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BUILD BIN report for DECIPHER on tokay2

This page was generated on 2020-10-17 11:56:25 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE DECIPHER PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 432/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 2.16.1
Erik Wright
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/DECIPHER
Branch: RELEASE_3_11
Last Commit: 237cc7d
Last Changed Date: 2020-05-11 09:00:15 -0400 (Mon, 11 May 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DECIPHER
Version: 2.16.1
Command: rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DECIPHER.buildbin-libdir DECIPHER_2.16.1.tar.gz
StartedAt: 2020-10-17 10:16:49 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 10:19:22 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 152.7 seconds
RetCode: 0
Status:  OK  
PackageFile: DECIPHER_2.16.1.zip
PackageFileSize: 11.58 MiB

Command output

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###
### Running command:
###
###   rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DECIPHER.buildbin-libdir DECIPHER_2.16.1.tar.gz
###
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install for i386

* installing *source* package 'DECIPHER' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function 'alignProfiles._omp_fn.0':
AlignProfiles.c:401:9: warning: 'lGp' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGp *= tot;
     ~~~~^~~~~~
AlignProfiles.c:39:39: note: 'lGp' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
                                       ^~~
AlignProfiles.c:403:9: warning: 'lGs' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGs *= tot;
     ~~~~^~~~~~
AlignProfiles.c:39:44: note: 'lGs' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
                                            ^~~
AlignProfiles.c: In function 'alignProfilesAA._omp_fn.1':
AlignProfiles.c:1220:9: warning: 'lGp' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGp *= tot;
     ~~~~^~~~~~
AlignProfiles.c:763:39: note: 'lGp' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
                                       ^~~
AlignProfiles.c:1222:9: warning: 'lGs' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGs *= tot;
     ~~~~^~~~~~
AlignProfiles.c:763:44: note: 'lGs' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
                                            ^~~
AlignProfiles.c: In function 'alignProfiles':
AlignProfiles.c:355:11: warning: 'subM' may be used uninitialized in this function [-Wmaybe-uninitialized]
   #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs) num_threads(nthreads)
           ^~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AssignIndels.c -o AssignIndels.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CalculateDeltaG.c -o CalculateDeltaG.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:25:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_DR[4][4] = {
                       ^
   -11.5, -7.8, -7, -8.3,
   {                    }
   -10.4, -12.8, -16.3, -9.1,
   {                        }
   -8.6, -8, -9.3, -5.9,
   {                   }
   -7.8, -5.5, -9, -7.8
   {
  };
  }
CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_DR[4][4] = {
                       ^
   -36.4, -21.6, -19.7, -23.9,
   {                         }
   -28.4, -31.9, -47.1, -23.5,
   {                         }
   -22.9, -17.1, -23.2, -12.3,
   {                         }
   -23.2, -13.5, -26.1, -21.9
   {
  };
  }
CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_DD[4][4] = {
                       ^
   -7.9, -8.4, -7.8, -7.2,
   {                     }
   -8.5, -8, -10.6, -7.8,
   {                    }
   -8.2, -9.8, -8, -8.4,
   {                   }
   -7.2, -8.2, -8.5, -7.9
   {
  };
  }
CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_DD[4][4] = {
                       ^
   -22.2, -22.4, -21, -20.4,
   {                       }
   -22.7, -19.9, -27.2, -21,
   {                       }
   -22.2, -24.4, -19.9, -22.4,
   {                         }
   -21.3, -22.2, -22.7, -22.2
   {
  };
  }
CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_RR[4][4] = {
                       ^
   -6.6, -10.17, -7.65, -5.76,
   {                         }
   -10.56, -12.21, -7.95, -7.65,
   {                           }
   -13.37, -14.21, -12.21, -10.17,
   {                             }
   -8.11, -13.37, -10.56, -6.6
   {
  };
  }
CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_RR[4][4] = {
                       ^
   -18.38, -26.03, -19.18, -15.67,
   {                             }
   -28.25, -30.02, -19.18, -19.18,
   {                             }
   -35.68, -34.85, -30.02, -26.03,
   {                             }
   -22.59, -35.68, -28.25, -18.38
   {
  };
  }
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:420:72: 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:420:67: 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:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Cluster.c -o Cluster.o
