BioC 3.3: CHECK report for DECIPHER on moscato2

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### Running command:
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###   rm -rf DECIPHER.buildbin-libdir DECIPHER.Rcheck && mkdir DECIPHER.buildbin-libdir DECIPHER.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_2.0.2.tar.gz >DECIPHER.Rcheck\00install.out 2>&1 && cp DECIPHER.Rcheck\00install.out DECIPHER-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=DECIPHER.buildbin-libdir --install="check:DECIPHER-install.out" --force-multiarch --no-vignettes --timings DECIPHER_2.0.2.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/DECIPHER.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 'DECIPHER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DECIPHER' version '2.0.2'
* 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 'DECIPHER' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       3.9Mb
    extdata   1.4Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... NOTE
.CalculateEfficiencyFISH: no visible global function definition for
  'uniroot'
.midpointRoot : .containsZero: no visible global function definition
  for 'is.leaf'
.midpointRoot : .findMax: no visible global function definition for
  'is.leaf'
.midpointRoot : .containsMax: no visible global function definition for
  'is.leaf'
.midpointRoot : .findMidpoint: no visible global function definition
  for 'is.leaf'
.midpointRoot : .adjustHeight: no visible global function definition
  for 'is.leaf'
.midpointRoot : .revertList: no visible global function definition for
  'is.leaf'
.midpointRoot : .adjustMidpoints: no visible global function definition
  for 'is.leaf'
.optimizeModel: no visible global function definition for 'optimize'
.optimizeModel: no visible global function definition for 'nlminb'
AdjustAlignment: no visible global function definition for 'data'
AlignDB: no visible global function definition for 'data'
AlignDB: no visible global function definition for 'txtProgressBar'
AlignDB: no visible global function definition for 'setTxtProgressBar'
AlignProfiles: no visible global function definition for 'data'
AlignSeqs: no visible global function definition for 'data'
AlignSeqs: no visible global function definition for 'flush.console'
AlignSeqs: no visible global function definition for 'txtProgressBar'
AlignSeqs: no visible global function definition for
  'setTxtProgressBar'
AlignSynteny: no visible global function definition for
  'txtProgressBar'
AlignSynteny: no visible global function definition for
  'setTxtProgressBar'
Array2Matrix: no visible global function definition for
  'txtProgressBar'
Array2Matrix: no visible global function definition for
  'setTxtProgressBar'
BrowseDB: no visible global function definition for 'browseURL'
BrowseSeqs: no visible global function definition for 'rainbow'
BrowseSeqs: no visible global function definition for 'browseURL'
CalculateEfficiencyArray: no visible global function definition for
  'data'
CalculateEfficiencyFISH: no visible global function definition for
  'step'
CalculateEfficiencyFISH: no visible global function definition for
  'uniroot'
CorrectFrameshifts: no visible global function definition for 'data'
CorrectFrameshifts: no visible global function definition for
  'flush.console'
CorrectFrameshifts: no visible global function definition for
  'txtProgressBar'
CorrectFrameshifts: no visible global function definition for
  'setTxtProgressBar'
CorrectFrameshifts: no visible binding for global variable 'setNames'
CreateChimeras: no visible global function definition for
  'txtProgressBar'
CreateChimeras: no visible global function definition for
  'setTxtProgressBar'
DB2Seqs: no visible global function definition for 'txtProgressBar'
DB2Seqs: no visible global function definition for 'setTxtProgressBar'
DesignArray: no visible global function definition for 'txtProgressBar'
DesignPrimers: no visible global function definition for
  'flush.console'
DesignPrimers: no visible global function definition for
  'txtProgressBar'
DesignPrimers: no visible global function definition for
  'setTxtProgressBar'
DesignProbes: no visible global function definition for 'flush.console'
DesignProbes: no visible global function definition for
  'txtProgressBar'
DesignProbes: no visible global function definition for
  'setTxtProgressBar'
DesignSignatures: no visible global function definition for 'data'
DesignSignatures: no visible binding for global variable 'deltaHrules'
DesignSignatures: no visible global function definition for
  'flush.console'
DesignSignatures: no visible global function definition for
  'txtProgressBar'
DesignSignatures: no visible global function definition for
  'setTxtProgressBar'
DesignSignatures: no visible global function definition for 'dist'
DigestDNA: no visible global function definition for 'setNames'
DistanceMatrix: no visible global function definition for
  'txtProgressBar'
FindChimeras: no visible global function definition for 'flush.console'
FindChimeras: no visible global function definition for
  'txtProgressBar'
FindChimeras: no visible global function definition for
  'setTxtProgressBar'
FindSynteny: no visible global function definition for 'setNames'
