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CHECK report for DECIPHER on tokay1

This page was generated on 2019-04-13 11:21:52 -0400 (Sat, 13 Apr 2019).

Package 377/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 2.10.2
Erik Wright
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/DECIPHER
Branch: RELEASE_3_8
Last Commit: db7b017
Last Changed Date: 2019-01-21 19:51:01 -0400 (Mon, 21 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DECIPHER
Version: 2.10.2
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DECIPHER.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DECIPHER_2.10.2.tar.gz
StartedAt: 2019-04-13 01:39:56 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:51:35 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 699.0 seconds
RetCode: 0
Status:  OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DECIPHER.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DECIPHER_2.10.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DECIPHER.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DECIPHER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DECIPHER' version '2.10.2'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'DECIPHER' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data      6.2Mb
    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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
IdTaxa: no visible binding for global variable 'L'
Undefined global functions or variables:
  L 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/DECIPHER/libs/i386/DECIPHER.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
AlignSeqs          45.89  11.74   57.62
BrowseSeqs         33.42   1.47   34.89
PredictDBN         34.37   0.31   34.69
StaggerAlignment   27.13   7.37   34.50
CorrectFrameshifts 31.00   3.21   34.20
IdTaxa             11.85   0.16   12.00
AlignTranslation    9.67   1.08   10.97
LearnTaxa           9.62   0.48   10.11
DesignArray        10.04   0.03   10.06
Array2Matrix        8.66   0.00    8.66
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
AlignSeqs          30.85  11.53   42.39
PredictDBN         24.88   0.25   25.13
StaggerAlignment   19.02   5.97   24.99
BrowseSeqs         21.86   0.94   22.81
CorrectFrameshifts 20.18   2.49   22.67
IdTaxa             10.22   0.08   10.30
AlignTranslation    8.08   1.12    9.21
DesignArray         6.81   0.00    6.81
Array2Matrix        6.75   0.03    6.78
TileSeqs            5.71   0.01    5.72
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/DECIPHER.Rcheck/00check.log'
for details.

Installation output

DECIPHER.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DECIPHER_2.10.2.tar.gz && rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DECIPHER.buildbin-libdir DECIPHER_2.10.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DECIPHER_2.10.2.zip && rm DECIPHER_2.10.2.tar.gz DECIPHER_2.10.2.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 8879k  100 8879k    0     0  73.5M      0 --:--:-- --:--:-- --:--:-- 76.0M

