrix_print(BitMatrix *bitmat)
             ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function 'SparseMIndex_endIndex':
MIndex_class.c:179:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
  IntAE *poffsets, *poffsets_order;
                    ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_Biostrings.c -o R_init_Biostrings.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c RoSeqs_utils.c -o RoSeqs_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c SparseList_utils.c -o SparseList_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XStringSetList_class.c -o XStringSetList_class.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
XStringSet_class.c:109:3: warning: 'lkup_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
   ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c: In function 'parse_FASTQ_file':
XStringSet_io.c:799:7: warning: 'load_rec' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (load_rec && loader->load_qual != NULL)
       ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XString_class.c -o XString_class.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function 'align_needwunsQS':
align_needwunsQS.c:155:22: warning: 'sc' may be used uninitialized in this function [-Wmaybe-uninitialized]
  INTEGER(ans_elt)[0] = score;
                      ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
align_utils.c:254:14: warning: 'indelWidthSubject' may be used uninitialized in this function [-Wmaybe-uninitialized]
     jPattern += indelWidthSubject;
              ^
align_utils.c:235:42: warning: 'indelStartSubject' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
                                          ^
align_utils.c:225:26: warning: 'indelWidthPattern' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
                          ^
align_utils.c:236:50: warning: 'indelStartPattern' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
                                                  ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c find_palindromes.c -o find_palindromes.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c gtestsim.c -o gtestsim.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c inject_code.c -o inject_code.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function 'XStringSet_two_way_letter_frequency':
letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
   int x_width, y_width, x_length, *ans_mat, i, x_pos;
                                                ^
letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
   SEXP ans, ans_dimnames;
             ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c lowlevel_matching.c -o lowlevel_matching.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_BOC.c -o match_BOC.o
match_BOC.c: In function 'split4_offsets':
match_BOC.c:193:79: warning: unused variable 'j' [-Wunused-variable]
  int tmp_codes[4], *tmp_offsets[4], tmp_noffsets[4], order[4], i, offset, ii, j;
                                                                               ^
match_BOC.c: In function 'BOC_exact_search':
match_BOC.c:292:3: warning: label 'continue0' defined but not used [-Wunused-label]
   continue0: ;
   ^
match_BOC.c:239:68: warning: unused variable 'noffsets' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                    ^
match_BOC.c:239:59: warning: unused variable 'offsets' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                           ^
match_BOC.c:239:55: warning: unused variable 'j' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                       ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_BOC2.c -o match_BOC2.o
match_BOC2.c: In function 'split4_offsets':
match_BOC2.c:167:79: warning: unused variable 'j' [-Wunused-variable]
  int tmp_codes[4], *tmp_offsets[4], tmp_noffsets[4], order[4], i, offset, ii, j;
                                                                               ^
match_BOC2.c: In function 'BOC2_exact_search':
match_BOC2.c:255:3: warning: label 'continue0' defined but not used [-Wunused-label]
   continue0: ;
   ^
match_BOC2.c:212:68: warning: unused variable 'noffsets' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                    ^
match_BOC2.c:212:59: warning: unused variable 'offsets' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                           ^
match_BOC2.c:212:55: warning: unused variable 'j' [-Wunused-variable]
      nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                       ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_PWM.c -o match_PWM.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pattern.c -o match_pattern.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: 'test_match_pattern_indels' defined but not used [-Wunused-function]
 static void test_match_pattern_indels(const char *p, const char *s,
             ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pdict.c -o match_pdict.o
match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
match_pdict.c:419:12: warning: 'ans_col' may be used uninitialized in this function [-Wmaybe-uninitialized]
    ans_col += tb_length;
            ^
match_pdict.c:392:58: note: 'ans_col' was declared here
  int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
                                                          ^
match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
match_pdict.c:470:13: warning: 'ans_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
     ans_elt += P_length;
             ^
match_pdict.c:441:57: note: 'ans_elt' was declared here
  int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
                                                         ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function 'split_and_move_pointers':
match_pdict_ACtree2.c:1031:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^
match_pdict_ACtree2.c: In function 'merge_pointers':
match_pdict_ACtree2.c:1076:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^
match_pdict_ACtree2.c: At top level:
match_pdict_ACtree2.c:139:13: warning: 'debug_node_counting_functions' defined but not used [-Wunused-function]
 static void debug_node_counting_functions(int maxdepth)
             ^
match_pdict_ACtree2.c:602:21: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used [-Wunused-function]
 static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
                     ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from match_pdict_Twobit.c:10:
match_pdict_Twobit.c: In function 'build_Twobit':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:661:20: warning: 'twobit_sign2pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
match_pdict_Twobit.c:110:12: note: 'twobit_sign2pos' was declared here
  SEXP ans, twobit_sign2pos;
            ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function 'match_ppheadtail0':
match_pdict_utils.c:652:49: warning: unused variable 'ncol' [-Wunused-variable]
  int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
                                                 ^
match_pdict_utils.c: In function 'match_ppheadtail':
match_pdict_utils.c:712:6: warning: unused variable 'nelt' [-Wunused-variable]
  int nelt, nkey0, nkey1, nkey2, i, key;
      ^
match_pdict_utils.c: In function '_match_pdict_all_flanks':
match_pdict_utils.c:819:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                            ^
match_pdict_utils.c:819:27: warning: unused variable 'total_NFC' [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                           ^
match_pdict_utils.c:818:33: warning: unused variable 'NFC' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                 ^
match_pdict_utils.c:818:26: warning: unused variable 'nloci' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                          ^
match_pdict_utils.c:818:20: warning: unused variable 'ndup' [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                    ^
match_pdict_utils.c: At top level:
match_pdict_utils.c:260:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function]
 static void match_headtail_by_loc(const HeadTail *headtail,
             ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c match_reporting.c -o match_reporting.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matchprobes.c -o matchprobes.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pmatchPattern.c -o pmatchPattern.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c replaceAt.c -o replaceAt.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c replace_letter_at.c -o replace_letter_at.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c strutils.c -o strutils.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c translate.c -o translate.o
translate.c: In function 'DNAStringSet_translate':
translate.c:101:8: warning: 'if_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (if_ambig == TRANSLATE_ERROR) {
        ^
translate.c:126:29: note: 'if_ambig0' was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
                             ^
translate.c:97:8: warning: 'if_non_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (if_non_ambig == TRANSLATE_TO_X)
        ^
translate.c:126:14: note: 'if_non_ambig0' was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
              ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c unstrsplit_methods.c -o unstrsplit_methods.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
utils.c: In function '_get_twobit_signature':
utils.c:157:2: warning: 'twobit_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return twobit_sign;
  ^
utils.c: In function '_get_twobit_signature_at':
utils.c:164:12: warning: 'twobit_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, twobit_sign;
