Back to the "Multiple platform build/check report" A  B  C [D] E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for DECIPHER on malbec1

This page was generated on 2017-04-15 16:10:39 -0400 (Sat, 15 Apr 2017).

Package 304/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 2.2.0
Erik Wright
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/DECIPHER
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DECIPHER
Version: 2.2.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DECIPHER_2.2.0.tar.gz
StartedAt: 2017-04-14 21:59:41 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:03:16 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 214.7 seconds
RetCode: 0
Status:  OK 
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DECIPHER_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DECIPHER.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.2.0’
* 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
CorrectFrameshifts 16.628  0.040  16.676
AlignSeqs          16.176  0.148  16.331
StaggerAlignment   14.492  0.080  14.578
PredictDBN          9.500  0.036   9.543
TileSeqs            6.028  0.000   6.028
BrowseSeqs          5.996  0.020   6.022
Array2Matrix        5.672  0.008   5.684
AlignTranslation    5.512  0.020   5.538
DesignArray         5.384  0.052   5.441
* 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-3.4-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.

DECIPHER.Rcheck/00install.out:

* installing *source* package ‘DECIPHER’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c AlignProfiles.c -o AlignProfiles.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ClusterML.c -o ClusterML.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include/Rdefines.h:40:0,
                 from ClusterNJ.c:11:
ClusterNJ.c: In function ‘clusterNJ’:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: 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-3.4-bioc/R/include/Rdefines.h:40:0,
                 from ClusterNJ.c:11:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: 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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include/Rdefines.h:40:0,
                 from ClusterUPGMA.c:11:
ClusterUPGMA.c: In function ‘clusterUPGMA’:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: 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-3.4-bioc/R/include/Rdefines.h:40:0,
                 from ClusterUPGMA.c:11:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: 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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c CommonGaps.c -o CommonGaps.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c Compositions.c -o Compositions.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c Diff.c -o Diff.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c DistanceMatrix.c -o DistanceMatrix.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: 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-3.4-bioc/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: 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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c GetPools.c -o GetPools.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c Import.c -o Import.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c InsertGaps.c -o InsertGaps.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c IntDist.c -o IntDist.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c MultiMatch.c -o MultiMatch.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchLists’:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:242:24: note: ‘utilsPackage’ was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:242:7: note: ‘percentComplete’ was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:325:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchListsDual’:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:350:24: note: ‘utilsPackage’ was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:350:7: note: ‘percentComplete’ was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:426:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchOrder’:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:451:24: note: ‘utilsPackage’ was declared here
  SEXP percentComplete, utilsPackage;
                        ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
MultiMatch.c:451:7: note: ‘percentComplete’ was declared here
  SEXP percentComplete, utilsPackage;
       ^
MultiMatch.c:545:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c NNLS.c -o NNLS.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
NNLS.c: In function ‘NNLS’:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: 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-3.4-bioc/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
/home/biocbuild/bbs-3.4-bioc/R/include/Rinternals.h:1173:16: 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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c Order.c -o Order.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c PredictDBN.c -o PredictDBN.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/include/Rdefines.h:37:0,
                 from PredictDBN.c:11:
PredictDBN.c: In function ‘predictDBN’:
/home/biocbuild/bbs-3.4-bioc/R/include/R_ext/RS.h:77:25: 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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c RemoveGaps.c -o RemoveGaps.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c Translate.c -o Translate.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/XVector/include"  -fopenmp -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -L/home/biocbuild/bbs-3.4-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 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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)

DECIPHER.Rcheck/DECIPHER-Ex.timings:

nameusersystemelapsed
Add2DB0.2880.0280.317
AdjustAlignment0.1960.0040.199
AlignDB0.9200.0400.958
AlignProfiles0.9360.0040.940
AlignSeqs16.176 0.14816.331
AlignSynteny1.6560.0321.689
AlignTranslation5.5120.0205.538
AmplifyDNA0.0040.0000.013
Array2Matrix5.6720.0085.684
BrowseDB0.0240.0000.022
BrowseSeqs5.9960.0206.022
CalculateEfficiencyArray0.0120.0000.014
CalculateEfficiencyFISH0.0080.0000.005
CalculateEfficiencyPCR0.0040.0000.005
Codec0.6840.0000.681
ConsensusSequence0.1640.0120.176
CorrectFrameshifts16.628 0.04016.676
CreateChimeras0.8760.0040.879
DB2Seqs0.0120.0080.020
DesignArray5.3840.0525.441
DesignPrimers0.0040.0000.000
DesignProbes0.0000.0000.001
DesignSignatures0.0000.0000.001
DigestDNA0.1280.0000.130
Disambiguate0.0440.0000.041
DistanceMatrix0.0080.0000.006
FindChimeras0.0560.0000.057
FindSynteny1.6080.0001.609
FormGroups0.0600.0000.061
HEC_MI0.2360.0160.255
IdClusters3.8760.0563.935
IdConsensus0.6440.0040.647
IdLengths0.0160.0000.016
IdentifyByRank0.0280.0000.030
MIQS0.0040.0000.006
MODELS000
MaskAlignment0.4840.0000.481
MeltDNA0.040.000.04
NNLS0.0040.0000.004
OrientNucleotides0.9200.0000.918
PredictDBN9.5000.0369.543
PredictHEC0.2760.0080.284
RESTRICTION_ENZYMES0.0040.0000.003
ReadDendrogram0.0240.0000.021
SearchDB0.0320.0000.031
Seqs2DB0.240.000.24
StaggerAlignment14.492 0.08014.578
Synteny-class0.740.000.74
TerminalChar0.0120.0000.013
TileSeqs6.0280.0006.028
TrimDNA0.0320.0000.034
WriteDendrogram0.0040.0000.007
deltaGrules0.0120.0000.010
deltaHrules0.020.000.02
deltaSrules0.0920.0000.092