FindSynteny: no visible global function definition for 'txtProgressBar'
FindSynteny: no visible global function definition for 'object.size'
FindSynteny: no visible global function definition for
  'setTxtProgressBar'
FormGroups: no visible global function definition for 'txtProgressBar'
FormGroups: no visible global function definition for
  'setTxtProgressBar'
IdClusters: no visible global function definition for 'txtProgressBar'
IdClusters: no visible global function definition for
  'setTxtProgressBar'
IdClusters: no visible global function definition for 'pbinom'
IdClusters: no visible global function definition for 'flush.console'
IdClusters : printLine: no visible global function definition for
  'flush.console'
IdClusters: no visible global function definition for
  'order.dendrogram'
IdClusters: no visible global function definition for 'colors'
IdClusters : colEdge: no visible global function definition for
  'is.leaf'
IdClusters: no visible global function definition for 'dendrapply'
IdClusters: no visible global function definition for 'reorder'
IdClusters: no visible global function definition for 'plot'
IdConsensus: no visible global function definition for 'txtProgressBar'
IdConsensus: no visible global function definition for
  'setTxtProgressBar'
IdLengths: no visible global function definition for 'txtProgressBar'
IdLengths: no visible global function definition for
  'setTxtProgressBar'
MaskAlignment: no visible global function definition for 'par'
MaskAlignment: no visible global function definition for 'plot'
MaskAlignment: no visible global function definition for 'points'
MaskAlignment: no visible global function definition for 'abline'
MaskAlignment: no visible global function definition for 'axis'
MaskAlignment: no visible global function definition for 'mtext'
MaskAlignment: no visible global function definition for 'legend'
MeltDNA: no visible global function definition for 'step'
NNLS: no visible global function definition for 'txtProgressBar'
OrientNucleotides: no visible global function definition for
  'txtProgressBar'
OrientNucleotides: no visible global function definition for
  'setTxtProgressBar'
PredictHEC: no visible global function definition for 'data'
ReadDendrogram: no visible global function definition for 'dendrapply'
Seqs2DB : .cat: no visible global function definition for
  'flush.console'
Seqs2DB: no visible global function definition for 'flush.console'
StaggerAlignment: no visible global function definition for
  'flush.console'
StaggerAlignment : .assignIndels: no visible global function definition
  for 'is.leaf'
StaggerAlignment : .groupIns: no visible global function definition for
  'is.leaf'
StaggerAlignment: no visible global function definition for
  'txtProgressBar'
StaggerAlignment: no visible global function definition for
  'setTxtProgressBar'
TileSeqs: no visible global function definition for 'txtProgressBar'
TileSeqs: no visible global function definition for 'setTxtProgressBar'
WriteDendrogram : .dendrogram2newick: no visible global function
  definition for 'is.leaf'
pairs.Synteny: no visible global function definition for 'par'
pairs.Synteny: no visible global function definition for 'dev.hold'
pairs.Synteny: no visible global function definition for 'dev.flush'
pairs.Synteny: no visible global function definition for 'strwidth'
pairs.Synteny: no visible global function definition for 'plot'
pairs.Synteny: no visible global function definition for 'box'
pairs.Synteny: no visible global function definition for 'axis'
pairs.Synteny: no visible global function definition for 'text'
pairs.Synteny: no visible global function definition for 'segments'
pairs.Synteny: no visible global function definition for 'rect'
pairs.Synteny: no visible global function definition for 'rainbow'
pairs.Synteny: no visible global function definition for 'mtext'
plot.Synteny: no visible global function definition for
  'colorRampPalette'
plot.Synteny: no visible global function definition for 'dev.hold'
plot.Synteny: no visible global function definition for 'dev.flush'
plot.Synteny: no visible global function definition for 'dev.size'
plot.Synteny: no visible global function definition for 'plot'
plot.Synteny: no visible global function definition for 'par'
plot.Synteny: no visible global function definition for 'strheight'
plot.Synteny: no visible global function definition for 'text'
plot.Synteny: no visible global function definition for 'rect'
plot.Synteny: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline axis box browseURL colorRampPalette colors data deltaHrules
  dendrapply dev.flush dev.hold dev.size dist flush.console is.leaf
  legend mtext nlminb object.size optimize order.dendrogram par pbinom
  plot points rainbow rect reorder segments setNames setTxtProgressBar
  step strheight strwidth text txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "colorRampPalette", "colors", "dev.flush",
             "dev.hold", "dev.size", "rainbow")
  importFrom("graphics", "abline", "axis", "box", "legend", "mtext",
             "par", "plot", "points", "rect", "segments", "strheight",
             "strwidth", "text")
  importFrom("stats", "dendrapply", "dist", "is.leaf", "nlminb",
