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BioC 3.4: CHECK report for DECIPHER on tokay1

This page was generated on 2017-04-15 16:16:55 -0400 (Sat, 15 Apr 2017).

Package 304/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 2.2.0
Erik Wright
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/DECIPHER
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DECIPHER
Version: 2.2.0
Command: rm -rf DECIPHER.buildbin-libdir DECIPHER.Rcheck && mkdir DECIPHER.buildbin-libdir DECIPHER.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_2.2.0.tar.gz >DECIPHER.Rcheck\00install.out 2>&1 && cp DECIPHER.Rcheck\00install.out DECIPHER-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DECIPHER.buildbin-libdir --install="check:DECIPHER-install.out" --force-multiarch --no-vignettes --timings DECIPHER_2.2.0.tar.gz
StartedAt: 2017-04-14 21:52:00 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:00:38 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 518.3 seconds
RetCode: 0
Status:  OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DECIPHER.buildbin-libdir DECIPHER.Rcheck && mkdir DECIPHER.buildbin-libdir DECIPHER.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_2.2.0.tar.gz >DECIPHER.Rcheck\00install.out 2>&1 && cp DECIPHER.Rcheck\00install.out DECIPHER-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DECIPHER.buildbin-libdir --install="check:DECIPHER-install.out" --force-multiarch --no-vignettes --timings DECIPHER_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/DECIPHER.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '2.2.0'
* 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  9.1Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       4.0Mb
    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
DesignSignatures: no visible binding for global variable 'deltaHrules'
Undefined global functions or variables:
  deltaHrules
* 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 'C:/Users/biocbuild/bbs-3.4-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
AlignSeqs          33.45  10.44   43.89
CorrectFrameshifts 22.54   4.05   26.60
StaggerAlignment   21.21   4.89   26.09
IdClusters          7.83   2.80   10.63
PredictDBN         10.39   0.12   10.51
BrowseSeqs          9.16   0.19    9.34
AlignTranslation    6.93   0.99    7.90
Array2Matrix        7.79   0.08    7.88
DesignArray         7.71   0.01    7.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
AlignSeqs          22.13   9.86   31.99
StaggerAlignment   18.55   4.97   23.51
CorrectFrameshifts 20.01   2.47   22.49
PredictDBN          8.63   0.17    8.79
IdClusters          5.27   3.10    8.36
Array2Matrix        7.23   0.05    7.28
BrowseSeqs          7.02   0.06    7.08
DesignArray         7.00   0.06    7.06
AlignTranslation    5.94   0.97    6.91
TileSeqs            5.62   0.00    5.62
* 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
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/DECIPHER.Rcheck/00check.log'
for details.

DECIPHER.Rcheck/00install.out:


install for i386

* installing *source* package 'DECIPHER' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from ClusterNJ.c:11:
ClusterNJ.c: In function 'clusterNJ':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from ClusterNJ.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from ClusterUPGMA.c:11:
ClusterUPGMA.c: In function 'clusterUPGMA':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from ClusterUPGMA.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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:975:11: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
      p[c] = (k - 1) & 0xFF; // length of run
           ^
Compression.c:513:12: note: 'k' was declared here
  int i, j, k, pos;
            ^
Compression.c:1007:12: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
       count++;
            ^
Compression.c:539:29: note: 'count' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                             ^
Compression.c:1006:20: warning: 'word' may be used uninitialized in this function [-Wmaybe-uninitialized]
       word = (word << 8) | (unsigned int)reorder(byte);
                    ^
Compression.c:539:23: note: 'word' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                       ^
Compression.c:1210:16: warning: 'lastHit' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = (unsigned char)lastHit;
                ^
Compression.c:539:36: note: 'lastHit' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                                    ^
Compression.c:1209:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = rev==0 ? 254 : 255;
              ^
Compression.c:540:27: note: 'rev' was declared here
   int lastTemp, currTemp, rev, len, len2, thresh = 1;
                           ^
Compression.c:626:25: warning: 'lastCase' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int run, lastTriplet, lastCase;
                         ^
Compression.c:1236:43: warning: 'lastTriplet' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
                                           ^
Compression.c:626:12: note: 'lastTriplet' was declared here
   int run, lastTriplet, lastCase;
            ^
Compression.c:1083:12: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
        dict[word] = j;
            ^
Compression.c:539:17: note: 'dict' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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:1578:10: warning: 'DBN' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *DBN, *s;
          ^
ConsensusSequence.c: In function 'consensusProfileAA':
ConsensusSequence.c:456:14: warning: 'length' may be used uninitialized in this function [-Wmaybe-uninitialized]
    } else if (length==2) { // run of length 3
              ^
ConsensusSequence.c:397:15: note: 'length' was declared here
  int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
               ^
ConsensusSequence.c:455:18: warning: 'lastPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
      *(runs + s) += weight;
                  ^
ConsensusSequence.c:397:23: note: 'lastPos' was declared here
  int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
                       ^
ConsensusSequence.c:1771:10: warning: 'HEC' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *HEC, *s;
          ^
ConsensusSequence.c: In function 'colScores':
ConsensusSequence.c:1938:20: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_DBN, n, l, d;
                    ^
ConsensusSequence.c:1937:10: warning: 'DBN' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *DBN, *s;
          ^
ConsensusSequence.c: In function 'colScoresAA':
ConsensusSequence.c:2063:20: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_HEC, n, l, d;
                    ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 'pop':
EnumerateSequence.c:266:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
  x = x + (x >> 4) & 0xF0F0F0F;
        ^
EnumerateSequence.c: In function 'enumerateGappedSequence':
EnumerateSequence.c:275:6: 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:397:6: 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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c GetPools.c -o GetPools.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c MovingAverage.c -o MovingAverage.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchListsDual':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchOrder':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
NNLS.c: In function 'NNLS':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c PredictDBN.c -o PredictDBN.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:37:0,
                 from PredictDBN.c:11:
PredictDBN.c: In function 'predictDBN':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/R_ext/RS.h:77:25: warning: 'MI2' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
                         ^
PredictDBN.c:399:10: note: 'MI2' was declared here
  double *MI2, *rowMax, *colMax;
          ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 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 GetPools.o Import.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o TerminalMismatch.o Translate.o XVector_stubs.o -fopenmp -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from ClusterNJ.c:11:
ClusterNJ.c: In function 'clusterNJ':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from ClusterNJ.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from ClusterUPGMA.c:11:
ClusterUPGMA.c: In function 'clusterUPGMA':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from ClusterUPGMA.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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:975:11: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
      p[c] = (k - 1) & 0xFF; // length of run
           ^
Compression.c:513:12: note: 'k' was declared here
  int i, j, k, pos;
            ^
Compression.c:1007:12: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
       count++;
            ^
Compression.c:539:29: note: 'count' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                             ^
Compression.c:1006:20: warning: 'word' may be used uninitialized in this function [-Wmaybe-uninitialized]
       word = (word << 8) | (unsigned int)reorder(byte);
                    ^
Compression.c:539:23: note: 'word' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                       ^
Compression.c:1210:16: warning: 'lastHit' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = (unsigned char)lastHit;
                ^
Compression.c:539:36: note: 'lastHit' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                                    ^
Compression.c:1209:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = rev==0 ? 254 : 255;
              ^
Compression.c:540:27: note: 'rev' was declared here
   int lastTemp, currTemp, rev, len, len2, thresh = 1;
                           ^
Compression.c:626:25: warning: 'lastCase' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int run, lastTriplet, lastCase;
                         ^
Compression.c:1236:43: warning: 'lastTriplet' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
                                           ^
Compression.c:626:12: note: 'lastTriplet' was declared here
   int run, lastTriplet, lastCase;
            ^
Compression.c:1054:23: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
         lastHit = dict[revcomp((word >> k) & 0xFF)]; // end of lastHit
                       ^
Compression.c:539:17: note: 'dict' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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:455:18: warning: 'lastPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
      *(runs + s) += weight;
                  ^
ConsensusSequence.c:397:23: note: 'lastPos' was declared here
  int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
                       ^
ConsensusSequence.c:1771:10: warning: 'HEC' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *HEC, *s;
          ^
ConsensusSequence.c: In function 'colScores':
ConsensusSequence.c:1938:20: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_DBN, n, l, d;
                    ^
ConsensusSequence.c: In function 'colScoresAA':
ConsensusSequence.c:2063:20: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_HEC, n, l, d;
                    ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 'pop':
EnumerateSequence.c:266:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
  x = x + (x >> 4) & 0xF0F0F0F;
        ^
EnumerateSequence.c: In function 'enumerateGappedSequence':
EnumerateSequence.c:275:6: 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:397:6: 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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c GetPools.c -o GetPools.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c MovingAverage.c -o MovingAverage.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchListsDual':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchOrder':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
NNLS.c: In function 'NNLS':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rinternals.h:1173:16: 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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/local323/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c PredictDBN.c -o PredictDBN.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/Rdefines.h:37:0,
                 from PredictDBN.c:11:
PredictDBN.c: In function 'predictDBN':
C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/R_ext/RS.h:77:25: warning: 'MI2' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
                         ^
PredictDBN.c:399:10: note: 'MI2' was declared here
  double *MI2, *rowMax, *colMax;
          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-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 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 GetPools.o Import.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o TerminalMismatch.o Translate.o XVector_stubs.o -fopenmp -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_2.2.0.zip
* DONE (DECIPHER)

