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This page was generated on 2021-09-20 15:04:47 -0400 (Mon, 20 Sep 2021).

INSTALL results for DECIPHER on nebbiolo1

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raw results

Package 454/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 2.20.0  (landing page)
Erik Wright
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/DECIPHER
git_branch: RELEASE_3_13
git_last_commit: bcd35a8
git_last_commit_date: 2021-05-19 11:50:12 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DECIPHER
Version: 2.20.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL DECIPHER
StartedAt: 2021-09-19 06:08:48 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 06:09:31 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 43.3 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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]
  401 |     lGp *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:39:39: note: ‘lGp’ was declared here
   39 |  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]
  403 |     lGs *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:39:44: note: ‘lGs’ was declared here
   39 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
      |                                            ^~~
AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’:
AlignProfiles.c:1220:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1220 |     lGp *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:763:39: note: ‘lGp’ was declared here
  763 |  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]
 1222 |     lGs *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:763:44: note: ‘lGs’ was declared here
  763 |  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]
  355 |   #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs) num_threads(nthreads)
      |           ^~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function ‘calculateHairpinDeltaG’:
CalculateDeltaG.c:375:26: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  375 |  int i, j, k, count, s1, s2;
      |                          ^~
CalculateDeltaG.c:375:22: warning: ‘s1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  375 |  int i, j, k, count, s1, s2;
      |                      ^~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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]
   25 |  double dH_DR[4][4] = {
      |                       ^
   26 |   -11.5, -7.8, -7, -8.3,
      |   {                    }
   27 |   -10.4, -12.8, -16.3, -9.1,
      |   {                        }
   28 |   -8.6, -8, -9.3, -5.9,
      |   {                   }
   29 |   -7.8, -5.5, -9, -7.8
      |   {
   30 |  };
      |  }
CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces]
   31 |  double dS_DR[4][4] = {
      |                       ^
   32 |   -36.4, -21.6, -19.7, -23.9,
      |   {                         }
   33 |   -28.4, -31.9, -47.1, -23.5,
      |   {                         }
   34 |   -22.9, -17.1, -23.2, -12.3,
      |   {                         }
   35 |   -23.2, -13.5, -26.1, -21.9
      |   {
   36 |  };
      |  }
CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces]
   37 |  double dH_DD[4][4] = {
      |                       ^
   38 |   -7.9, -8.4, -7.8, -7.2,
      |   {                     }
   39 |   -8.5, -8, -10.6, -7.8,
      |   {                    }
   40 |   -8.2, -9.8, -8, -8.4,
      |   {                   }
   41 |   -7.2, -8.2, -8.5, -7.9
      |   {
   42 |  };
      |  }
CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces]
   43 |  double dS_DD[4][4] = {
      |                       ^
   44 |   -22.2, -22.4, -21, -20.4,
      |   {                       }
   45 |   -22.7, -19.9, -27.2, -21,
      |   {                       }
   46 |   -22.2, -24.4, -19.9, -22.4,
      |   {                         }
   47 |   -21.3, -22.2, -22.7, -22.2
      |   {
   48 |  };
      |  }
CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces]
   49 |  double dH_RR[4][4] = {
      |                       ^
   50 |   -6.6, -10.17, -7.65, -5.76,
      |   {                         }
   51 |   -10.56, -12.21, -7.95, -7.65,
      |   {                           }
   52 |   -13.37, -14.21, -12.21, -10.17,
      |   {                             }
   53 |   -8.11, -13.37, -10.56, -6.6
      |   {
   54 |  };
      |  }
CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces]