             "optimize", "order.dendrogram", "pbinom", "reorder",
             "setNames", "step", "uniroot")
  importFrom("utils", "browseURL", "data", "flush.console",
             "object.size", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* 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 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.3-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/i386/DECIPHER.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 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
StaggerAlignment   45.33   9.60   55.75
CorrectFrameshifts 48.42   3.54   51.96
AlignSeqs          26.57   7.79   34.65
AlignTranslation   21.93   1.45   24.39
IdClusters         13.66   4.99   19.20
BrowseSeqs         13.67   0.02   13.68
DesignArray        13.54   0.05   13.59
Array2Matrix       11.31   0.04   11.87
TileSeqs           10.03   0.00   10.03
AlignSynteny        5.60   1.96    7.56
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
StaggerAlignment   42.62   8.55   51.21
CorrectFrameshifts 40.08   3.54   43.61
AlignSeqs          21.22   7.92   29.27
AlignTranslation   20.56   1.45   22.01
TileSeqs           14.36   0.00   14.37
IdClusters          8.41   4.55   12.96
Array2Matrix       11.52   0.11   11.63
DesignArray        11.09   0.07   11.15
BrowseSeqs         11.00   0.00   11.00
AlignSynteny        4.71   1.87    6.58
* 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: 3 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/DECIPHER.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'DECIPHER' ...
** 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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c AlignProfiles.c -o AlignProfiles.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c AppendXStringSets.c -o AppendXStringSets.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c AssignIndels.c -o AssignIndels.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c CalculateDeltaG.c -o CalculateDeltaG.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
   -11.5, -7.8, -7, -8.3,
   ^
CalculateFISH.c:26:3: warning: (near initialization for 'dH_DR[0]') [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
   -36.4, -21.6, -19.7, -23.9,
   ^
CalculateFISH.c:32:3: warning: (near initialization for 'dS_DR[0]') [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
   -7.9, -8.4, -7.8, -7.2,
   ^
CalculateFISH.c:38:3: warning: (near initialization for 'dH_DD[0]') [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
   -22.2, -22.4, -21, -20.4,
   ^
CalculateFISH.c:44:3: warning: (near initialization for 'dS_DD[0]') [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
   -6.6, -10.17, -7.65, -5.76,
   ^
CalculateFISH.c:50:3: warning: (near initialization for 'dH_RR[0]') [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
   -18.38, -26.03, -19.18, -15.67,
   ^
CalculateFISH.c:56:3: warning: (near initialization for 'dS_RR[0]') [-Wmissing-braces]
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:414:72: warning: 'upY' may be used uninitialized in this function [-Wmaybe-uninitialized]
    int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
                                                                        ^
ChainSegments.c:414:67: warning: 'upX' may be used uninitialized in this function [-Wmaybe-uninitialized]
    int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
                                                                   ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ._omp_fn.0':
ClusterNJ.c:195:62: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC;
                                                              ^
ClusterNJ.c:195:56: warning: 'minR' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC;
                                                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from ClusterNJ.c:11:
ClusterNJ.c: In function 'clusterNJ':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
ClusterNJ.c:198:29: note: 'utilsPackage' was declared here
  SEXP ans, percentComplete, utilsPackage;
                             ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from ClusterNJ.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
ClusterNJ.c:198:12: note: 'percentComplete' was declared here
  SEXP ans, percentComplete, utilsPackage;
            ^
ClusterNJ.c:487:24: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *rPercentComplete = floor(100*soFar/total);
                        ^
ClusterNJ.c:492:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA._omp_fn.0':
ClusterUPGMA.c:124:62: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC, met;
                                                              ^
ClusterUPGMA.c:124:56: warning: 'minR' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC, met;
                                                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from ClusterUPGMA.c:11:
ClusterUPGMA.c: In function 'clusterUPGMA':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
ClusterUPGMA.c:127:29: note: 'utilsPackage' was declared here
  SEXP ans, percentComplete, utilsPackage;
                             ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from ClusterUPGMA.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