Cluster.c: In function 'cluster._omp_fn.0':
Cluster.c:403:15: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
        minCol = minC;
        ~~~~~~~^~~~~~
Cluster.c:229:50: note: 'minC' was declared here
  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
                                                  ^~~~
Cluster.c: In function 'cluster._omp_fn.1':
Cluster.c:418:30: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
       minCols[rowIndices[i]] = minC;
       ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:229:50: note: 'minC' was declared here
  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
                                                  ^~~~
Cluster.c: In function 'cluster':
Cluster.c:229:50: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
Cluster.c:766:19: warning: 'nDiv' may be used uninitialized in this function [-Wmaybe-uninitialized]
      nDiv[minCol] -= dMatrix2[length*colIndices[minCol] - colIndices[minCol]*(colIndices[minCol] + 1)/2 + rowIndices[j] - colIndices[minCol]]; // col sums
                   ^~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ClusterML.c -o ClusterML.o
ClusterML.c: In function 'clusterML._omp_fn.2':
ClusterML.c:556:40: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
       node[count*maxWidth*4 + i*4 + 0] += *(Ls + 0*length + j);
                                        ^~
ClusterML.c:420:6: note: 'count' was declared here
  int count;
      ^~~~~
ClusterML.c: In function 'clusterML':
ClusterML.c:441:11: warning: 'node' may be used uninitialized in this function [-Wmaybe-uninitialized]
   #pragma omp parallel for private(i,j,y_i,row,count) schedule(guided) num_threads(nthreads)
           ^~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CommonGaps.c -o CommonGaps.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Compositions.c -o Compositions.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:966:8: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (k==1 && letter >= 11) {
        ^
Compression.c:516:12: note: 'k' was declared here
  int i, j, k, pos;
            ^
Compression.c:1010:12: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
       count++;
       ~~~~~^~
Compression.c:542:29: note: 'count' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                             ^~~~~
Compression.c:1009:20: warning: 'word' may be used uninitialized in this function [-Wmaybe-uninitialized]
       word = (word << 8) | (unsigned int)reorder(byte);
              ~~~~~~^~~~~
Compression.c:542:23: note: 'word' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                       ^~~~
Compression.c:1167:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = rev==0 ? 254 : 255;
       ~~~~~~~^~~~~~~~~~~~~~~~~~~~
Compression.c:543:27: note: 'rev' was declared here
   int lastTemp, currTemp, rev, len, len2, thresh = 1;
                           ^~~
Compression.c:556:7: warning: 'lower' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int lower = 0;
       ^~~~~
Compression.c:1239:43: warning: 'lastTriplet' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
                                        ~~~^~~~~~~~~~~~~~
Compression.c:629:12: note: 'lastTriplet' was declared here
   int run, lastTriplet, lastCase;
            ^~~~~~~~~~~
Compression.c:1057:23: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
         lastHit = dict[revcomp((word >> k) & 0xFF)]; // end of lastHit
                       ^
Compression.c:542:17: note: 'dict' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ConsensusSequence.c -o ConsensusSequence.o
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: 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:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ConsolidateGaps.c -o ConsolidateGaps.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:70:20: warning: missing braces around initializer [-Wmissing-braces]
  double NN[4][4] = {
                    ^
   -0.816507461,-2.5401714,-1.647430026,-1.184658548
   {
   ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
   }{
   ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
   }{
   ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
   }{
  };
  }
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
  double PM[4][4] = {
                    ^
   -0.141370102,-0.439805276,-0.285236035,-0.205111781
   {
   ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
   }{
   ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
   }{
   ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
   }{
  };
  }
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
  double sMM[4][5][5][4] = {
                           ^
   0,0,0,0
   {{{
   ,1.545032445,1.254355018,1.491691514,1.329138183
   }{
   ,1.150635633,0.582415494,1.075877275,1.187937642
   }{
   ,1.203555051,1.001540513,0.864287715,0.717125848