   55 |  double dS_RR[4][4] = {
      |                       ^
   56 |   -18.38, -26.03, -19.18, -15.67,
      |   {                             }
   57 |   -28.25, -30.02, -19.18, -19.18,
      |   {                             }
   58 |   -35.68, -34.85, -30.02, -26.03,
      |   {                             }
   59 |   -22.59, -35.68, -28.25, -18.38
      |   {
   60 |  };
      |  }
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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:422:72: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  422 |    int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
      |                                                                        ^~~
ChainSegments.c:470:8: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  470 |     if (upX) { // new chain is last
      |        ^
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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]
  403 |        minCol = minC;
      |        ~~~~~~~^~~~~~
Cluster.c:229:50: note: ‘minC’ was declared here
  229 |  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]
  418 |       minCols[rowIndices[i]] = minC;
      |       ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:229:50: note: ‘minC’ was declared here
  229 |  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]
  451 |      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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -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]
  556 |       node[count*maxWidth*4 + i*4 + 0] += *(Ls + 0*length + j);
      |                                        ^~
ClusterML.c:420:6: note: ‘count’ was declared here
  420 |  int count;
      |      ^~~~~
ClusterML.c: In function ‘clusterML’:
ClusterML.c:441:11: warning: ‘node’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  441 |   #pragma omp parallel for private(i,j,y_i,row,count) schedule(guided) num_threads(nthreads)
      |           ^~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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:976:17: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  976 |      p[c] = ((k - 1) >> 8) & 0xFF; // length of run
      |              ~~~^~~~
Compression.c:516:12: note: ‘k’ was declared here
  516 |  int i, j, k, pos;
      |            ^
Compression.c:1010:12: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1010 |       count++;
      |       ~~~~~^~
Compression.c:542:29: note: ‘count’ was declared here
  542 |   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                             ^~~~~
Compression.c:1009:20: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1009 |       word = (word << 8) | (unsigned int)reorder(byte);
      |              ~~~~~~^~~~~
Compression.c:542:23: note: ‘word’ was declared here
  542 |   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                       ^~~~
Compression.c:1212:14: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1212 |       p[c++] = rev==0 ? 254 : 255;
      |       ~~~~~~~^~~~~~~~~~~~~~~~~~~~
Compression.c:543:27: note: ‘rev’ was declared here
  543 |   int lastTemp, currTemp, rev, len, len2, thresh = 1;
      |                           ^~~
Compression.c:556:7: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  556 |   int lower = 0;
      |       ^~~~~
Compression.c:1239:43: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1239 |     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
      |                                        ~~~^~~~~~~~~~~~~~
Compression.c:629:12: note: ‘lastTriplet’ was declared here
  629 |   int run, lastTriplet, lastCase;
      |            ^~~~~~~~~~~
Compression.c:1325:4: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1325 |    free(dict);
      |    ^~~~~~~~~~
Compression.c:542:17: note: ‘dict’ was declared here
  542 |   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                 ^~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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]
 1578 |  double *DBN, *s;
      |          ^~~
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:456:14: warning: ‘length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  456 |    } else if (length==2) { // run of length 3
      |              ^
ConsensusSequence.c:397:15: note: ‘length’ was declared here
  397 |  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]