ClusterUPGMA.c:127:12: note: 'percentComplete' was declared here
  SEXP ans, percentComplete, utilsPackage;
            ^
ClusterUPGMA.c:426:24: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *rPercentComplete = floor(100*soFar/total);
                        ^
ClusterUPGMA.c:431:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c Compositions.c -o Compositions.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:884:11: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
      p[c] = (k - 1) & 0xFF; // length of run
           ^
Compression.c:411:12: note: 'k' was declared here
  int i, j, k, pos;
            ^
Compression.c:916:12: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
       count++;
            ^
Compression.c:437:29: note: 'count' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                             ^
Compression.c:915:20: warning: 'word' may be used uninitialized in this function [-Wmaybe-uninitialized]
       word = (word << 8) | (unsigned int)reorder(byte);
                    ^
Compression.c:437:23: note: 'word' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                       ^
Compression.c:1119:16: warning: 'lastHit' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = (unsigned char)lastHit;
                ^
Compression.c:437:36: note: 'lastHit' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                                    ^
Compression.c:1118:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = rev==0 ? 254 : 255;
              ^
Compression.c:438:27: note: 'rev' was declared here
   int lastTemp, currTemp, rev, len, len2, thresh = 1;
                           ^
Compression.c:535:25: warning: 'lastCase' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int run, lastTriplet, lastCase;
                         ^
Compression.c:1145:43: warning: 'lastTriplet' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
                                           ^
Compression.c:535:12: note: 'lastTriplet' was declared here
   int run, lastTriplet, lastCase;
            ^
Compression.c:992:12: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
        dict[word] = j;
            ^
Compression.c:437:17: note: 'dict' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function 'consensusProfile':
ConsensusSequence.c:1555:10: warning: 'DBN' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *DBN, *s;
          ^
ConsensusSequence.c: In function 'consensusProfileAA':
ConsensusSequence.c:444:14: warning: 'length' may be used uninitialized in this function [-Wmaybe-uninitialized]
    } else if (length==2) { // run of length 3
              ^
ConsensusSequence.c:385:15: note: 'length' was declared here
  int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
               ^
ConsensusSequence.c:443:18: warning: 'lastPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
      *(runs + s) += weight;
                  ^
ConsensusSequence.c:385:23: note: 'lastPos' was declared here
  int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
                       ^
ConsensusSequence.c:1748:10: warning: 'HEC' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *HEC, *s;
          ^
ConsensusSequence.c: In function 'colScores':
ConsensusSequence.c:1915:20: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_DBN, n, l, d;
                    ^
ConsensusSequence.c:1914:10: warning: 'DBN' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *DBN, *s;
          ^
ConsensusSequence.c: In function 'colScoresAA':
ConsensusSequence.c:2040:20: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_HEC, n, l, d;
                    ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ConsolidateGaps.c -o ConsolidateGaps.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
   -0.816507461,-2.5401714,-1.647430026,-1.184658548
   ^
DesignProbes.c:71:3: warning: (near initialization for 'NN[0]') [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
   -0.141370102,-0.439805276,-0.285236035,-0.205111781
   ^
DesignProbes.c:78:3: warning: (near initialization for 'PM[0]') [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
   0,0,0,0
   ^
DesignProbes.c:85:3: warning: (near initialization for 'sMM[0]') [-Wmissing-braces]
DesignProbes.c: In function 'designProbes._omp_fn.0':
DesignProbes.c:834:29: warning: 'lastCycle' may be used uninitialized in this function [-Wmaybe-uninitialized]
         cycles += lastCycle - thisCycle;
                             ^
DesignProbes.c:267:37: note: 'lastCycle' was declared here
    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
                                     ^
DesignProbes.c:834:29: warning: 'thisCycle' may be used uninitialized in this function [-Wmaybe-uninitialized]
         cycles += lastCycle - thisCycle;
                             ^
DesignProbes.c:267:48: note: 'thisCycle' was declared here
    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
                                                ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c Diff.c -o Diff.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function 'enumerateGappedSequence':
