Back to Multiple platform build/check report for BioC 3.13
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-17 15:06:02 -0400 (Fri, 17 Sep 2021).

CHECK results for DECIPHER on tokay2

To the developers/maintainers of the DECIPHER package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DECIPHER.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 454/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 2.20.0  (landing page)
Erik Wright
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/DECIPHER
git_branch: RELEASE_3_13
git_last_commit: bcd35a8
git_last_commit_date: 2021-05-19 11:50:12 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DECIPHER
Version: 2.20.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DECIPHER.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DECIPHER_2.20.0.tar.gz
StartedAt: 2021-09-16 22:00:25 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 22:29:48 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 1763.0 seconds
RetCode: 0
Status:   OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DECIPHER.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DECIPHER_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DECIPHER.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '2.20.0'
* 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 whether package 'DECIPHER' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    data      7.3Mb
    extdata   2.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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'
FindGenes: no visible binding for global variable 'deltaHrulesRNA'
FindNonCoding: no visible binding for global variable 'deltaHrulesRNA'
LearnNonCoding: no visible binding for global variable 'deltaHrulesRNA'
PredictDBN: no visible binding for global variable 'deltaHrulesRNA'
Undefined global functions or variables:
  deltaHrules deltaHrulesRNA
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/DECIPHER/libs/i386/DECIPHER.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/DECIPHER/libs/x64/DECIPHER.dll':
  Found '_exit', possibly from '_exit' (C)
  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 (user + system) or elapsed time > 5s
                     user system elapsed
PredictDBN         126.02   0.23  126.75
DetectRepeats       93.89   0.45   94.37
FindNonCoding       58.17   9.42   67.60
BrowseSeqs          57.87   0.69   58.56
LearnNonCoding      50.09   6.96   57.06
Genes-class         54.76   1.36   56.18
ExtractGenes        50.30   1.14   51.46
WriteGenes          47.82   2.56   50.41
FindGenes           48.08   1.00   49.09
MapCharacters       35.02   1.16   36.60
AlignSeqs           27.87   2.30   30.17
CorrectFrameshifts  21.28   0.66   21.95
StaggerAlignment    13.65   1.57   15.24
Taxa-class          12.79   2.07   14.88
AlignTranslation    14.19   0.35   14.60
IdTaxa              13.79   0.30   14.09
LearnTaxa            8.36   2.94   11.30
Array2Matrix         7.56   0.01    7.58
DesignArray          7.44   0.00    7.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
PredictDBN         116.19   0.14  116.33
DetectRepeats       99.77   0.59  100.37
FindNonCoding       51.87   8.14   60.04
LearnNonCoding      45.81   5.72   51.55
BrowseSeqs          49.66   0.60   50.25
Genes-class         48.87   0.94   49.81
ExtractGenes        48.43   1.31   49.76
FindGenes           46.03   1.17   47.21
WriteGenes          45.75   0.22   45.97
MapCharacters       29.14   1.40   30.56
AlignSeqs           21.55   2.24   23.78
CorrectFrameshifts  16.18   0.47   16.99
StaggerAlignment    12.94   1.92   14.86
Taxa-class          12.52   0.44   12.95
AlignTranslation    11.12   0.39   11.53
IdTaxa              11.24   0.02   11.25
LearnTaxa            7.32   1.84    9.16
Array2Matrix         6.28   0.01    6.30
DesignArray          6.22   0.00    6.22
TileSeqs             5.50   0.00    5.50
* 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-3.13-bioc/meat/DECIPHER.Rcheck/00check.log'
for details.