  455 |      *(runs + s) += weight;
      |                  ^~
ConsensusSequence.c:397:23: note: ‘lastPos’ was declared here
  397 |  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]
 1771 |  double *HEC, *s;
      |          ^~~
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:1938:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1938 |  int do_DBN, n, l, d;
      |                    ^
ConsensusSequence.c:1937:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1937 |  double *DBN, *s;
      |          ^~~
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2063:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2063 |  int do_HEC, n, l, d;
      |                    ^
ConsensusSequence.c:2062:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2062 |  double *HEC, *s;
      |          ^~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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]
   70 |  double NN[4][4] = {
      |                    ^
   71 |   -0.816507461,-2.5401714,-1.647430026,-1.184658548
      |   {
   72 |   ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
      |   }{
   73 |   ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
      |   }{
   74 |   ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
      |   }{
   75 |  };
      |  }
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
   77 |  double PM[4][4] = {
      |                    ^
   78 |   -0.141370102,-0.439805276,-0.285236035,-0.205111781
      |   {
   79 |   ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
      |   }{
   80 |   ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
      |   }{
   81 |   ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
      |   }{
   82 |  };
      |  }
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
   84 |  double sMM[4][5][5][4] = {
      |                           ^
   85 |   0,0,0,0
      |   {{{
   86 |   ,1.545032445,1.254355018,1.491691514,1.329138183
      |   }{
   87 |   ,1.150635633,0.582415494,1.075877275,1.187937642
      |   }{
   88 |   ,1.203555051,1.001540513,0.864287715,0.717125848
      |   }{
   89 |   ,0.75,0.65,0.69,0.78
      |   }{
   90 |   ,0.630005348,0.18553379,0.730763505,0.709272397
      |   -
      |   }},{{
   91 |   ,0,0,0,0
      |   }{
   92 |   ,0.856582783,-0.143236405,0.716721488,0.603652831
      |   }{
   93 |   ,0.851622883,0.653168672,0.676545316,1.187937642
      |   }{
   94 |   ,0.75,0.65,0.69,0.78
      |   }{
   95 |   ,1.231861002,0.746214538,1.087821916,0.989140748
      |   -
      |   }},{{
   96 |   ,1.822113278,1.270687029,1.336192565,1.364584949
      |   }{
   97 |   ,0,0,0,0
      |   }{
   98 |   ,1.443665704,1.385046493,1.256013166,1.329138183
      |   }{
   99 |   ,0.75,0.65,0.69,0.78
      |   }{
  100 |   ,1.478009492,0.882097231,1.20450984,1.061002478
      |   -
      |   }},{{
  101 |   ,1.496720812,0.846496194,0.967868114,0.989140748
      |   }{
  102 |   ,0.766581547,-0.024857805,0.50754303,0.709272397
      |   }{
  103 |   ,0,0,0,0
      |   }{
  104 |   ,0.75,0.65,0.69,0.78
      |   }{
  105 |   ,0.75,0.65,0.69,0.78
      |   -
      |   }},{{
  106 |   ,0.75,0.65,0.69,0.78
      |   }{
  107 |   ,0.75,0.65,0.69,0.78
      |   }{
  108 |   ,0.76,0.65,0.69,0.78
      |   }{
  109 |   ,0,0,0,0
      |   }{
  110 |   ,0,0,0,0
      |   -
      |   }}},{{{
  111 |   ,1.295827995,0.84547091,0.91019099,1.256013166
      |   }{
  112 |   ,0.755889609,0.241428373,0.396379912,0.676545316
      |   }{
  113 |   ,0.99945386,0.740323132,0.435659206,0.864287715
      |   }{
  114 |   ,0.65,0.55,0.48,0.69
      |   }{
  115 |   ,0.843147406,0.101248351,0.49063599,0.50754303
      |   -
      |   }},{{
  116 |   ,0,0,0,0
      |   }{
  117 |   ,1.0651638,0.249934344,0.699352949,0.716721488
      |   }{
  118 |   ,0.871921533,0.59458138,0.396379912,1.075877275
      |   }{
  119 |   ,0.65,0.56,0.49,0.69
      |   }{
  120 |   ,1.07531714,0.318907854,0.653287717,0.967868114
      |   -
      |   }},{{
  121 |   ,1.099899195,0.730184613,0.661798984,1.336192565
      |   }{
  122 |   ,0,0,0,0
      |   }{
  123 |   ,1.45897431,1.318532145,0.91019099,1.491691514
      |   }{
  124 |   ,0.65,0.56,0.49,0.69
      |   }{
  125 |   ,1.242135174,0.894838095,1.108555445,1.20450984
      |   -
      |   }},{{
  126 |   ,0.911428974,0.524430101,0.653287717,1.087821916
      |   }{
