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CHECK report for DECIPHER on malbec1

This page was generated on 2021-05-06 12:27:18 -0400 (Thu, 06 May 2021).

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 436/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 2.18.1  (landing page)
Erik Wright
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/DECIPHER
Branch: RELEASE_3_12
Last Commit: 6a70842
Last Changed Date: 2020-10-28 14:49:22 -0400 (Wed, 28 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: DECIPHER
Version: 2.18.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings DECIPHER_2.18.1.tar.gz
StartedAt: 2021-05-06 00:43:32 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:58:26 -0400 (Thu, 06 May 2021)
EllapsedTime: 894.1 seconds
RetCode: 0
Status:   OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings DECIPHER_2.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/DECIPHER.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘2.18.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data      6.4Mb
    extdata   2.2Mb
    libs      1.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DesignSignatures: no visible binding for global variable ‘deltaHrules’
FindGenes: no visible binding for global variable ‘deltaHrulesRNA’
Undefined global functions or variables:
  deltaHrules deltaHrulesRNA
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
Genes-class        119.048  0.084 124.738
FindGenes          110.272  0.312 110.814
ExtractGenes       107.560  0.432 108.205
WriteGenes         106.872  0.260 107.267
BrowseSeqs          42.800  0.172  43.056
MapCharacters       40.572  0.192  40.846
PredictDBN          38.848  0.052  38.969
AlignSeqs           27.212  0.424  27.666
CorrectFrameshifts  23.620  0.124  23.796
AlignTranslation    18.460  0.108  18.611
Taxa-class          15.728  0.008  15.768
StaggerAlignment    14.396  0.136  14.549
IdTaxa              14.036  0.008  14.056
Array2Matrix         7.956  0.024   8.027
DesignArray          6.732  0.116   6.857
TileSeqs             6.404  0.008   6.429
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.

Installation output

DECIPHER.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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: ‘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)
           ^~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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: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;
                                                                   ^~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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]
       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)
           ^~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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]
      p[c] = ((k - 1) >> 8) & 0xFF; // length of run
              ~~~^~~~
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:1325:4: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    free(dict);
    ^~~~~~~~~~
Compression.c:542:17: note: ‘dict’ was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h:1555:16: 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-3.12-bioc/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h:1555:16: 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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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:362:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c:406:29: warning: ‘lastVal’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      score += codons[lastVal*64 + val];
                      ~~~~~~~^~~
GeneFinding.c: In function ‘startCodonModel’:
GeneFinding.c:765:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    val = getBaseRC(x_i.ptr[j++]);
                           ^
GeneFinding.c: In function ‘scoreStartCodonModel’:
GeneFinding.c:866:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    val = getBaseRC(x_i.ptr[j++]);
                           ^
GeneFinding.c: In function ‘initialCodonModel’:
GeneFinding.c:947:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     val += 4*getBaseRC(x_i.ptr[j++]);
                               ^
GeneFinding.c: In function ‘scoreInitialCodonModel’:
GeneFinding.c:1033:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     val += 4*getBaseRC(x_i.ptr[j++]);
                               ^
GeneFinding.c: In function ‘terminationCodonModel’:
GeneFinding.c:1105:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     val += 4*getBaseRC(x_i.ptr[j++]);
                               ^
GeneFinding.c: In function ‘scoreTerminationCodonModel’:
GeneFinding.c:1190:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     val += 4*getBaseRC(x_i.ptr[j++]);
                               ^
GeneFinding.c: In function ‘getRegion’:
GeneFinding.c:1250:14: warning: ‘x_i.length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    if ((s==1 && j < x_i.length) ||
        ~~~~~~^~~~~~~~~~~~~~~~~~
GeneFinding.c:1225:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function ‘autocorrelationModel’:
GeneFinding.c:1336:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     val += 4*getBaseRC(x_i.ptr[j++]);
                               ^
GeneFinding.c: In function ‘scoreAutocorrelationModel’:
GeneFinding.c:1453:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     val += 4*getBaseRC(x_i.ptr[j++]);
                               ^
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1529:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function ‘scoreNucleotideBiasModel’:
GeneFinding.c:1623:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function ‘upstreamMotifModel’:
GeneFinding.c:1731:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
                                          ^
GeneFinding.c: In function ‘scoreUpstreamMotifModel’:
GeneFinding.c:1831:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
                                          ^
GeneFinding.c: In function ‘scoreRunLengthModel’:
GeneFinding.c:2017:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function ‘stopCodonModel’:
GeneFinding.c:2160:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    val = getBaseRC(x_i.ptr[j++]);
                           ^
GeneFinding.c: In function ‘scoreStopCodonModel’:
GeneFinding.c:2261:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    val = getBaseRC(x_i.ptr[j++]);
                           ^
GeneFinding.c: In function ‘codonFrequencies’:
GeneFinding.c:2319:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     val += 4*getBaseRC(x_i.ptr[j++]);
                               ^
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchLists’:
/home/biocbuild/bbs-3.12-bioc/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 /home/biocbuild/bbs-3.12-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.12-bioc/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;
     ~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchListsDual’:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h:1555:16: 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-3.12-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h:1555:16: 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-3.12-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchOrder’:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h:1555:16: 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-3.12-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h:1555:16: 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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
NNLS.c: In function ‘NNLS’:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h:1555:16: 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-3.12-bioc/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h:1555:16: 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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-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-3.12-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-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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)