Installation output

DECIPHER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DECIPHER_2.20.0.tar.gz && rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DECIPHER.buildbin-libdir DECIPHER_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DECIPHER_2.20.0.zip && rm DECIPHER_2.20.0.tar.gz DECIPHER_2.20.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 13 10.8M   13 1496k    0     0  1676k      0  0:00:06 --:--:--  0:00:06 1677k
 36 10.8M   36 4039k    0     0  2158k      0  0:00:05  0:00:01  0:00:04 2158k
 70 10.8M   70 7812k    0     0  2704k      0  0:00:04  0:00:02  0:00:02 2704k
100 10.8M  100 10.8M    0     0  3049k      0  0:00:03  0:00:03 --:--:-- 3049k

install for i386

* installing *source* package 'DECIPHER' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function 'alignProfiles._omp_fn.0':
AlignProfiles.c:401:9: warning: 'lGp' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGp *= tot;
     ~~~~^~~~~~
AlignProfiles.c:39:39: note: 'lGp' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
                                       ^~~
AlignProfiles.c:403:9: warning: 'lGs' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGs *= tot;
     ~~~~^~~~~~
AlignProfiles.c:39:44: note: 'lGs' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
                                            ^~~
AlignProfiles.c: In function 'alignProfilesAA._omp_fn.1':
AlignProfiles.c:1220:9: warning: 'lGp' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGp *= tot;
     ~~~~^~~~~~
AlignProfiles.c:763:39: note: 'lGp' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
                                       ^~~
AlignProfiles.c:1222:9: warning: 'lGs' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGs *= tot;
     ~~~~^~~~~~
AlignProfiles.c:763:44: note: 'lGs' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
                                            ^~~
AlignProfiles.c: In function 'alignProfiles':
AlignProfiles.c:355:11: warning: 'subM' may be used uninitialized in this function [-Wmaybe-uninitialized]
   #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs) num_threads(nthreads)
           ^~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c AssignIndels.c -o AssignIndels.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateHairpinDeltaG':
CalculateDeltaG.c:375:26: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, k, count, s1, s2;
                          ^~
CalculateDeltaG.c:375:22: warning: 's1' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, k, count, s1, s2;
                      ^~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:25:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_DR[4][4] = {
                       ^
   -11.5, -7.8, -7, -8.3,
   {                    }
   -10.4, -12.8, -16.3, -9.1,
   {                        }
   -8.6, -8, -9.3, -5.9,
   {                   }
   -7.8, -5.5, -9, -7.8
   {
  };
  }
CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_DR[4][4] = {
                       ^
   -36.4, -21.6, -19.7, -23.9,
   {                         }
   -28.4, -31.9, -47.1, -23.5,
   {                         }
   -22.9, -17.1, -23.2, -12.3,
   {                         }
   -23.2, -13.5, -26.1, -21.9
   {
  };
  }
CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_DD[4][4] = {
                       ^
   -7.9, -8.4, -7.8, -7.2,
   {                     }
   -8.5, -8, -10.6, -7.8,
   {                    }
   -8.2, -9.8, -8, -8.4,
   {                   }
   -7.2, -8.2, -8.5, -7.9
   {
  };
  }
CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_DD[4][4] = {
                       ^
   -22.2, -22.4, -21, -20.4,
   {                       }
   -22.7, -19.9, -27.2, -21,
   {                       }
   -22.2, -24.4, -19.9, -22.4,
   {                         }
   -21.3, -22.2, -22.7, -22.2
   {
  };
  }
CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_RR[4][4] = {
                       ^
   -6.6, -10.17, -7.65, -5.76,
   {                         }
   -10.56, -12.21, -7.95, -7.65,
   {                           }
   -13.37, -14.21, -12.21, -10.17,
   {                             }
   -8.11, -13.37, -10.56, -6.6
   {
  };
  }
CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_RR[4][4] = {
                       ^
   -18.38, -26.03, -19.18, -15.67,
   {                             }