  127 |   ,0.503209827,0.274849491,0.49063599,0.730763505
      |   }{
  128 |   ,0,0,0,0
      |   }{
  129 |   ,0.65,0.55,0.48,0.69
      |   }{
  130 |   ,0.65,0.55,0.48,0.69
      |   -
      |   }},{{
  131 |   ,0.65,0.56,0.49,0.69
      |   }{
  132 |   ,0.65,0.56,0.49,0.69
      |   }{
  133 |   ,0.65,0.55,0.48,0.69
      |   }{
  134 |   ,0,0,0,0
      |   }{
  135 |   ,0,0,0,0
      |   -
      |   }}},{{{
  136 |   ,1.100661785,0.969784756,1.318532145,1.385046493
      |   }{
  137 |   ,0.565895968,-0.060347902,0.59458138,0.653168672
      |   }{
  138 |   ,0.782168488,0.788161238,0.740323132,1.001540513
      |   }{
  139 |   ,0.68,0.46,0.55,0.65
      |   }{
  140 |   ,0.468913405,-0.469855984,0.274849491,-0.024857805
      |   -
      |   }},{{
  141 |   ,0,0,0,0
      |   }{
  142 |   ,0.258195131,-0.70438632,0.249934344,-0.143236405
      |   }{
  143 |   ,0.502914193,-0.060347902,0.241428373,0.582415494
      |   }{
  144 |   ,0.68,0.47,0.56,0.65
      |   }{
  145 |   ,0.584083861,0.258975454,0.524430101,0.846496194
      |   -
      |   }},{{
  146 |   ,0.968040559,0.797499702,0.730184613,1.270687029
      |   }{
  147 |   ,0,0,0,0
      |   }{
  148 |   ,1.081040749,0.969784756,0.84547091,1.254355018
      |   }{
  149 |   ,0.68,0.47,0.56,0.65
      |   }{
  150 |   ,1.048553951,0.728354541,0.894838095,0.882097231
      |   -
      |   }},{{
  151 |   ,0.88611252,0.258975454,0.318907854,0.746214538
      |   }{
  152 |   ,0.239520858,-0.469855984,0.101248351,0.18553379
      |   }{
  153 |   ,0,0,0,0
      |   }{
  154 |   ,0.68,0.46,0.55,0.65
      |   }{
  155 |   ,0.68,0.46,0.55,0.65
      |   -
      |   }},{{
  156 |   ,0.68,0.47,0.56,0.65
      |   }{
  157 |   ,0.68,0.47,0.56,0.65
      |   }{
  158 |   ,0.68,0.46,0.55,0.65
      |   }{
  159 |   ,0,0,0,0
      |   }{
  160 |   ,0,0,0,0
      |   -
      |   }}},{{{
  161 |   ,1.566899704,1.081040749,1.45897431,1.443665704
      |   }{
  162 |   ,0.976725675,0.502914193,0.871921533,0.851622883
      |   }{
  163 |   ,1.482046826,0.782168488,0.99945386,1.203555051
      |   }{
  164 |   ,0.85,0.68,0.65,0.76
      |   }{
  165 |   ,0.798628781,0.239520858,0.503209827,0.766581547
      |   -
      |   }},{{
  166 |   ,0,0,0,0
      |   }{
  167 |   ,1.141098246,0.258195131,1.0651638,0.856582783
      |   }{
  168 |   ,0.976725675,0.565895968,0.755889609,1.150635633
      |   }{
  169 |   ,0.85,0.68,0.65,0.75
      |   }{
  170 |   ,1.125403302,0.88611252,0.911428974,1.496720812
      |   -
      |   }},{{
  171 |   ,1.68169282,0.968040559,1.099899195,1.822113278
      |   }{
  172 |   ,0,0,0,0
      |   }{
  173 |   ,1.566899704,1.100661785,1.295827995,1.545032445
      |   }{
  174 |   ,0.85,0.68,0.65,0.75
      |   }{
  175 |   ,1.35948517,1.048553951,1.242135174,1.478009492
      |   -
      |   }},{{
  176 |   ,1.125403302,0.584083861,1.07531714,1.231861002
      |   }{
  177 |   ,0.798628781,0.468913405,0.843147406,0.630005348
      |   }{
  178 |   ,0,0,0,0
      |   }{
  179 |   ,0.85,0.68,0.65,0.75
      |   }{
  180 |   ,0.85,0.68,0.65,0.75
      |   -
      |   }},{{
  181 |   ,0.85,0.68,0.65,0.75
      |   }{
  182 |   ,0.85,0.68,0.65,0.75
      |   }{
  183 |   ,0.85,0.68,0.65,0.75
      |   }{
  184 |   ,0,0,0,0
      |   }{
  185 |  };
      |  }}}
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c:834:29: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  834 |         cycles += lastCycle - thisCycle;
      |                   ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:37: note: ‘lastCycle’ was declared here
  267 |    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                     ^~~~~~~~~
DesignProbes.c:834:29: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  834 |         cycles += lastCycle - thisCycle;
      |                   ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:48: note: ‘thisCycle’ was declared here
  267 |    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                                ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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]
  625 |   if (!ci)
      |   ^~
DistanceMatrix.c:628:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  628 |    while (i < ex) {
      |    ^~~~~
DistanceMatrix.c:647:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  647 |   if (!cj)
      |   ^~