install for i386

* installing *source* package 'DECIPHER' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -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;
                                            ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c AssignIndels.c -o AssignIndels.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c CalculateDeltaG.c -o CalculateDeltaG.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
   -11.5, -7.8, -7, -8.3,
   ^
CalculateFISH.c:26:3: warning: (near initialization for 'dH_DR[0]') [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
   -36.4, -21.6, -19.7, -23.9,
   ^
CalculateFISH.c:32:3: warning: (near initialization for 'dS_DR[0]') [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
   -7.9, -8.4, -7.8, -7.2,
   ^
CalculateFISH.c:38:3: warning: (near initialization for 'dH_DD[0]') [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
   -22.2, -22.4, -21, -20.4,
   ^
CalculateFISH.c:44:3: warning: (near initialization for 'dS_DD[0]') [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
   -6.6, -10.17, -7.65, -5.76,
   ^
CalculateFISH.c:50:3: warning: (near initialization for 'dH_RR[0]') [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
   -18.38, -26.03, -19.18, -15.67,
   ^
CalculateFISH.c:56:3: warning: (near initialization for 'dS_RR[0]') [-Wmissing-braces]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -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;
                                                                   ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c Cluster.c -o Cluster.o
Cluster.c: In function 'cluster._omp_fn.0':
Cluster.c:229:50: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
                                                  ^
Cluster.c: In function 'cluster._omp_fn.1':
Cluster.c:229:50: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
Cluster.c: In function 'cluster':
Cluster.c:229:50: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from Cluster.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: warning: 'utilsPackage' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
Cluster.c:233:29: note: 'utilsPackage' was declared here
  SEXP ans, percentComplete, utilsPackage;
                             ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from Cluster.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: warning: 'percentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define eval   Rf_eval
                ^
Cluster.c:233:12: note: 'percentComplete' was declared here
  SEXP ans, percentComplete, utilsPackage;
            ^
Cluster.c:789:24: warning: 'total' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *rPercentComplete = floor(100*soFar/total);
                        ^
Cluster.c:794:12: warning: 'rPercentComplete' may be used uninitialized in this function [-Wmaybe-uninitialized]
     before = *rPercentComplete;
            ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c ClusterML.c -o ClusterML.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c CommonGaps.c -o CommonGaps.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c Compositions.c -o Compositions.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -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:1210:16: warning: 'lastHit' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = (unsigned char)lastHit;
                ^
Compression.c:539:36: note: 'lastHit' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                                    ^
Compression.c:1209:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = rev==0 ? 254 : 255;
              ^
Compression.c:540:27: note: 'rev' was declared here
   int lastTemp, currTemp, rev, len, len2, thresh = 1;
                           ^
Compression.c: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:1083:12: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
        dict[word] = j;
            ^
Compression.c:539:17: note: 'dict' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -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:456:14: warning: 'length' may be used uninitialized in this function [-Wmaybe-uninitialized]
    } else if (length==2) { // run of length 3
              ^
ConsensusSequence.c:397:15: note: 'length' was declared here
  int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
               ^
ConsensusSequence.c:455:18: warning: 'lastPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
      *(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;
                    ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c ConsolidateGaps.c -o ConsolidateGaps.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
   -0.816507461,-2.5401714,-1.647430026,-1.184658548
   ^
DesignProbes.c:71:3: warning: (near initialization for 'NN[0]') [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
   -0.141370102,-0.439805276,-0.285236035,-0.205111781
   ^
DesignProbes.c:78:3: warning: (near initialization for 'PM[0]') [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
   0,0,0,0
   ^
DesignProbes.c:85:3: warning: (near initialization for 'sMM[0]') [-Wmissing-braces]
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;
                                                ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c Diff.c -o Diff.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c DistanceMatrix.c -o DistanceMatrix.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -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;
        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c ExpandAmbiguities.c -o ExpandAmbiguities.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:135:27: warning: 'K' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
                           ^
FindFrameshifts.c:135:24: warning: 'J' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
                        ^
FindFrameshifts.c:135:21: warning: 'I' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
                     ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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;
            ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c GetPools.c -o GetPools.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c Import.c -o Import.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c InformationContent.c -o InformationContent.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c InsertGaps.c -o InsertGaps.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c IntDist.c -o IntDist.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:80:3: warning: missing braces around initializer [-Wmissing-braces]
   -7.9,-8.4,-7.8,-7.2
   ^
MeltPolymer.c:80:3: warning: (near initialization for 'dH[0]') [-Wmissing-braces]
MeltPolymer.c:89:3: warning: missing braces around initializer [-Wmissing-braces]
   -22.2,-22.4,-21.0,-20.4
