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INSTALL report for DECIPHER on malbec2

This page was generated on 2019-04-09 11:31:27 -0400 (Tue, 09 Apr 2019).

Package 390/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 2.11.2
Erik Wright
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/DECIPHER
Branch: master
Last Commit: 112f9cf
Last Changed Date: 2019-01-21 19:51:01 -0400 (Mon, 21 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: DECIPHER
Version: 2.11.2
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DECIPHER
StartedAt: 2019-04-08 18:11:52 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 18:12:55 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 63.2 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -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: ‘Ps’ 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)
           ^˜˜
AlignProfiles.c:355:11: warning: ‘Pp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
AlignProfiles.c:355:11: warning: ‘Os’ may be used uninitialized in this function [-Wmaybe-uninitialized]
AlignProfiles.c:355:11: warning: ‘Op’ may be used uninitialized in this function [-Wmaybe-uninitialized]
AlignProfiles.c:355:11: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -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
   {
  };
  }
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -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;
                                                                   ^˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -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
                                                                                                                                                                        ^
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c ClusterML.c -o ClusterML.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c CommonGaps.c -o CommonGaps.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c Compositions.c -o Compositions.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c Compression.c -o Compression.o
Compression.c: In function ‘nbit._omp_fn.0’:
Compression.c:973:17: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      p[c] = ((k - 1) >> 8) & 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: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:553:7: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int lower = 0;
       ^˜˜˜˜
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:1026:23: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         lastHit = dict[(word >> k) & 0xFF];
                       ^
Compression.c:539:17: note: ‘dict’ was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -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;
          ^˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -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;
                                                ^˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c Diff.c -o Diff.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -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) {
    ^˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -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;
      ˜˜^˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -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: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 /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: 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 /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: 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;
     ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c GetPools.c -o GetPools.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c Import.c -o Import.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c InformationContent.c -o InformationContent.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c InsertGaps.c -o InsertGaps.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c IntDist.c -o IntDist.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -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:339:16: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     *(rans + k + (seq_length - 1)*l) = V_10_LR[seq_length]/Q_tot;
      ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c MultiMatch.c -o MultiMatch.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchLists’:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: 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 /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: 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;
     ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchListsDual’:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^˜˜˜˜˜˜
MultiMatch.c:352:24: note: ‘utilsPackage’ was declared here
  SEXP percentComplete, utilsPackage;
                        ^˜˜˜˜˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^˜˜˜˜˜˜
MultiMatch.c:352:7: note: ‘percentComplete’ was declared here
  SEXP percentComplete, utilsPackage;
       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MultiMatch.c:428:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
     ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchOrder’:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^˜˜˜˜˜˜
MultiMatch.c:454:24: note: ‘utilsPackage’ was declared here
  SEXP percentComplete, utilsPackage;
                        ^˜˜˜˜˜˜˜˜˜˜˜
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^˜˜˜˜˜˜
MultiMatch.c:454:7: note: ‘percentComplete’ was declared here
  SEXP percentComplete, utilsPackage;
       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
MultiMatch.c:543:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
     ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c NNLS.c -o NNLS.o
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
NNLS.c: In function ‘NNLS’:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: 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 /home/biocbuild/bbs-3.9-bioc/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
/home/biocbuild/bbs-3.9-bioc/R/include/Rinternals.h:1409:16: 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;
      ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c Order.c -o Order.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -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;
                             ^
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -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;
                        ^˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c RemoveGaps.c -o RemoveGaps.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c Translate.c -o Translate.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c VectorSums.c -o VectorSums.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -fopenmp -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o DECIPHER.so 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 -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-DECIPHER/00new/DECIPHER/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DECIPHER)