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

nameusersystemelapsed
Add2DB0.230.020.25
AdjustAlignment0.250.000.25
AlignDB1.030.121.16
AlignProfiles1.340.171.52
AlignSeqs33.4510.4443.89
AlignSynteny2.861.144.00
AlignTranslation6.930.997.90
AmplifyDNA0.000.010.06
Array2Matrix7.790.087.88
BrowseDB0.030.000.03
BrowseSeqs9.160.199.34
CalculateEfficiencyArray0.020.000.02
CalculateEfficiencyFISH000
CalculateEfficiencyPCR000
Codec0.550.000.54
ConsensusSequence0.210.000.20
CorrectFrameshifts22.54 4.0526.60
CreateChimeras0.770.000.76
DB2Seqs0.010.000.02
DesignArray7.710.017.72
DesignPrimers000
DesignProbes000
DesignSignatures000
DigestDNA0.120.020.14
Disambiguate0.030.000.03
DistanceMatrix0.020.000.01
FindChimeras0.050.000.05
FindSynteny1.260.021.28
FormGroups0.060.000.06
HEC_MI0.250.010.26
IdClusters 7.83 2.8010.63
IdConsensus0.660.030.69
IdLengths0.010.000.01
IdentifyByRank0.040.000.03
MIQS0.010.000.02
MODELS000
MaskAlignment0.560.020.58
MeltDNA0.050.000.04
NNLS000
OrientNucleotides0.890.030.93
PredictDBN10.39 0.1210.51
PredictHEC0.300.020.31
RESTRICTION_ENZYMES0.000.010.02
ReadDendrogram0.010.000.02
SearchDB0.020.020.03
Seqs2DB0.090.000.09
StaggerAlignment21.21 4.8926.09
Synteny-class0.730.020.75
TerminalChar0.020.000.02
TileSeqs4.170.004.17
TrimDNA0.030.000.03
WriteDendrogram000
deltaGrules0.020.000.02
deltaHrules0.020.000.02
deltaSrules0.090.000.09

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

nameusersystemelapsed
Add2DB0.340.000.35
AdjustAlignment0.230.030.26
AlignDB1.100.141.24
AlignProfiles1.230.171.40
AlignSeqs22.13 9.8631.99
AlignSynteny2.151.133.28
AlignTranslation5.940.976.91
AmplifyDNA000
Array2Matrix7.230.057.28
BrowseDB0.030.000.03
BrowseSeqs7.020.067.08
CalculateEfficiencyArray0.000.010.04
CalculateEfficiencyFISH000
CalculateEfficiencyPCR000
Codec0.740.000.74
ConsensusSequence0.220.000.21
CorrectFrameshifts20.01 2.4722.49
CreateChimeras1.020.001.01
DB2Seqs0.010.000.05
DesignArray7.000.067.06
DesignPrimers000
DesignProbes000
DesignSignatures000
DigestDNA0.140.000.14
Disambiguate0.050.000.05
DistanceMatrix0.020.000.02
FindChimeras0.060.000.06
FindSynteny1.670.001.67
FormGroups0.080.000.08
HEC_MI0.230.000.23
IdClusters5.273.108.36
IdConsensus0.730.010.75
IdLengths0.020.000.02
IdentifyByRank0.030.000.03
MIQS0.000.020.02
MODELS000
MaskAlignment0.610.000.60
MeltDNA0.050.000.05
NNLS0.010.000.02
OrientNucleotides0.960.030.98
PredictDBN8.630.178.79
PredictHEC0.280.020.30
RESTRICTION_ENZYMES000
ReadDendrogram0.030.000.03
SearchDB0.030.000.11
Seqs2DB0.230.030.27
StaggerAlignment18.55 4.9723.51
Synteny-class0.810.040.86
TerminalChar0.020.000.02
TileSeqs5.620.005.62
TrimDNA0.040.000.03
WriteDendrogram000
deltaGrules0.010.000.02
deltaHrules0.010.000.01
deltaSrules0.060.020.08