   -28.25, -30.02, -19.18, -19.18,
   {                             }
   -35.68, -34.85, -30.02, -26.03,
   {                             }
   -22.59, -35.68, -28.25, -18.38
   {
  };
  }
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:422:72: warning: 'upY' may be used uninitialized in this function [-Wmaybe-uninitialized]
    int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
                                                                        ^~~
ChainSegments.c:422:67: 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:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Cluster.c -o Cluster.o
Cluster.c: In function 'cluster._omp_fn.0':
Cluster.c:403:15: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
        minCol = minC;
        ~~~~~~~^~~~~~
Cluster.c:229:50: note: 'minC' was declared here
  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
                                                  ^~~~
Cluster.c: In function 'cluster._omp_fn.1':
Cluster.c:418:30: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
       minCols[rowIndices[i]] = minC;
       ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:229:50: note: 'minC' was declared here
  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
                                                  ^~~~
Cluster.c: In function 'cluster':
Cluster.c:229:50: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
Cluster.c:766:19: warning: 'nDiv' may be used uninitialized in this function [-Wmaybe-uninitialized]
      nDiv[minCol] -= dMatrix2[length*colIndices[minCol] - colIndices[minCol]*(colIndices[minCol] + 1)/2 + rowIndices[j] - colIndices[minCol]]; // col sums
                   ^~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ClusterML.c -o ClusterML.o
ClusterML.c: In function 'clusterML._omp_fn.2':
ClusterML.c:556:40: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
       node[count*maxWidth*4 + i*4 + 0] += *(Ls + 0*length + j);
                                        ^~
ClusterML.c:420:6: note: 'count' was declared here
  int count;
      ^~~~~
ClusterML.c: In function 'clusterML':
ClusterML.c:441:11: warning: 'node' may be used uninitialized in this function [-Wmaybe-uninitialized]
   #pragma omp parallel for private(i,j,y_i,row,count) schedule(guided) num_threads(nthreads)
           ^~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CommonGaps.c -o CommonGaps.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Compositions.c -o Compositions.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:966:8: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (k==1 && letter >= 11) {
        ^
Compression.c:516:12: note: 'k' was declared here
  int i, j, k, pos;
            ^
Compression.c:1010:12: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
       count++;
       ~~~~~^~
Compression.c:542:29: note: 'count' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                             ^~~~~
Compression.c:1009:20: warning: 'word' may be used uninitialized in this function [-Wmaybe-uninitialized]
       word = (word << 8) | (unsigned int)reorder(byte);
              ~~~~~~^~~~~
Compression.c:542:23: note: 'word' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                       ^~~~
Compression.c:1167:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = rev==0 ? 254 : 255;
       ~~~~~~~^~~~~~~~~~~~~~~~~~~~
Compression.c:543:27: note: 'rev' was declared here
   int lastTemp, currTemp, rev, len, len2, thresh = 1;
                           ^~~
Compression.c:556:7: warning: 'lower' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int lower = 0;
       ^~~~~
Compression.c:1239:43: warning: 'lastTriplet' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
                                        ~~~^~~~~~~~~~~~~~
Compression.c:629:12: note: 'lastTriplet' was declared here
   int run, lastTriplet, lastCase;
            ^~~~~~~~~~~
Compression.c:1057:23: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
         lastHit = dict[revcomp((word >> k) & 0xFF)]; // end of lastHit
                       ^
Compression.c:542:17: note: 'dict' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ConsensusSequence.c -o ConsensusSequence.o