   ^
MeltPolymer.c:89:3: warning: (near initialization for 'dS[0]') [-Wmissing-braces]
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]]);
                                 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c MovingAverage.c -o MovingAverage.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c MultiMatch.c -o MultiMatch.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchListsDual':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchOrder':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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;
            ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c NNLS.c -o NNLS.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
NNLS.c: In function 'NNLS':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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;
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c Order.c -o Order.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -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;
                             ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:37:0,
                 from PredictDBN.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/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:445:10: note: 'MI2' was declared here
  double *MI2, *rowMax, *colMax;
          ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -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:233:16: warning: 'states' may be used uninitialized in this function [-Wmaybe-uninitialized]
      states[j] = 'C';
                ^
PredictHEC.c:41:24: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double H, E, C, sum, *rans;
                        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_decipher.c -o R_init_decipher.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c RemoveGaps.c -o RemoveGaps.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c ReplaceChars.c -o ReplaceChars.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c TerminalMismatch.c -o TerminalMismatch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c Translate.c -o Translate.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c VectorSums.c -o VectorSums.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.o CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GetPools.o Import.o InformationContent.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DECIPHER'
    finding HTML links ... done
    AA_REDUCED                              html  
    Add2DB                                  html  
    AdjustAlignment                         html  
    AlignDB                                 html  
    AlignProfiles                           html  
    AlignSeqs                               html  
    AlignSynteny                            html  
    AlignTranslation                        html  
    AmplifyDNA                              html  
    Array2Matrix                            html  
    BrowseDB                                html  
    BrowseSeqs                              html  
    CalculateEfficiencyArray                html  
    CalculateEfficiencyFISH                 html  
    CalculateEfficiencyPCR                  html  
    Codec                                   html  
    ConsensusSequence                       html  
    CorrectFrameshifts                      html  
    CreateChimeras                          html  
    DB2Seqs                                 html  
    DECIPHER-package                        html  
    DesignArray                             html  
    DesignPrimers                           html  
    DesignProbes                            html  
    DesignSignatures                        html  
    DigestDNA                               html  
    Disambiguate                            html  
    DistanceMatrix                          html  
    FindChimeras                            html  
    FindSynteny                             html  
    FormGroups                              html  
    HEC_MI                                  html  
    IdClusters                              html  
    IdConsensus                             html  
    IdLengths                               html  
    IdTaxa                                  html  
    IdentifyByRank                          html  
    LearnTaxa                               html  
    MIQS                                    html  
    MODELS                                  html  
    MaskAlignment                           html  
    MeltDNA                                 html  
    NNLS                                    html  
    OrientNucleotides                       html  
    PFASUM                                  html  
    PredictDBN                              html  
    PredictHEC                              html  
    RESTRICTION_ENZYMES                     html  
    ReadDendrogram                          html  
    RemoveGaps                              html  
    SearchDB                                html  
    Seqs2DB                                 html  
    StaggerAlignment                        html  
    Synteny-class                           html  
    Taxa-class                              html  
    TerminalChar                            html  
    TileSeqs                                html  
    TrainingSet_16S                         html  
    TrimDNA                                 html  
    WriteDendrogram                         html  
    deltaGrules                             html  
    deltaHrules                             html  
    deltaSrules                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DECIPHER' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -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;
                                            ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c AssignIndels.c -o AssignIndels.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c CalculateDeltaG.c -o CalculateDeltaG.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:26:3: warning: missing braces around initializer [-Wmissing-braces]
   -11.5, -7.8, -7, -8.3,
   ^
CalculateFISH.c:26:3: warning: (near initialization for 'dH_DR[0]') [-Wmissing-braces]
CalculateFISH.c:32:3: warning: missing braces around initializer [-Wmissing-braces]
   -36.4, -21.6, -19.7, -23.9,
   ^
CalculateFISH.c:32:3: warning: (near initialization for 'dS_DR[0]') [-Wmissing-braces]
CalculateFISH.c:38:3: warning: missing braces around initializer [-Wmissing-braces]
   -7.9, -8.4, -7.8, -7.2,
   ^
CalculateFISH.c:38:3: warning: (near initialization for 'dH_DD[0]') [-Wmissing-braces]
CalculateFISH.c:44:3: warning: missing braces around initializer [-Wmissing-braces]
   -22.2, -22.4, -21, -20.4,
   ^
CalculateFISH.c:44:3: warning: (near initialization for 'dS_DD[0]') [-Wmissing-braces]