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.630005348,0.18553379,0.730763505,0.709272397
   -
   }},{{
   ,0,0,0,0
   }{
   ,0.856582783,-0.143236405,0.716721488,0.603652831
   }{
   ,0.851622883,0.653168672,0.676545316,1.187937642
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,1.231861002,0.746214538,1.087821916,0.989140748
   -
   }},{{
   ,1.822113278,1.270687029,1.336192565,1.364584949
   }{
   ,0,0,0,0
   }{
   ,1.443665704,1.385046493,1.256013166,1.329138183
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,1.478009492,0.882097231,1.20450984,1.061002478
   -
   }},{{
   ,1.496720812,0.846496194,0.967868114,0.989140748
   }{
   ,0.766581547,-0.024857805,0.50754303,0.709272397
   }{
   ,0,0,0,0
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.75,0.65,0.69,0.78
   -
   }},{{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.76,0.65,0.69,0.78
   }{
   ,0,0,0,0
   }{
   ,0,0,0,0
   -
   }}},{{{
   ,1.295827995,0.84547091,0.91019099,1.256013166
   }{
   ,0.755889609,0.241428373,0.396379912,0.676545316
   }{
   ,0.99945386,0.740323132,0.435659206,0.864287715
   }{
   ,0.65,0.55,0.48,0.69
   }{
   ,0.843147406,0.101248351,0.49063599,0.50754303
   -
   }},{{
   ,0,0,0,0
   }{
   ,1.0651638,0.249934344,0.699352949,0.716721488
   }{
   ,0.871921533,0.59458138,0.396379912,1.075877275
   }{
   ,0.65,0.56,0.49,0.69
   }{
   ,1.07531714,0.318907854,0.653287717,0.967868114
   -
   }},{{
   ,1.099899195,0.730184613,0.661798984,1.336192565
   }{
   ,0,0,0,0
   }{
   ,1.45897431,1.318532145,0.91019099,1.491691514
   }{
   ,0.65,0.56,0.49,0.69
   }{
   ,1.242135174,0.894838095,1.108555445,1.20450984
   -
   }},{{
   ,0.911428974,0.524430101,0.653287717,1.087821916
   }{
   ,0.503209827,0.274849491,0.49063599,0.730763505
   }{
   ,0,0,0,0
   }{
   ,0.65,0.55,0.48,0.69
   }{
   ,0.65,0.55,0.48,0.69
   -
   }},{{
   ,0.65,0.56,0.49,0.69
   }{
   ,0.65,0.56,0.49,0.69
   }{
   ,0.65,0.55,0.48,0.69
   }{
   ,0,0,0,0
   }{
   ,0,0,0,0
   -
   }}},{{{
   ,1.100661785,0.969784756,1.318532145,1.385046493
   }{
   ,0.565895968,-0.060347902,0.59458138,0.653168672
   }{
   ,0.782168488,0.788161238,0.740323132,1.001540513
   }{
   ,0.68,0.46,0.55,0.65
   }{
   ,0.468913405,-0.469855984,0.274849491,-0.024857805
   -
   }},{{
   ,0,0,0,0
   }{
   ,0.258195131,-0.70438632,0.249934344,-0.143236405
   }{
   ,0.502914193,-0.060347902,0.241428373,0.582415494
   }{
   ,0.68,0.47,0.56,0.65
   }{
   ,0.584083861,0.258975454,0.524430101,0.846496194
   -
   }},{{
   ,0.968040559,0.797499702,0.730184613,1.270687029
   }{
   ,0,0,0,0
   }{
   ,1.081040749,0.969784756,0.84547091,1.254355018
   }{
   ,0.68,0.47,0.56,0.65
   }{
   ,1.048553951,0.728354541,0.894838095,0.882097231
   -
   }},{{
   ,0.88611252,0.258975454,0.318907854,0.746214538
   }{
   ,0.239520858,-0.469855984,0.101248351,0.18553379
   }{
   ,0,0,0,0
   }{
   ,0.68,0.46,0.55,0.65
   }{
   ,0.68,0.46,0.55,0.65
   -
   }},{{
   ,0.68,0.47,0.56,0.65
   }{
   ,0.68,0.47,0.56,0.65
   }{
   ,0.68,0.46,0.55,0.65
   }{
   ,0,0,0,0
   }{
   ,0,0,0,0
   -
   }}},{{{
   ,1.566899704,1.081040749,1.45897431,1.443665704
   }{
   ,0.976725675,0.502914193,0.871921533,0.851622883
   }{
   ,1.482046826,0.782168488,0.99945386,1.203555051
   }{
   ,0.85,0.68,0.65,0.76
   }{
   ,0.798628781,0.239520858,0.503209827,0.766581547
   -
   }},{{
   ,0,0,0,0
   }{
   ,1.141098246,0.258195131,1.0651638,0.856582783
   }{
   ,0.976725675,0.565895968,0.755889609,1.150635633
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,1.125403302,0.88611252,0.911428974,1.496720812
   -
   }},{{
   ,1.68169282,0.968040559,1.099899195,1.822113278
   }{
   ,0,0,0,0
   }{
   ,1.566899704,1.100661785,1.295827995,1.545032445
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,1.35948517,1.048553951,1.242135174,1.478009492
   -
   }},{{
   ,1.125403302,0.584083861,1.07531714,1.231861002
   }{
   ,0.798628781,0.468913405,0.843147406,0.630005348
   }{
   ,0,0,0,0
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,0.85,0.68,0.65,0.75
   -
   }},{{
   ,0.85,0.68,0.65,0.75
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,0,0,0,0
   }{
  };
  }}}
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:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Diff.c -o Diff.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'firstSeqsPosEqual':
DistanceMatrix.c:625:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if (!ci)
   ^~
DistanceMatrix.c:628:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    while (i < ex) {
    ^~~~~
DistanceMatrix.c:647:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if (!cj)
   ^~
DistanceMatrix.c:650:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    while (j < ey) {
    ^~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function 'pop':
EnumerateSequence.c:268:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
  x = x + (x >> 4) & 0xF0F0F0F;
      ~~^~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ExpandAmbiguities.c -o ExpandAmbiguities.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:376:7: warning: 'K' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (k==1) {
