BioC 3.5: CHECK report for DECIPHER on malbec2

Package: DECIPHER

Version: 2.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DECIPHER_2.4.0.tar.gz

StartedAt: 2017-08-15 22:25:46 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:29:36 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 229.7 seconds

RetCode: 0

Status:  OK

CheckDir: DECIPHER.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DECIPHER_2.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/DECIPHER.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       3.8Mb
    extdata   1.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DesignSignatures: no visible binding for global variable ‘deltaHrules’
Undefined global functions or variables:
  deltaHrules
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
AlignSeqs          18.144  0.164  18.320
CorrectFrameshifts 16.780  0.076  16.868
BrowseSeqs         13.516  0.068  13.593
StaggerAlignment   12.928  0.048  12.988
PredictDBN          8.484  0.056   8.540
AlignTranslation    6.056  0.060   6.120
Array2Matrix        5.916  0.032   5.950
DesignArray         5.724  0.072   5.797
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.

* installing *source* package ‘DECIPHER’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c AlignProfiles.c -o AlignProfiles.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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] = {
                       ^
CalculateFISH.c:25:23: note: (near initialization for ‘dH_DR’)
CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_DR[4][4] = {
                       ^
CalculateFISH.c:31:23: note: (near initialization for ‘dS_DR’)
CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_DD[4][4] = {
                       ^
CalculateFISH.c:37:23: note: (near initialization for ‘dH_DD’)
CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_DD[4][4] = {
                       ^
CalculateFISH.c:43:23: note: (near initialization for ‘dS_DD’)
CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_RR[4][4] = {
                       ^
CalculateFISH.c:49:23: note: (near initialization for ‘dH_RR’)
CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_RR[4][4] = {
                       ^
CalculateFISH.c:55:23: note: (near initialization for ‘dS_RR’)
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function ‘chainSegments’:
ChainSegments.c:414:72: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
                                                                        ^
ChainSegments.c:414:67: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
                                                                   ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ClusterML.c -o ClusterML.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function ‘clusterNJ._omp_fn.0’:
ClusterNJ.c:281:12: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     minCol = minC;
            ^
ClusterNJ.c:195:62: note: ‘minC’ was declared here
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC;
                                                              ^
ClusterNJ.c:280:12: warning: ‘minR’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     minRow = minR;
            ^
ClusterNJ.c:195:56: note: ‘minR’ was declared here
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC;
                                                        ^
In file included from /home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:40:0,
                 from ClusterNJ.c:11:
ClusterNJ.c: In function ‘clusterNJ’:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
ClusterNJ.c:198:29: note: ‘utilsPackage’ was declared here
  SEXP ans, percentComplete, utilsPackage;
                             ^
In file included from /home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:40:0,
                 from ClusterNJ.c:11:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
ClusterNJ.c:198:12: note: ‘percentComplete’ was declared here
  SEXP ans, percentComplete, utilsPackage;
            ^
ClusterNJ.c:487:24: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    *rPercentComplete = floor(100*soFar/total);
                        ^
ClusterNJ.c:492:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function ‘clusterUPGMA._omp_fn.0’:
ClusterUPGMA.c:200:12: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     minCol = minC;
            ^
ClusterUPGMA.c:124:62: note: ‘minC’ was declared here
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC, met;
                                                              ^
ClusterUPGMA.c:199:12: warning: ‘minR’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     minRow = minR;
            ^
ClusterUPGMA.c:124:56: note: ‘minR’ was declared here
  int i, j, k, clusterNum, size, minRow, minCol, index, minR, minC, met;
                                                        ^
In file included from /home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:40:0,
                 from ClusterUPGMA.c:11:
ClusterUPGMA.c: In function ‘clusterUPGMA’:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
ClusterUPGMA.c:127:29: note: ‘utilsPackage’ was declared here
  SEXP ans, percentComplete, utilsPackage;
                             ^
In file included from /home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:40:0,
                 from ClusterUPGMA.c:11:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
ClusterUPGMA.c:127:12: note: ‘percentComplete’ was declared here
  SEXP ans, percentComplete, utilsPackage;
            ^
ClusterUPGMA.c:426:24: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    *rPercentComplete = floor(100*soFar/total);
                        ^
ClusterUPGMA.c:431:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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:975:11: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      p[c] = (k - 1) & 0xFF; // length of run
           ^
Compression.c:513:12: note: ‘k’ was declared here
  int i, j, k, pos;
            ^
Compression.c:1007:12: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       count++;
            ^
Compression.c:539:29: note: ‘count’ was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                             ^
Compression.c:1006:20: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       word = (word << 8) | (unsigned int)reorder(byte);
                    ^
Compression.c:539:23: note: ‘word’ was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                       ^
Compression.c:1164:14: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = rev==0 ? 254 : 255;
              ^
Compression.c:540:27: note: ‘rev’ was declared here
   int lastTemp, currTemp, rev, len, len2, thresh = 1;
                           ^
Compression.c:626:25: warning: ‘lastCase’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int run, lastTriplet, lastCase;
                         ^
Compression.c:1236:43: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
                                           ^
Compression.c:626:12: note: ‘lastTriplet’ was declared here
   int run, lastTriplet, lastCase;
            ^
Compression.c:1054:23: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         lastHit = dict[revcomp((word >> k) & 0xFF)]; // end of lastHit
                       ^
Compression.c:539:17: note: ‘dict’ was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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: In function ‘colScoresAA’:
ConsensusSequence.c:2063:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_HEC, n, l, d;
                    ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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] = {
                    ^
DesignProbes.c:70:20: note: (near initialization for ‘NN’)
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
  double PM[4][4] = {
                    ^
DesignProbes.c:77:20: note: (near initialization for ‘PM’)
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
  double sMM[4][5][5][4] = {
                           ^
DesignProbes.c:84:27: note: (near initialization for ‘sMM’)
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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c DistanceMatrix.c -o DistanceMatrix.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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:266:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  x = x + (x >> 4) & 0xF0F0F0F;
        ^
EnumerateSequence.c: In function ‘enumerateGappedSequence’:
EnumerateSequence.c:275:6: warning: variable ‘x_length’ set but not used [-Wunused-but-set-variable]
  int x_length, i, j, k, wS, sum, ambiguous, *rans, *p;
      ^
EnumerateSequence.c: In function ‘enumerateGappedSequenceAA’:
EnumerateSequence.c:397:6: warning: variable ‘x_length’ set but not used [-Wunused-but-set-variable]
  int x_length, i, j, k, wS, sum, ambiguous, *rans, *p;
      ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: 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-3.5-bioc/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: 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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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] = {
                    ^
MeltPolymer.c:79:20: note: (near initialization for ‘dH’)
MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces]
  double dS[4][4] = {
                    ^
MeltPolymer.c:88:20: note: (near initialization for ‘dS’)
MeltPolymer.c:373:33: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
      slope = (*(rans + stack[0] + l*s) - *(rans + stack[pos] + l*s))/(t[stack[0]] - t[stack[pos]]);
                                 ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchLists’:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: 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-3.5-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: 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-3.5-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchListsDual’:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: 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-3.5-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: 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-3.5-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchOrder’:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:453:24: note: ‘utilsPackage’ was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from /home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:453:7: note: ‘percentComplete’ was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:547:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
NNLS.c: In function ‘NNLS’:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: 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-3.5-bioc/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:1222:16: 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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c PredictDBN.c -o PredictDBN.o
In file included from /home/biocbuild/bbs-3.5-bioc/R/include/Rdefines.h:37:0,
                 from PredictDBN.c:11:
PredictDBN.c: In function ‘predictDBN’:
/home/biocbuild/bbs-3.5-bioc/R/include/R_ext/RS.h:74:25: warning: ‘MI2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
                         ^
PredictDBN.c:399:10: note: ‘MI2’ was declared here
  double *MI2, *rowMax, *colMax;
          ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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:246:18: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     *(rans + 3*j + 2) = C/sum;
                  ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GetPools.o Import.o 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 TerminalMismatch.o Translate.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/DECIPHER.Rcheck/DECIPHER/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DECIPHER)