DistanceMatrix.c:650:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  650 |    while (j < ey) {
      |    ^~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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:315:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  315 |  x = x + (x >> 4) & 0xF0F0F0F;
      |      ~~^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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:381:14: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  381 |    } else if (k==2) {
      |              ^
FindFrameshifts.c:318:19: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  318 |     if (C[k*rc + j*r + i] >= 0) {
      |                  ~^~
FindFrameshifts.c:320:13: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  320 |      pos = i*3 + k + 1;
      |            ~^~
In file included from /home/biocbuild/bbs-3.13-bioc/R/include/Rdefines.h:42,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.13-bioc/R/include/Rinternals.h:1557:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1557 | #define eval   Rf_eval
      |                ^~~~~~~
FindFrameshifts.c:162:24: note: ‘utilsPackage’ was declared here
  162 |  SEXP percentComplete, utilsPackage;
      |                        ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/include/Rdefines.h:42,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.13-bioc/R/include/Rinternals.h:1557:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1557 | #define eval   Rf_eval
      |                ^~~~~~~
FindFrameshifts.c:162:7: note: ‘percentComplete’ was declared here
  162 |  SEXP percentComplete, utilsPackage;
      |       ^~~~~~~~~~~~~~~
FindFrameshifts.c:468:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  468 |     before = *rPercentComplete;
      |     ~~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function ‘scoreCodonModel’:
GeneFinding.c:388:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  388 |  Chars_holder x_i;
      |               ^~~
GeneFinding.c:432:29: warning: ‘lastVal’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  432 |      score += codons[lastVal*64 + val];
      |                      ~~~~~~~^~~
GeneFinding.c: In function ‘startCodonModel’:
GeneFinding.c:791:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  791 |    val = getBaseRC(x_i.ptr[j++]);
      |                           ^
GeneFinding.c: In function ‘scoreStartCodonModel’:
GeneFinding.c:892:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  892 |    val = getBaseRC(x_i.ptr[j++]);
      |                           ^
GeneFinding.c: In function ‘initialCodonModel’:
GeneFinding.c:973:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  973 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘scoreInitialCodonModel’:
GeneFinding.c:1059:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1059 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘terminationCodonModel’:
GeneFinding.c:1131:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1131 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘scoreTerminationCodonModel’:
GeneFinding.c:1216:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1216 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘getRegion’:
GeneFinding.c:1286:21: warning: ‘x_i.length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1286 |     (s==0 && j >= 0 && j + w <= x_i.length)) {
      |     ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1252:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1252 |  Chars_holder x_i;
      |               ^~~
GeneFinding.c: In function ‘autocorrelationModel’:
GeneFinding.c:1379:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1379 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘scoreAutocorrelationModel’:
GeneFinding.c:1496:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1496 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘couplingModel’:
GeneFinding.c:1598:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1598 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘scoreCouplingModel’:
GeneFinding.c:1681:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1681 |  Chars_holder x_i;
      |               ^~~
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1788:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1788 |  Chars_holder x_i;
      |               ^~~
GeneFinding.c: In function ‘scoreNucleotideBiasModel’:
GeneFinding.c:1882:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1882 |  Chars_holder x_i;
      |               ^~~
GeneFinding.c: In function ‘upstreamMotifModel’:
GeneFinding.c:1990:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1990 |      val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
      |                                          ^
GeneFinding.c: In function ‘scoreUpstreamMotifModel’:
GeneFinding.c:2090:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2090 |      val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
      |                                          ^
GeneFinding.c: In function ‘scoreRunLengthModel’:
GeneFinding.c:2276:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2276 |  Chars_holder x_i;
      |               ^~~
GeneFinding.c: In function ‘stopCodonModel’:
GeneFinding.c:2419:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2419 |    val = getBaseRC(x_i.ptr[j++]);
      |                           ^
GeneFinding.c: In function ‘scoreStopCodonModel’:
GeneFinding.c:2520:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2520 |    val = getBaseRC(x_i.ptr[j++]);
      |                           ^
GeneFinding.c: In function ‘codonFrequencies’:
GeneFinding.c:2578:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2578 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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]
   79 |  double dH[4][4] = {
      |                    ^
   80 |   -7.9,-8.4,-7.8,-7.2
      |   {
   81 |   ,-8.5,-8.0,-10.6,-7.8
      |   }{
   82 |   ,-8.2,-9.8,-8.0,-8.4
      |   }{
   83 |   ,-7.2,-8.2,-8.5,-7.9
      |   }{
   84 |  };
      |  }
MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces]
   88 |  double dS[4][4] = {
      |                    ^
   89 |   -22.2,-22.4,-21.0,-20.4
      |   {
   90 |   ,-22.7,-19.9,-27.2,-21.0
      |   }{
   91 |   ,-22.2,-24.4,-19.9,-22.4
      |   }{
   92 |   ,-21.3,-22.2,-22.7,-22.2
      |   }{
   93 |  };
      |  }
MeltPolymer.c:54:10: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   54 |  double *rans;
      |          ^~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function ‘intMatchSelfOnce’:
MultiMatch.c:866:21: warning: variable ‘start’ set but not used [-Wunused-but-set-variable]
  866 |  int i, j, k, temp, start = 0;
      |                     ^~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/include/Rdefines.h:42,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchLists’:
/home/biocbuild/bbs-3.13-bioc/R/include/Rinternals.h:1557:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1557 | #define eval   Rf_eval
      |                ^~~~~~~
MultiMatch.c:244:24: note: ‘utilsPackage’ was declared here
  244 |  SEXP percentComplete, utilsPackage;
      |                        ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/include/Rdefines.h:42,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.13-bioc/R/include/Rinternals.h:1557:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1557 | #define eval   Rf_eval
      |                ^~~~~~~
MultiMatch.c:244:7: note: ‘percentComplete’ was declared here
  244 |  SEXP percentComplete, utilsPackage;
      |       ^~~~~~~~~~~~~~~
MultiMatch.c:327:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  327 |     before = *rPercentComplete;
      |     ~~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c NNLS.c -o NNLS.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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:869:29: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  869 |         range2[0] = nucs[pos[prev]];// + 1;
      |                             ^
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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]
  255 |    SET_VECTOR_ELT(ret, i, ans);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:42:8: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   42 |  char *states;
      |        ^~~~~~
PredictHEC.c:41:24: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   41 |  double H, E, C, sum, *rans;
      |                        ^~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-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-3.13-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 GeneFinding.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-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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)