       ^
FindFrameshifts.c:372:8: warning: 'J' may be used uninitialized in this function [-Wmaybe-uninitialized]
      j -= B[k*rc + j*r + i];
      ~~^~~~~~~~~~~~~~~~~~~~
FindFrameshifts.c:320:13: warning: 'I' may be used uninitialized in this function [-Wmaybe-uninitialized]
      pos = i*3 + k + 1;
            ~^~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c GetPools.c -o GetPools.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Import.c -o Import.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c InformationContent.c -o InformationContent.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c InsertGaps.c -o InsertGaps.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IntDist.c -o IntDist.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:79:20: warning: missing braces around initializer [-Wmissing-braces]
  double dH[4][4] = {
                    ^
   -7.9,-8.4,-7.8,-7.2
   {
   ,-8.5,-8.0,-10.6,-7.8
   }{
   ,-8.2,-9.8,-8.0,-8.4
   }{
   ,-7.2,-8.2,-8.5,-7.9
   }{
  };
  }
MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces]
  double dS[4][4] = {
                    ^
   -22.2,-22.4,-21.0,-20.4
   {
   ,-22.7,-19.9,-27.2,-21.0
   }{
   ,-22.2,-24.4,-19.9,-22.4
   }{
   ,-21.3,-22.2,-22.7,-22.2
   }{
  };
  }
MeltPolymer.c:54:10: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *rans;
          ^~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MovingAverage.c -o MovingAverage.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MultiMatch.c -o MultiMatch.o
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rdefines.h:40,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rinternals.h:1555:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^~~~~~~
MultiMatch.c:244:24: note: 'utilsPackage' was declared here
  SEXP percentComplete, utilsPackage;
                        ^~~~~~~~~~~~
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rdefines.h:40,
                 from MultiMatch.c:11:
C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rinternals.h:1555:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^~~~~~~
MultiMatch.c:244:7: note: 'percentComplete' was declared here
  SEXP percentComplete, utilsPackage;
       ^~~~~~~~~~~~~~~
MultiMatch.c:327:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
     ~~~~~~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c NNLS.c -o NNLS.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Order.c -o Order.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function 'predictDBN':
PredictDBN.c:833:29: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
         range2[0] = nucs[pos[prev]];// + 1;
                             ^
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:231:16: warning: 'states' may be used uninitialized in this function [-Wmaybe-uninitialized]
      states[j] = 'E';
      ~~~~~~~~~~^~~~~
PredictHEC.c:41:24: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double H, E, C, sum, *rans;
                        ^~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_decipher.c -o R_init_decipher.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RemoveGaps.c -o RemoveGaps.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ReplaceChars.c -o ReplaceChars.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c TerminalMismatch.c -o TerminalMismatch.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Translate.c -o Translate.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c VectorSums.c -o VectorSums.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.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 InformationContent.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 S4Vectors_stubs.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/DECIPHER.buildbin-libdir/00LOCK-DECIPHER/00new/DECIPHER/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DECIPHER'
    finding HTML links ... done
    AA_REDUCED                              html  
    Add2DB                                  html  
    AdjustAlignment                         html  
    AlignDB                                 html  
    AlignProfiles                           html  
    AlignSeqs                               html  
    AlignSynteny                            html  
    AlignTranslation                        html  
    AmplifyDNA                              html  
    Array2Matrix                            html  
    BrowseDB                                html  
    BrowseSeqs                              html  
    CalculateEfficiencyArray                html  
    CalculateEfficiencyFISH                 html  
    CalculateEfficiencyPCR                  html  
    Codec                                   html  
    ConsensusSequence                       html  
    Cophenetic                              html  
    CorrectFrameshifts                      html  