EnumerateSequence.c:267:6: warning: variable 'x_length' set but not used [-Wunused-but-set-variable]
  int x_length, i, j, k, wS, sum, ambiguous, *rans, *p;
      ^
EnumerateSequence.c: In function 'enumerateGappedSequenceAA':
EnumerateSequence.c:364:6: warning: variable 'x_length' set but not used [-Wunused-but-set-variable]
  int x_length, i, j, k, wS, sum, ambiguous, *rans, *p;
      ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ExpandAmbiguities.c -o ExpandAmbiguities.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:135:27: warning: 'K' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
                           ^
FindFrameshifts.c:135:24: warning: 'J' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
                        ^
FindFrameshifts.c:135:21: warning: 'I' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
                     ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from FindFrameshifts.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
FindFrameshifts.c:162:24: note: 'utilsPackage' was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from FindFrameshifts.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
FindFrameshifts.c:162:7: note: 'percentComplete' was declared here
  SEXP percentComplete, utilsPackage;
       ^
FindFrameshifts.c:468:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c Import.c -o Import.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c InsertGaps.c -o InsertGaps.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c IntDist.c -o IntDist.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:80:3: warning: missing braces around initializer [-Wmissing-braces]
   -7.9,-8.4,-7.8,-7.2
   ^
MeltPolymer.c:80:3: warning: (near initialization for 'dH[0]') [-Wmissing-braces]
MeltPolymer.c:89:3: warning: missing braces around initializer [-Wmissing-braces]
   -22.2,-22.4,-21.0,-20.4
   ^
MeltPolymer.c:89:3: warning: (near initialization for 'dS[0]') [-Wmissing-braces]
MeltPolymer.c:373:33: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
      slope = (*(rans + stack[0] + l*s) - *(rans + stack[pos] + l*s))/(t[stack[0]] - t[stack[pos]]);
                                 ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c MultiMatch.c -o MultiMatch.o
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:242:24: note: 'utilsPackage' was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from MultiMatch.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:242:7: note: 'percentComplete' was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:325:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchListsDual':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:350:24: note: 'utilsPackage' was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from MultiMatch.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:350:7: note: 'percentComplete' was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:426:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchOrder':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:451:24: note: 'utilsPackage' was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from MultiMatch.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:451:7: note: 'percentComplete' was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:545:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c NNLS.c -o NNLS.o
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from NNLS.c:11:
NNLS.c: In function 'NNLS':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
NNLS.c:47:24: note: 'utilsPackage' was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from NNLS.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
NNLS.c:47:7: note: 'percentComplete' was declared here
  SEXP percentComplete, utilsPackage;
       ^
NNLS.c:82:13: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
      before = *rPercentComplete;
             ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c Order.c -o Order.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function 'predictHEC':
PredictHEC.c:255:4: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
    SET_VECTOR_ELT(ret, i, ans);
    ^
PredictHEC.c:233:16: warning: 'states' may be used uninitialized in this function [-Wmaybe-uninitialized]
      states[j] = 'C';
                ^
PredictHEC.c:41:24: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double H, E, C, sum, *rans;
                        ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c RemoveGaps.c -o RemoveGaps.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c SubsetXStringSet.c -o SubsetXStringSet.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c TerminalMismatch.c -o TerminalMismatch.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c Translate.c -o Translate.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def AlignProfiles.o AppendXStringSets.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o Import.o InsertGaps.o IntDist.o MeltPolymer.o MultiMatch.o NNLS.o Order.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o SubsetXStringSet.o TerminalMismatch.o Translate.o XVector_stubs.o -fopenmp -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/DECIPHER.buildbin-libdir/DECIPHER/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'DECIPHER' ...