            ^
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c xscat.c -o xscat.o
In file included from E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function 'XString_xscat':
E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:94:21: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define NEW_RAW(n)  Rf_allocVector(RAWSXP,n)
                     ^
xscat.c:18:13: note: 'ans_length' was declared here
  int nargs, ans_length, tag_offset, j;
             ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:661:20: warning: 'ans_classname' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^
xscat.c:20:14: note: 'ans_classname' was declared here
  const char *ans_classname;
              ^
In file included from E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function 'XStringSet_xscat':
E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:88:25: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define NEW_INTEGER(n)  Rf_allocVector(INTSXP,n)
                         ^
xscat.c:66:32: note: 'ans_length' was declared here
  int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
                                ^
xscat.c:110:6: warning: 'ans_element_type' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (snprintf(ans_classname, sizeof(ans_classname),
      ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Biostrings.dll tmp.def BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/Biostrings.buildbin-libdir/Biostrings/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Biostrings' as Biostrings_2.40.2.zip
* DONE (Biostrings)

Biostrings.Rcheck/examples_i386/Biostrings-Ex.timings:

nameusersystemelapsed
AAString-class000
AMINO_ACID_CODE000
AlignedXStringSet-class0.090.000.09
DNAString-class000
GENETIC_CODE0.020.000.02
HNF4alpha0.030.020.05
IUPAC_CODE_MAP000
MIndex-class0.020.000.01
MaskedXString-class0.250.000.41
MultipleAlignment-class1.70.01.7
PDict-class4.680.035.12
PairwiseAlignments-class0.220.000.21
PairwiseAlignments-io3.020.043.09
QualityScaledXStringSet-class0.050.000.05
RNAString-class0.010.000.02
XString-class0.020.000.01
XStringQuality-class0.20.00.2
XStringSet-class12.37 0.1814.98
XStringSet-comparison4.360.184.54
XStringSet-io 9.87 0.2410.44
XStringSetList-class0.390.000.39
XStringViews-class0.170.000.17
align-utils0.010.000.03
chartr1.380.031.64
detail0.530.010.55
dinucleotideFrequencyTest0.010.000.01
findPalindromes42.11 0.5743.19
getSeq0.110.000.11
gregexpr2000
injectHardMask0.060.000.06
letter0.040.000.03
letterFrequency2.010.052.06
longestConsecutive000
lowlevel-matching0.590.010.61
maskMotif2.480.102.71
match-utils0.030.000.03
matchLRPatterns1.780.042.11
matchPDict-exact415.35 1.02416.44
matchPDict-inexact56.29 0.3956.69
matchPWM3.110.033.60
matchPattern9.470.119.58
matchProbePair2.310.012.32
matchprobes0.360.000.36
misc000
needwunsQS000
nucleotideFrequency0.920.020.94
padAndClip0.610.000.61
pairwiseAlignment0.870.020.89
phiX174Phage0.710.000.70
pid0.370.000.37
replaceAt3.770.073.85
replaceLetterAt0.810.000.81
reverseComplement1.930.032.03
stringDist12.68 0.0212.70
substitution_matrices0.660.050.70
toComplex0.010.000.02
translate0.830.010.84
trimLRPatterns0.050.000.04
xscat1.480.001.49
yeastSEQCHR1000

Biostrings.Rcheck/examples_x64/Biostrings-Ex.timings:

nameusersystemelapsed
AAString-class000
AMINO_ACID_CODE000
AlignedXStringSet-class0.050.020.06
DNAString-class000
GENETIC_CODE0.010.000.02
HNF4alpha0.030.000.03
IUPAC_CODE_MAP000
MIndex-class000
MaskedXString-class0.280.000.28
MultipleAlignment-class1.700.001.81
PDict-class5.150.095.24
PairwiseAlignments-class0.220.000.22
PairwiseAlignments-io3.040.053.09
QualityScaledXStringSet-class0.070.000.06
RNAString-class000
XString-class0.020.000.01
XStringQuality-class0.250.000.25
XStringSet-class12.99 0.3613.36
XStringSet-comparison4.320.224.54
XStringSet-io 9.17 0.2113.04
XStringSetList-class0.390.030.42
XStringViews-class0.250.000.25
align-utils0.050.001.23
chartr1.420.041.45
detail0.840.010.86
dinucleotideFrequencyTest0.010.000.01
findPalindromes45.26 0.7345.99
getSeq0.040.050.09
gregexpr2000
injectHardMask0.050.000.05
letter0.030.000.03
letterFrequency2.540.052.59
longestConsecutive000
lowlevel-matching0.810.010.83
maskMotif2.290.052.34
match-utils0.030.000.04
matchLRPatterns1.650.021.67
matchPDict-exact395.26 1.43396.80
matchPDict-inexact62.04 0.3662.41
matchPWM4.420.024.43
matchPattern8.890.038.95
matchProbePair2.340.032.61
matchprobes0.340.010.35
misc0.020.000.02
needwunsQS000
nucleotideFrequency0.840.000.84
padAndClip0.620.000.63
pairwiseAlignment1.060.021.08
phiX174Phage0.580.000.58
pid0.300.000.29
replaceAt3.680.143.90
replaceLetterAt0.630.000.62
reverseComplement1.790.061.86
stringDist7.720.007.72
substitution_matrices0.740.030.76
toComplex000
translate1.670.001.67
trimLRPatterns0.080.000.08
xscat1.800.021.83
yeastSEQCHR1000