name	user	system	elapsed
Add2DB	0.556	0.040	0.597
AdjustAlignment	0.464	0.004	0.465
AlignDB	1.820	0.072	1.893
AlignProfiles	1.768	0.004	1.771
AlignSeqs	18.144	0.164	18.320
AlignSynteny	1.744	0.028	1.773
AlignTranslation	6.056	0.060	6.120
AmplifyDNA	0.000	0.004	0.015
Array2Matrix	5.916	0.032	5.950
BrowseDB	0.02	0.00	0.02
BrowseSeqs	13.516	0.068	13.593
CalculateEfficiencyArray	0.020	0.000	0.021
CalculateEfficiencyFISH	0.008	0.000	0.009
CalculateEfficiencyPCR	0.008	0.000	0.010
Codec	0.892	0.004	0.894
ConsensusSequence	0.168	0.000	0.169
CorrectFrameshifts	16.780	0.076	16.868
CreateChimeras	0.832	0.000	0.832
DB2Seqs	0.012	0.008	0.249
DesignArray	5.724	0.072	5.797
DesignPrimers	0.000	0.000	0.001
DesignProbes	0	0	0
DesignSignatures	0.000	0.000	0.002
DigestDNA	0.36	0.00	0.36
Disambiguate	0.032	0.000	0.031
DistanceMatrix	0.004	0.000	0.005
FindChimeras	0.056	0.000	0.054
FindSynteny	2.376	0.004	2.383
FormGroups	0.052	0.008	0.060
HEC_MI	0.208	0.020	0.228
IdClusters	3.860	0.048	3.912
IdConsensus	0.584	0.008	0.592
IdLengths	0.020	0.000	0.017
IdentifyByRank	0.032	0.000	0.034
MIQS	0.008	0.000	0.021
MODELS	0	0	0
MaskAlignment	0.568	0.000	0.566
MeltDNA	0.064	0.000	0.063
NNLS	0.044	0.004	0.050
OrientNucleotides	0.916	0.004	0.923
PredictDBN	8.484	0.056	8.540
PredictHEC	0.444	0.012	0.457
RESTRICTION_ENZYMES	0.004	0.000	0.003
ReadDendrogram	0.248	0.004	0.250
SearchDB	0.024	0.004	0.028
Seqs2DB	0.08	0.00	0.08
StaggerAlignment	12.928	0.048	12.988
Synteny-class	1.236	0.008	1.246
TerminalChar	0.012	0.000	0.012
TileSeqs	4.852	0.000	4.857
TrimDNA	0.068	0.000	0.068
WriteDendrogram	0.036	0.000	0.038
deltaGrules	0.012	0.000	0.010
deltaHrules	0.016	0.004	0.020
deltaSrules	0.060	0.000	0.059