** 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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c AlignProfiles.c -o AlignProfiles.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c AppendXStringSets.c -o AppendXStringSets.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c AssignIndels.c -o AssignIndels.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c CalculateDeltaG.c -o CalculateDeltaG.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
   -11.5, -7.8, -7, -8.3,
   ^
CalculateFISH.c:26:3: warning: (near initialization for 'dH_DR[0]') [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
   -36.4, -21.6, -19.7, -23.9,
   ^
CalculateFISH.c:32:3: warning: (near initialization for 'dS_DR[0]') [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
   -7.9, -8.4, -7.8, -7.2,
   ^
CalculateFISH.c:38:3: warning: (near initialization for 'dH_DD[0]') [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
   -22.2, -22.4, -21, -20.4,
   ^
CalculateFISH.c:44:3: warning: (near initialization for 'dS_DD[0]') [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
   -6.6, -10.17, -7.65, -5.76,
   ^
CalculateFISH.c:50:3: warning: (near initialization for 'dH_RR[0]') [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
   -18.38, -26.03, -19.18, -15.67,
   ^
CalculateFISH.c:56:3: warning: (near initialization for 'dS_RR[0]') [-Wmissing-braces]
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:414:72: warning: 'upY' may be used uninitialized in this function [-Wmaybe-uninitialized]
    int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
                                                                        ^
ChainSegments.c:414:67: warning: 'upX' may be used uninitialized in this function [-Wmaybe-uninitialized]
    int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
                                                                   ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ._omp_fn.0':
ClusterNJ.c:281:12: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
     minCol = minC;
            ^
ClusterNJ.c:195:62: note: 'minC' was declared here
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC;
                                                              ^
ClusterNJ.c:280:12: warning: 'minR' may be used uninitialized in this function [-Wmaybe-uninitialized]
     minRow = minR;
            ^
ClusterNJ.c:195:56: note: 'minR' was declared here
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC;
                                                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from ClusterNJ.c:11:
ClusterNJ.c: In function 'clusterNJ':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
ClusterNJ.c:198:29: note: 'utilsPackage' was declared here
  SEXP ans, percentComplete, utilsPackage;
                             ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from ClusterNJ.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
ClusterNJ.c:198:12: note: 'percentComplete' was declared here
  SEXP ans, percentComplete, utilsPackage;
            ^
ClusterNJ.c:487:24: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *rPercentComplete = floor(100*soFar/total);
                        ^
ClusterNJ.c:492:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA._omp_fn.0':
ClusterUPGMA.c:200:12: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
     minCol = minC;
            ^
ClusterUPGMA.c:124:62: note: 'minC' was declared here
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC, met;
                                                              ^
ClusterUPGMA.c:199:12: warning: 'minR' may be used uninitialized in this function [-Wmaybe-uninitialized]
     minRow = minR;
            ^
ClusterUPGMA.c:124:56: note: 'minR' was declared here
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC, met;
                                                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from ClusterUPGMA.c:11:
ClusterUPGMA.c: In function 'clusterUPGMA':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
ClusterUPGMA.c:127:29: note: 'utilsPackage' was declared here
  SEXP ans, percentComplete, utilsPackage;
                             ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from ClusterUPGMA.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
ClusterUPGMA.c:127:12: note: 'percentComplete' was declared here
  SEXP ans, percentComplete, utilsPackage;
            ^
ClusterUPGMA.c:426:24: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *rPercentComplete = floor(100*soFar/total);
                        ^
ClusterUPGMA.c:431:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c Compositions.c -o Compositions.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:884:11: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
      p[c] = (k - 1) & 0xFF; // length of run
           ^
Compression.c:411:12: note: 'k' was declared here
  int i, j, k, pos;
            ^
Compression.c:916:12: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
       count++;
            ^
Compression.c:437:29: note: 'count' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                             ^
Compression.c:915:20: warning: 'word' may be used uninitialized in this function [-Wmaybe-uninitialized]
       word = (word << 8) | (unsigned int)reorder(byte);
                    ^