CalculateFISH.c:50:3: warning: missing braces around initializer [-Wmissing-braces]
   -6.6, -10.17, -7.65, -5.76,
   ^
CalculateFISH.c:50:3: warning: (near initialization for 'dH_RR[0]') [-Wmissing-braces]
CalculateFISH.c:56:3: warning: missing braces around initializer [-Wmissing-braces]
   -18.38, -26.03, -19.18, -15.67,
   ^
CalculateFISH.c:56:3: warning: (near initialization for 'dS_RR[0]') [-Wmissing-braces]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -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;
                                                                   ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -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]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c ClusterML.c -o ClusterML.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c CommonGaps.c -o CommonGaps.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c Compositions.c -o Compositions.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -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:1210:16: warning: 'lastHit' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = (unsigned char)lastHit;
                ^
Compression.c:539:36: note: 'lastHit' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                                    ^
Compression.c:1209:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = rev==0 ? 254 : 255;
              ^
Compression.c:540:27: note: 'rev' was declared here
   int lastTemp, currTemp, rev, len, len2, thresh = 1;
                           ^
Compression.c: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;
                 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c ConsensusSequence.c -o ConsensusSequence.o
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;
                    ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c ConsolidateGaps.c -o ConsolidateGaps.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:71:3: warning: missing braces around initializer [-Wmissing-braces]
   -0.816507461,-2.5401714,-1.647430026,-1.184658548
   ^
DesignProbes.c:71:3: warning: (near initialization for 'NN[0]') [-Wmissing-braces]
DesignProbes.c:78:3: warning: missing braces around initializer [-Wmissing-braces]
   -0.141370102,-0.439805276,-0.285236035,-0.205111781
   ^
DesignProbes.c:78:3: warning: (near initialization for 'PM[0]') [-Wmissing-braces]
DesignProbes.c:85:3: warning: missing braces around initializer [-Wmissing-braces]
   0,0,0,0
   ^
DesignProbes.c:85:3: warning: (near initialization for 'sMM[0]') [-Wmissing-braces]
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;
                                                ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c Diff.c -o Diff.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c DistanceMatrix.c -o DistanceMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -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;
        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c ExpandAmbiguities.c -o ExpandAmbiguities.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:318:12: warning: 'K' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (C[k*rc + j*r + i] >= 0) {
            ^
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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from FindFrameshifts.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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;
            ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c GetPools.c -o GetPools.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c Import.c -o Import.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c InformationContent.c -o InformationContent.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c InsertGaps.c -o InsertGaps.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c IntDist.c -o IntDist.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:80:3: warning: missing braces around initializer [-Wmissing-braces]
   -7.9,-8.4,-7.8,-7.2
   ^
MeltPolymer.c:80:3: warning: (near initialization for 'dH[0]') [-Wmissing-braces]
MeltPolymer.c:89:3: warning: missing braces around initializer [-Wmissing-braces]
   -22.2,-22.4,-21.0,-20.4
   ^
MeltPolymer.c:89:3: warning: (near initialization for 'dS[0]') [-Wmissing-braces]
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]]);
                                 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c MovingAverage.c -o MovingAverage.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c MultiMatch.c -o MultiMatch.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchListsDual':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchOrder':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from MultiMatch.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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;
            ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c NNLS.c -o NNLS.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
NNLS.c: In function 'NNLS':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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 C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from NNLS.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1356:16: 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;
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c Order.c -o Order.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -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;
                             ^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:37:0,
                 from PredictDBN.c:11:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/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:445:10: note: 'MI2' was declared here
  double *MI2, *rowMax, *colMax;
          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -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;
                        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_decipher.c -o R_init_decipher.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c RemoveGaps.c -o RemoveGaps.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c ReplaceChars.c -o ReplaceChars.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c TerminalMismatch.c -o TerminalMismatch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c Translate.c -o Translate.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c VectorSums.c -o VectorSums.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/XVector/include"   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.o CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GetPools.o Import.o InformationContent.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_2.10.2.zip
* DONE (DECIPHER)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DECIPHER' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