    CreateChimeras                          html  
    DB2Seqs                                 html  
    DECIPHER-package                        html  
    DesignArray                             html  
    DesignPrimers                           html  
    DesignProbes                            html  
    DesignSignatures                        html  
    DigestDNA                               html  
    Disambiguate                            html  
    DistanceMatrix                          html  
    FindChimeras                            html  
    FindSynteny                             html  
    FormGroups                              html  
    HEC_MI                                  html  
    IdClusters                              html  
    IdConsensus                             html  
    IdLengths                               html  
    IdTaxa                                  html  
    IdentifyByRank                          html  
    LearnTaxa                               html  
    MIQS                                    html  
    MODELS                                  html  
    MapCharacters                           html  
    MaskAlignment                           html  
    MeltDNA                                 html  
    NNLS                                    html  
    OrientNucleotides                       html  
    PFASUM                                  html  
    PredictDBN                              html  
    PredictHEC                              html  
    RESTRICTION_ENZYMES                     html  
    ReadDendrogram                          html  
    RemoveGaps                              html  
    SearchDB                                html  
    Seqs2DB                                 html  
    StaggerAlignment                        html  
    Synteny-class                           html  
    Taxa-class                              html  
    TerminalChar                            html  
    TileSeqs                                html  
    TrainingSet_16S                         html  
    TrimDNA                                 html  
    WriteDendrogram                         html  
    deltaGrules                             html  
    deltaHrules                             html  
    deltaSrules                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'DECIPHER' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function 'alignProfiles._omp_fn.0':
AlignProfiles.c:401:9: warning: 'lGp' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGp *= tot;
     ~~~~^~~~~~
AlignProfiles.c:39:39: note: 'lGp' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
                                       ^~~
AlignProfiles.c:403:9: warning: 'lGs' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGs *= tot;
     ~~~~^~~~~~
AlignProfiles.c:39:44: note: 'lGs' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
                                            ^~~
AlignProfiles.c: In function 'alignProfilesAA._omp_fn.1':
AlignProfiles.c:1220:9: warning: 'lGp' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGp *= tot;
     ~~~~^~~~~~
AlignProfiles.c:763:39: note: 'lGp' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
                                       ^~~
AlignProfiles.c:1222:9: warning: 'lGs' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGs *= tot;
     ~~~~^~~~~~
AlignProfiles.c:763:44: note: 'lGs' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
                                            ^~~
AlignProfiles.c: In function 'alignProfiles':
AlignProfiles.c:355:11: warning: 'subM' may be used uninitialized in this function [-Wmaybe-uninitialized]
   #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs) num_threads(nthreads)
           ^~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AssignIndels.c -o AssignIndels.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CalculateDeltaG.c -o CalculateDeltaG.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:25:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_DR[4][4] = {
                       ^
   -11.5, -7.8, -7, -8.3,
   {                    }
   -10.4, -12.8, -16.3, -9.1,
   {                        }
   -8.6, -8, -9.3, -5.9,
   {                   }
   -7.8, -5.5, -9, -7.8
   {
  };
  }
CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_DR[4][4] = {
                       ^
   -36.4, -21.6, -19.7, -23.9,
   {                         }
   -28.4, -31.9, -47.1, -23.5,
   {                         }
   -22.9, -17.1, -23.2, -12.3,
   {                         }
   -23.2, -13.5, -26.1, -21.9
   {
  };
  }
CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_DD[4][4] = {
                       ^
   -7.9, -8.4, -7.8, -7.2,
   {                     }
   -8.5, -8, -10.6, -7.8,
   {                    }
   -8.2, -9.8, -8, -8.4,
   {                   }
   -7.2, -8.2, -8.5, -7.9
   {
  };
  }
CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_DD[4][4] = {