Tests output

Example timings

DECIPHER.Rcheck/DECIPHER-Ex.timings

nameusersystemelapsed
AA_REDUCED0.1000.0160.115
Add2DB0.2920.0320.348
AdjustAlignment0.2160.0040.223
AlignDB1.3840.0241.423
AlignProfiles0.7840.0040.803
AlignSeqs27.212 0.42427.666
AlignSynteny3.9920.0084.002
AlignTranslation18.460 0.10818.611
AmplifyDNA0.0040.0000.004
Array2Matrix7.9560.0248.027
BrowseDB0.0240.0000.025
BrowseSeqs42.800 0.17243.056
CalculateEfficiencyArray0.0120.0000.014
CalculateEfficiencyFISH0.0040.0000.005
CalculateEfficiencyPCR0.0040.0000.004
Codec1.0200.0001.018
ConsensusSequence0.1720.0000.173
Cophenetic1.4840.0001.487
CorrectFrameshifts23.620 0.12423.796
CreateChimeras1.0480.0081.064
DB2Seqs0.0120.0200.036
DesignArray6.7320.1166.857
DesignPrimers0.0040.0000.001
DesignProbes0.0000.0000.001
DesignSignatures0.0000.0000.001
DigestDNA0.2360.0000.235
Disambiguate0.0520.0000.052
DistanceMatrix0.0480.0000.050
ExtractGenes107.560 0.432108.205
FindChimeras0.0840.0000.087
FindGenes110.272 0.312110.814
FindSynteny2.4120.0002.417
FormGroups0.1120.0040.117
Genes-class119.048 0.084124.738
HEC_MI0.2760.0040.280
IdClusters0.8560.0120.869
IdConsensus1.1400.0041.146
IdLengths0.0280.0000.028
IdTaxa14.036 0.00814.056
IdentifyByRank0.0320.0000.031
LearnTaxa0.0080.0000.009
MIQS0.0160.0040.018
MODELS000
MapCharacters40.572 0.19240.846
MaskAlignment0.8920.0000.894
MeltDNA0.0800.0040.094
NNLS0.0040.0000.005
OrientNucleotides1.5200.0001.522
PFASUM0.0280.0000.028
PredictDBN38.848 0.05238.969
PredictHEC0.4080.0040.411
RESTRICTION_ENZYMES0.0000.0040.004
ReadDendrogram0.0560.0000.058
RemoveGaps0.0240.0000.020
SearchDB0.0480.0000.052
Seqs2DB0.1640.0000.166
StaggerAlignment14.396 0.13614.549
Synteny-class2.5840.0042.589
Taxa-class15.728 0.00815.768
TerminalChar0.0160.0000.018
TileSeqs6.4040.0086.429
TrainingSet_16S2.2880.0322.320
TrimDNA0.0960.0000.097
WriteDendrogram0.0080.0000.006
WriteGenes106.872 0.260107.267
deltaGrules0.0160.0000.016
deltaHrules0.0280.0000.029
deltaHrulesRNA0.0200.0000.024
deltaSrules0.0880.0040.093
deltaSrulesRNA0.0200.0040.025