Compression.c:437:23: note: 'word' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                       ^
Compression.c:1119:16: warning: 'lastHit' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = (unsigned char)lastHit;
                ^
Compression.c:437:36: note: 'lastHit' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                                    ^
Compression.c:1118:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = rev==0 ? 254 : 255;
              ^
Compression.c:438:27: note: 'rev' was declared here
   int lastTemp, currTemp, rev, len, len2, thresh = 1;
                           ^
Compression.c:535:25: warning: 'lastCase' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int run, lastTriplet, lastCase;
                         ^
Compression.c:1145:43: warning: 'lastTriplet' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
                                           ^
Compression.c:535:12: note: 'lastTriplet' was declared here
   int run, lastTriplet, lastCase;
            ^
Compression.c:963:23: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
         lastHit = dict[revcomp((word >> k) & 0xFF)]; // end of lastHit
                       ^
Compression.c:437:17: note: 'dict' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function 'consensusProfileAA':
ConsensusSequence.c:443:18: warning: 'lastPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
      *(runs + s) += weight;
                  ^
ConsensusSequence.c:385:23: note: 'lastPos' was declared here
  int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
                       ^
ConsensusSequence.c:1748:10: warning: 'HEC' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *HEC, *s;
          ^
ConsensusSequence.c: In function 'colScores':
ConsensusSequence.c:1915:20: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_DBN, n, l, d;
                    ^
ConsensusSequence.c: In function 'colScoresAA':
ConsensusSequence.c:2040:20: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_HEC, n, l, d;
                    ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ConsolidateGaps.c -o ConsolidateGaps.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
   -0.816507461,-2.5401714,-1.647430026,-1.184658548
   ^
DesignProbes.c:71:3: warning: (near initialization for 'NN[0]') [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
   -0.141370102,-0.439805276,-0.285236035,-0.205111781
   ^
DesignProbes.c:78:3: warning: (near initialization for 'PM[0]') [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
   0,0,0,0
   ^
DesignProbes.c:85:3: warning: (near initialization for 'sMM[0]') [-Wmissing-braces]
DesignProbes.c: In function 'designProbes._omp_fn.0':
DesignProbes.c:834:29: warning: 'lastCycle' may be used uninitialized in this function [-Wmaybe-uninitialized]
         cycles += lastCycle - thisCycle;
                             ^
DesignProbes.c:267:37: note: 'lastCycle' was declared here
    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
                                     ^
DesignProbes.c:834:29: warning: 'thisCycle' may be used uninitialized in this function [-Wmaybe-uninitialized]
         cycles += lastCycle - thisCycle;
                             ^
DesignProbes.c:267:48: note: 'thisCycle' was declared here
    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
                                                ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c Diff.c -o Diff.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function 'enumerateGappedSequence':
EnumerateSequence.c:267:6: warning: variable 'x_length' set but not used [-Wunused-but-set-variable]
  int x_length, i, j, k, wS, sum, ambiguous, *rans, *p;
      ^
EnumerateSequence.c: In function 'enumerateGappedSequenceAA':
EnumerateSequence.c:364:6: warning: variable 'x_length' set but not used [-Wunused-but-set-variable]
  int x_length, i, j, k, wS, sum, ambiguous, *rans, *p;
      ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ExpandAmbiguities.c -o ExpandAmbiguities.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:318:12: warning: 'K' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (C[k*rc + j*r + i] >= 0) {
            ^
FindFrameshifts.c:372:8: warning: 'J' may be used uninitialized in this function [-Wmaybe-uninitialized]
      j -= B[k*rc + j*r + i];
        ^
FindFrameshifts.c:318:22: warning: 'I' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (C[k*rc + j*r + i] >= 0) {
                      ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from FindFrameshifts.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
FindFrameshifts.c:162:24: note: 'utilsPackage' was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from FindFrameshifts.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
FindFrameshifts.c:162:7: note: 'percentComplete' was declared here
  SEXP percentComplete, utilsPackage;
       ^
FindFrameshifts.c:468:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c Import.c -o Import.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c InsertGaps.c -o InsertGaps.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c IntDist.c -o IntDist.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:80:3: warning: missing braces around initializer [-Wmissing-braces]
   -7.9,-8.4,-7.8,-7.2
   ^
MeltPolymer.c:80:3: warning: (near initialization for 'dH[0]') [-Wmissing-braces]