                       ^
   -22.2, -22.4, -21, -20.4,
   {                       }
   -22.7, -19.9, -27.2, -21,
   {                       }
   -22.2, -24.4, -19.9, -22.4,
   {                         }
   -21.3, -22.2, -22.7, -22.2
   {
  };
  }
CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_RR[4][4] = {
                       ^
   -6.6, -10.17, -7.65, -5.76,
   {                         }
   -10.56, -12.21, -7.95, -7.65,
   {                           }
   -13.37, -14.21, -12.21, -10.17,
   {                             }
   -8.11, -13.37, -10.56, -6.6
   {
  };
  }
CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_RR[4][4] = {
                       ^
   -18.38, -26.03, -19.18, -15.67,
   {                             }
   -28.25, -30.02, -19.18, -19.18,
   {                             }
   -35.68, -34.85, -30.02, -26.03,
   {                             }
   -22.59, -35.68, -28.25, -18.38
   {
  };
  }
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:420:72: 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:420:67: 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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Cluster.c -o Cluster.o
Cluster.c: In function 'cluster._omp_fn.0':
Cluster.c:403:15: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
        minCol = minC;
        ~~~~~~~^~~~~~
Cluster.c:229:50: note: 'minC' was declared here
  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
                                                  ^~~~
Cluster.c: In function 'cluster._omp_fn.1':
Cluster.c:418:30: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
       minCols[rowIndices[i]] = minC;
       ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:229:50: note: 'minC' was declared here
  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
                                                  ^~~~
Cluster.c: In function 'cluster':
Cluster.c:229:50: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
Cluster.c:451:168: warning: 'nDiv' may be used uninitialized in this function [-Wmaybe-uninitialized]
      rans[4*(length - 1) + k] = dMatrix2[length*colIndices[minCol] - colIndices[minCol]*(colIndices[minCol] + 1)/2 + rowIndices[minRow] - colIndices[minCol]]/2 + (nDiv[minCol] - nDiv[minRow + 1])/(2*(size-2)); // col
                                                                                                                                                                        ^
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ClusterML.c -o ClusterML.o
ClusterML.c: In function 'clusterML._omp_fn.2':
ClusterML.c:556:40: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
       node[count*maxWidth*4 + i*4 + 0] += *(Ls + 0*length + j);
                                        ^~
ClusterML.c:420:6: note: 'count' was declared here
  int count;
      ^~~~~
ClusterML.c: In function 'clusterML':
ClusterML.c:441:11: warning: 'node' may be used uninitialized in this function [-Wmaybe-uninitialized]
   #pragma omp parallel for private(i,j,y_i,row,count) schedule(guided) num_threads(nthreads)
           ^~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CommonGaps.c -o CommonGaps.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Compositions.c -o Compositions.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:966:8: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (k==1 && letter >= 11) {
        ^
Compression.c:516:12: note: 'k' was declared here
  int i, j, k, pos;
            ^
Compression.c:1010:12: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
       count++;
       ~~~~~^~
Compression.c:542:29: note: 'count' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                             ^~~~~
Compression.c:1009:20: warning: 'word' may be used uninitialized in this function [-Wmaybe-uninitialized]
       word = (word << 8) | (unsigned int)reorder(byte);
              ~~~~~~^~~~~
Compression.c:542:23: note: 'word' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                       ^~~~
Compression.c:1212:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = rev==0 ? 254 : 255;
       ~~~~~~~^~~~~~~~~~~~~~~~~~~~
Compression.c:543:27: note: 'rev' was declared here
   int lastTemp, currTemp, rev, len, len2, thresh = 1;
                           ^~~
Compression.c:556:7: warning: 'lower' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int lower = 0;
       ^~~~~
Compression.c:1239:43: warning: 'lastTriplet' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
                                        ~~~^~~~~~~~~~~~~~
Compression.c:629:12: note: 'lastTriplet' was declared here
   int run, lastTriplet, lastCase;
            ^~~~~~~~~~~
Compression.c:1029:23: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
         lastHit = dict[(word >> k) & 0xFF];
                       ^
Compression.c:542:17: note: 'dict' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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: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;