DECIPHER.Rcheck/examples_i386/DECIPHER-Ex.timings

nameusersystemelapsed
AA_REDUCED0.080.000.07
Add2DB0.300.060.46
AdjustAlignment0.400.050.48
AlignDB1.250.201.69
AlignProfiles1.500.151.77
AlignSeqs45.8911.7457.62
AlignSynteny2.960.423.41
AlignTranslation 9.67 1.0810.97
AmplifyDNA000
Array2Matrix8.660.008.66
BrowseDB0.030.000.03
BrowseSeqs33.42 1.4734.89
CalculateEfficiencyArray0.020.010.03
CalculateEfficiencyFISH0.010.000.02
CalculateEfficiencyPCR000
Codec1.240.001.23
ConsensusSequence0.280.000.28
CorrectFrameshifts31.00 3.2134.20
CreateChimeras1.330.001.33
DB2Seqs0.010.000.02
DesignArray10.04 0.0310.06
DesignPrimers000
DesignProbes000
DesignSignatures0.010.000.02
DigestDNA0.220.000.22
Disambiguate0.080.000.07
DistanceMatrix0.030.010.05
FindChimeras0.110.020.13
FindSynteny1.610.001.60
FormGroups0.060.000.07
HEC_MI0.310.010.33
IdClusters3.661.224.87
IdConsensus0.940.020.95
IdLengths0.010.000.02
IdTaxa11.85 0.1612.00
IdentifyByRank0.030.000.03
LearnTaxa 9.62 0.4810.11
MIQS0.030.000.03
MODELS000
MaskAlignment0.600.000.59
MeltDNA0.060.000.08
NNLS0.020.000.02
OrientNucleotides1.040.001.05
PFASUM0.020.000.01
PredictDBN34.37 0.3134.69
PredictHEC0.380.030.40
RESTRICTION_ENZYMES000
ReadDendrogram0.030.000.04
RemoveGaps0.010.000.01
SearchDB0.040.000.03
Seqs2DB0.070.020.10
StaggerAlignment27.13 7.3734.50
Synteny-class3.190.023.20
Taxa-class2.260.022.28
TerminalChar0.020.000.02
TileSeqs4.450.014.47
TrainingSet_16S2.450.052.50
TrimDNA0.060.000.06
WriteDendrogram000
deltaGrules0.020.000.02
deltaHrules0.030.000.03
deltaSrules0.080.010.09

DECIPHER.Rcheck/examples_x64/DECIPHER-Ex.timings

nameusersystemelapsed
AA_REDUCED0.140.000.14
Add2DB0.520.020.54
AdjustAlignment0.280.020.29
AlignDB0.980.141.13
AlignProfiles1.110.141.25
AlignSeqs30.8511.5342.39
AlignSynteny3.480.503.98
AlignTranslation8.081.129.21
AmplifyDNA000
Array2Matrix6.750.036.78
BrowseDB0.030.000.03
BrowseSeqs21.86 0.9422.81
CalculateEfficiencyArray0.010.000.02
CalculateEfficiencyFISH000
CalculateEfficiencyPCR0.020.000.01
Codec0.970.000.97
ConsensusSequence0.220.000.22
CorrectFrameshifts20.18 2.4922.67
CreateChimeras0.880.000.88
DB2Seqs0.020.000.01
DesignArray6.810.006.81
DesignPrimers000
DesignProbes000
DesignSignatures000
DigestDNA0.150.000.16
Disambiguate0.050.000.05
DistanceMatrix0.030.000.03
FindChimeras0.080.000.08
FindSynteny1.550.001.54
FormGroups0.080.000.08
HEC_MI0.200.030.24
IdClusters2.260.763.03
IdConsensus0.800.000.79
IdLengths0.020.000.02
IdTaxa10.22 0.0810.30
IdentifyByRank0.040.000.04
LearnTaxa3.440.393.83
MIQS0.050.000.05
MODELS000
MaskAlignment0.530.020.55
MeltDNA0.040.000.04
NNLS0.020.000.02
OrientNucleotides0.780.010.79
PFASUM0.000.020.02
PredictDBN24.88 0.2525.13
PredictHEC0.260.010.28
RESTRICTION_ENZYMES000
ReadDendrogram0.010.000.02
RemoveGaps0.020.000.01
SearchDB0.030.000.03
Seqs2DB0.090.020.11
StaggerAlignment19.02 5.9724.99
Synteny-class2.500.012.51
Taxa-class2.860.042.89
TerminalChar0.010.000.02
TileSeqs5.710.015.72
TrainingSet_16S2.480.022.50
TrimDNA0.080.000.08
WriteDendrogram0.020.000.01
deltaGrules0.010.000.02
deltaHrules0.020.000.01
deltaSrules0.080.000.08