MeltPolymer.c:89:3: warning: missing braces around initializer [-Wmissing-braces]
   -22.2,-22.4,-21.0,-20.4
   ^
MeltPolymer.c:89:3: warning: (near initialization for 'dS[0]') [-Wmissing-braces]
MeltPolymer.c:373:33: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
      slope = (*(rans + stack[0] + l*s) - *(rans + stack[pos] + l*s))/(t[stack[0]] - t[stack[pos]]);
                                 ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c MultiMatch.c -o MultiMatch.o
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:242:24: note: 'utilsPackage' was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from MultiMatch.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:242:7: note: 'percentComplete' was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:325:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchListsDual':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:350:24: note: 'utilsPackage' was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from MultiMatch.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:350:7: note: 'percentComplete' was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:426:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchOrder':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:451:24: note: 'utilsPackage' was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from MultiMatch.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:451:7: note: 'percentComplete' was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:545:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c NNLS.c -o NNLS.o
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from NNLS.c:11:
NNLS.c: In function 'NNLS':
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
NNLS.c:47:24: note: 'utilsPackage' was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from E:/biocbld/BBS-3˜1.3-B/R/include/Rdefines.h:36:0,
                 from NNLS.c:11:
E:/biocbld/BBS-3˜1.3-B/R/include/Rinternals.h:1155:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
NNLS.c:47:7: note: 'percentComplete' was declared here
  SEXP percentComplete, utilsPackage;
       ^
NNLS.c:82:13: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
      before = *rPercentComplete;
             ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c Order.c -o Order.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function 'predictHEC':
PredictHEC.c:255:4: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
    SET_VECTOR_ELT(ret, i, ans);
    ^
PredictHEC.c:42:8: warning: 'states' may be used uninitialized in this function [-Wmaybe-uninitialized]
  char *states;
        ^
PredictHEC.c:41:24: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double H, E, C, sum, *rans;
                        ^
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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c RemoveGaps.c -o RemoveGaps.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c SubsetXStringSet.c -o SubsetXStringSet.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c TerminalMismatch.c -o TerminalMismatch.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c Translate.c -o Translate.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/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/RSQLite/include" -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"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def AlignProfiles.o AppendXStringSets.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o Import.o InsertGaps.o IntDist.o MeltPolymer.o MultiMatch.o NNLS.o Order.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o SubsetXStringSet.o TerminalMismatch.o Translate.o XVector_stubs.o -fopenmp -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/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_2.0.2.zip
* DONE (DECIPHER)

BioC 3.3: CHECK report for DECIPHER on moscato2

Summary

Command output

name	user	system	elapsed
Add2DB	0.31	0.00	0.39
AdjustAlignment	0.39	0.00	1.14
AlignDB	1.84	0.13	2.03
AlignProfiles	2.61	0.29	2.94
AlignSeqs	26.57	7.79	34.65
AlignSynteny	5.60	1.96	7.56
AlignTranslation	21.93	1.45	24.39
AmplifyDNA	0.02	0.00	0.34
Array2Matrix	11.31	0.04	11.87
BrowseDB	0.03	0.00	0.03
BrowseSeqs	13.67	0.02	13.68
CalculateEfficiencyArray	0.03	0.00	0.09
CalculateEfficiencyFISH	0.02	0.00	0.02
CalculateEfficiencyPCR	0.00	0.01	0.01
Codec	0.62	0.02	0.64
ConsensusSequence	0.05	0.00	0.05
CorrectFrameshifts	48.42	3.54	51.96
CreateChimeras	1.51	0.00	2.54
DB2Seqs	0.02	0.00	0.02
DesignArray	13.54	0.05	13.59
DesignPrimers	0	0	0
DesignProbes	0	0	0
DesignSignatures	0	0	0
DigestDNA	0.29	0.00	0.30
Disambiguate	0.10	0.00	0.09
DistanceMatrix	0.01	0.00	0.02
FindChimeras	0.08	0.00	0.08
FindSynteny	2.14	0.00	2.13
FormGroups	0.08	0.00	0.08
HEC_MI	0.34	0.01	0.36
IdClusters	13.66	4.99	19.20
IdConsensus	1.21	0.02	1.22
IdLengths	0.01	0.00	0.02
IdentifyByRank	0.01	0.00	0.02
MIQS	0.02	0.01	0.18
MODELS	0	0	0
MaskAlignment	1.11	0.02	1.13
MeltDNA	0.07	0.00	0.08
NNLS	0.02	0.00	0.01
OrientNucleotides	1.96	0.06	2.56
PredictHEC	0.43	0.02	0.44
RESTRICTION_ENZYMES	0.00	0.01	0.01
ReadDendrogram	0.04	0.00	0.05
SearchDB	0.05	0.00	0.05
Seqs2DB	0.14	0.00	0.14
StaggerAlignment	45.33	9.60	55.75
Synteny-class	0.89	0.01	0.91
TerminalChar	0.03	0.00	0.03
TileSeqs	10.03	0.00	10.03
WriteDendrogram	0.02	0.00	0.01
deltaGrules	0.03	0.00	0.04
deltaHrules	0.05	0.00	0.04
deltaSrules	0.08	0.02	0.38