                    ^
ConsensusSequence.c:2062:10: warning: 'HEC' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *HEC, *s;
          ^~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ConsolidateGaps.c -o ConsolidateGaps.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:70:20: warning: missing braces around initializer [-Wmissing-braces]
  double NN[4][4] = {
                    ^
   -0.816507461,-2.5401714,-1.647430026,-1.184658548
   {
   ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
   }{
   ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
   }{
   ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
   }{
  };
  }
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
  double PM[4][4] = {
                    ^
   -0.141370102,-0.439805276,-0.285236035,-0.205111781
   {
   ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
   }{
   ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
   }{
   ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
   }{
  };
  }
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
  double sMM[4][5][5][4] = {
                           ^
   0,0,0,0
   {{{
   ,1.545032445,1.254355018,1.491691514,1.329138183
   }{
   ,1.150635633,0.582415494,1.075877275,1.187937642
   }{
   ,1.203555051,1.001540513,0.864287715,0.717125848
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.630005348,0.18553379,0.730763505,0.709272397
   -
   }},{{
   ,0,0,0,0
   }{
   ,0.856582783,-0.143236405,0.716721488,0.603652831
   }{
   ,0.851622883,0.653168672,0.676545316,1.187937642
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,1.231861002,0.746214538,1.087821916,0.989140748
   -
   }},{{
   ,1.822113278,1.270687029,1.336192565,1.364584949
   }{
   ,0,0,0,0
   }{
   ,1.443665704,1.385046493,1.256013166,1.329138183
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,1.478009492,0.882097231,1.20450984,1.061002478
   -
   }},{{
   ,1.496720812,0.846496194,0.967868114,0.989140748
   }{
   ,0.766581547,-0.024857805,0.50754303,0.709272397
   }{
   ,0,0,0,0
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.75,0.65,0.69,0.78
   -
   }},{{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.76,0.65,0.69,0.78
   }{
   ,0,0,0,0
   }{
   ,0,0,0,0
   -
   }}},{{{
   ,1.295827995,0.84547091,0.91019099,1.256013166
   }{
   ,0.755889609,0.241428373,0.396379912,0.676545316
   }{
   ,0.99945386,0.740323132,0.435659206,0.864287715
   }{
   ,0.65,0.55,0.48,0.69
   }{
   ,0.843147406,0.101248351,0.49063599,0.50754303
   -
   }},{{
   ,0,0,0,0
   }{
   ,1.0651638,0.249934344,0.699352949,0.716721488
   }{
   ,0.871921533,0.59458138,0.396379912,1.075877275
   }{
   ,0.65,0.56,0.49,0.69
   }{
   ,1.07531714,0.318907854,0.653287717,0.967868114
   -
   }},{{
   ,1.099899195,0.730184613,0.661798984,1.336192565
   }{
   ,0,0,0,0
   }{
   ,1.45897431,1.318532145,0.91019099,1.491691514
   }{
   ,0.65,0.56,0.49,0.69
   }{
   ,1.242135174,0.894838095,1.108555445,1.20450984
   -
   }},{{
   ,0.911428974,0.524430101,0.653287717,1.087821916
   }{
   ,0.503209827,0.274849491,0.49063599,0.730763505
   }{
   ,0,0,0,0
   }{
   ,0.65,0.55,0.48,0.69
   }{
   ,0.65,0.55,0.48,0.69
   -
   }},{{
   ,0.65,0.56,0.49,0.69
   }{
   ,0.65,0.56,0.49,0.69
   }{
   ,0.65,0.55,0.48,0.69
   }{
   ,0,0,0,0
   }{
   ,0,0,0,0
   -
   }}},{{{
   ,1.100661785,0.969784756,1.318532145,1.385046493
   }{
   ,0.565895968,-0.060347902,0.59458138,0.653168672
   }{
   ,0.782168488,0.788161238,0.740323132,1.001540513
   }{
   ,0.68,0.46,0.55,0.65
   }{
   ,0.468913405,-0.469855984,0.274849491,-0.024857805
   -
   }},{{
   ,0,0,0,0
   }{
   ,0.258195131,-0.70438632,0.249934344,-0.143236405
   }{
   ,0.502914193,-0.060347902,0.241428373,0.582415494
   }{
   ,0.68,0.47,0.56,0.65
   }{
   ,0.584083861,0.258975454,0.524430101,0.846496194
   -
   }},{{
   ,0.968040559,0.797499702,0.730184613,1.270687029
   }{
   ,0,0,0,0
   }{
   ,1.081040749,0.969784756,0.84547091,1.254355018
   }{
   ,0.68,0.47,0.56,0.65
   }{
   ,1.048553951,0.728354541,0.894838095,0.882097231
   -
   }},{{
   ,0.88611252,0.258975454,0.318907854,0.746214538
   }{
   ,0.239520858,-0.469855984,0.101248351,0.18553379
   }{
   ,0,0,0,0
   }{
   ,0.68,0.46,0.55,0.65
   }{
   ,0.68,0.46,0.55,0.65
   -
   }},{{
   ,0.68,0.47,0.56,0.65
   }{
   ,0.68,0.47,0.56,0.65
   }{
   ,0.68,0.46,0.55,0.65
   }{
   ,0,0,0,0
   }{
   ,0,0,0,0
   -
   }}},{{{
   ,1.566899704,1.081040749,1.45897431,1.443665704
   }{
   ,0.976725675,0.502914193,0.871921533,0.851622883
   }{
   ,1.482046826,0.782168488,0.99945386,1.203555051
   }{
   ,0.85,0.68,0.65,0.76
   }{
   ,0.798628781,0.239520858,0.503209827,0.766581547
   -
   }},{{
   ,0,0,0,0
   }{
   ,1.141098246,0.258195131,1.0651638,0.856582783
   }{
   ,0.976725675,0.565895968,0.755889609,1.150635633
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,1.125403302,0.88611252,0.911428974,1.496720812
   -
   }},{{
   ,1.68169282,0.968040559,1.099899195,1.822113278
   }{
   ,0,0,0,0
   }{
   ,1.566899704,1.100661785,1.295827995,1.545032445
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,1.35948517,1.048553951,1.242135174,1.478009492
   -
   }},{{
   ,1.125403302,0.584083861,1.07531714,1.231861002
   }{
   ,0.798628781,0.468913405,0.843147406,0.630005348
   }{
   ,0,0,0,0
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,0.85,0.68,0.65,0.75
   -
   }},{{
   ,0.85,0.68,0.65,0.75
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,0,0,0,0
   }{
  };
  }}}
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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Diff.c -o Diff.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'firstSeqsPosEqual':
DistanceMatrix.c:625:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if (!ci)
   ^~
DistanceMatrix.c:628:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    while (i < ex) {
    ^~~~~
DistanceMatrix.c:647:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if (!cj)
   ^~
DistanceMatrix.c:650:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    while (j < ey) {
    ^~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function 'pop':
EnumerateSequence.c:268:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
  x = x + (x >> 4) & 0xF0F0F0F;
      ~~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ExpandAmbiguities.c -o ExpandAmbiguities.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:376:7: warning: 'K' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (k==1) {
       ^
FindFrameshifts.c:372:8: warning: 'J' may be used uninitialized in this function [-Wmaybe-uninitialized]
      j -= B[k*rc + j*r + i];
      ~~^~~~~~~~~~~~~~~~~~~~
FindFrameshifts.c:320:13: warning: 'I' may be used uninitialized in this function [-Wmaybe-uninitialized]
      pos = i*3 + k + 1;
            ~^~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c GetPools.c -o GetPools.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Import.c -o Import.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c InformationContent.c -o InformationContent.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c InsertGaps.c -o InsertGaps.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IntDist.c -o IntDist.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:79:20: warning: missing braces around initializer [-Wmissing-braces]
  double dH[4][4] = {
                    ^
   -7.9,-8.4,-7.8,-7.2
   {
   ,-8.5,-8.0,-10.6,-7.8
   }{
   ,-8.2,-9.8,-8.0,-8.4
   }{
   ,-7.2,-8.2,-8.5,-7.9
   }{
  };
  }
MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces]
  double dS[4][4] = {
                    ^
   -22.2,-22.4,-21.0,-20.4
   {
   ,-22.7,-19.9,-27.2,-21.0
   }{
   ,-22.2,-24.4,-19.9,-22.4
   }{
   ,-21.3,-22.2,-22.7,-22.2
   }{
  };
  }
MeltPolymer.c:54:10: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *rans;
          ^~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MovingAverage.c -o MovingAverage.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MultiMatch.c -o MultiMatch.o
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rdefines.h:40,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rinternals.h:1555:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^~~~~~~
MultiMatch.c:244:24: note: 'utilsPackage' was declared here
  SEXP percentComplete, utilsPackage;
                        ^~~~~~~~~~~~
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rdefines.h:40,
                 from MultiMatch.c:11:
C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rinternals.h:1555:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^~~~~~~
MultiMatch.c:244:7: note: 'percentComplete' was declared here
  SEXP percentComplete, utilsPackage;
       ^~~~~~~~~~~~~~~
MultiMatch.c:327:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
     ~~~~~~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c NNLS.c -o NNLS.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Order.c -o Order.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function 'predictDBN':
PredictDBN.c:833:29: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
         range2[0] = nucs[pos[prev]];// + 1;
                             ^
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_decipher.c -o R_init_decipher.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RemoveGaps.c -o RemoveGaps.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ReplaceChars.c -o ReplaceChars.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c TerminalMismatch.c -o TerminalMismatch.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Translate.c -o Translate.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c VectorSums.c -o VectorSums.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.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 InformationContent.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 S4Vectors_stubs.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_2.16.1.zip
* DONE (DECIPHER)