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: 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:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ConsolidateGaps.c -o ConsolidateGaps.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:70:20: warning: missing braces around initializer [-Wmissing-braces]
  double NN[4][4] = {
                    ^
   -0.816507461,-2.5401714,-1.647430026,-1.184658548
   {
   ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
   }{
   ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
   }{
   ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
   }{
  };
  }
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
  double PM[4][4] = {
                    ^
   -0.141370102,-0.439805276,-0.285236035,-0.205111781
   {
   ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
   }{
   ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
   }{
   ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
   }{
  };
  }
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
  double sMM[4][5][5][4] = {
                           ^
   0,0,0,0
   {{{
   ,1.545032445,1.254355018,1.491691514,1.329138183
   }{
   ,1.150635633,0.582415494,1.075877275,1.187937642
   }{
   ,1.203555051,1.001540513,0.864287715,0.717125848
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.630005348,0.18553379,0.730763505,0.709272397
   -
   }},{{
   ,0,0,0,0
   }{
   ,0.856582783,-0.143236405,0.716721488,0.603652831
   }{
   ,0.851622883,0.653168672,0.676545316,1.187937642
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,1.231861002,0.746214538,1.087821916,0.989140748
   -
   }},{{
   ,1.822113278,1.270687029,1.336192565,1.364584949
   }{
   ,0,0,0,0
   }{
   ,1.443665704,1.385046493,1.256013166,1.329138183
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,1.478009492,0.882097231,1.20450984,1.061002478
   -
   }},{{
   ,1.496720812,0.846496194,0.967868114,0.989140748
   }{
   ,0.766581547,-0.024857805,0.50754303,0.709272397
   }{
   ,0,0,0,0
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.75,0.65,0.69,0.78
   -
   }},{{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.76,0.65,0.69,0.78
   }{
   ,0,0,0,0
   }{
   ,0,0,0,0
   -
   }}},{{{
   ,1.295827995,0.84547091,0.91019099,1.256013166
   }{
   ,0.755889609,0.241428373,0.396379912,0.676545316
   }{
   ,0.99945386,0.740323132,0.435659206,0.864287715
   }{
   ,0.65,0.55,0.48,0.69
   }{
   ,0.843147406,0.101248351,0.49063599,0.50754303
   -
   }},{{
   ,0,0,0,0
   }{
   ,1.0651638,0.249934344,0.699352949,0.716721488
   }{
   ,0.871921533,0.59458138,0.396379912,1.075877275
   }{
   ,0.65,0.56,0.49,0.69
   }{
   ,1.07531714,0.318907854,0.653287717,0.967868114
   -
   }},{{
   ,1.099899195,0.730184613,0.661798984,1.336192565
   }{
   ,0,0,0,0
   }{
   ,1.45897431,1.318532145,0.91019099,1.491691514
   }{
   ,0.65,0.56,0.49,0.69
   }{
   ,1.242135174,0.894838095,1.108555445,1.20450984
   -
   }},{{
   ,0.911428974,0.524430101,0.653287717,1.087821916
   }{
   ,0.503209827,0.274849491,0.49063599,0.730763505
   }{
   ,0,0,0,0
   }{
   ,0.65,0.55,0.48,0.69
   }{
   ,0.65,0.55,0.48,0.69
   -
   }},{{
   ,0.65,0.56,0.49,0.69
   }{
   ,0.65,0.56,0.49,0.69
   }{
   ,0.65,0.55,0.48,0.69
   }{
   ,0,0,0,0
   }{
   ,0,0,0,0
   -
   }}},{{{
   ,1.100661785,0.969784756,1.318532145,1.385046493
   }{
   ,0.565895968,-0.060347902,0.59458138,0.653168672
   }{
   ,0.782168488,0.788161238,0.740323132,1.001540513
   }{
   ,0.68,0.46,0.55,0.65
   }{
   ,0.468913405,-0.469855984,0.274849491,-0.024857805
   -
   }},{{
   ,0,0,0,0
   }{
   ,0.258195131,-0.70438632,0.249934344,-0.143236405
   }{
   ,0.502914193,-0.060347902,0.241428373,0.582415494
   }{
   ,0.68,0.47,0.56,0.65
   }{
   ,0.584083861,0.258975454,0.524430101,0.846496194
   -
   }},{{
   ,0.968040559,0.797499702,0.730184613,1.270687029
   }{
   ,0,0,0,0
   }{
   ,1.081040749,0.969784756,0.84547091,1.254355018
   }{
   ,0.68,0.47,0.56,0.65
   }{
   ,1.048553951,0.728354541,0.894838095,0.882097231
   -
   }},{{
   ,0.88611252,0.258975454,0.318907854,0.746214538
   }{
   ,0.239520858,-0.469855984,0.101248351,0.18553379
   }{
   ,0,0,0,0
   }{
   ,0.68,0.46,0.55,0.65
   }{
   ,0.68,0.46,0.55,0.65
   -
   }},{{
   ,0.68,0.47,0.56,0.65
   }{
   ,0.68,0.47,0.56,0.65
   }{
   ,0.68,0.46,0.55,0.65
   }{
   ,0,0,0,0
   }{
   ,0,0,0,0
   -
   }}},{{{
   ,1.566899704,1.081040749,1.45897431,1.443665704
   }{
   ,0.976725675,0.502914193,0.871921533,0.851622883
   }{
   ,1.482046826,0.782168488,0.99945386,1.203555051
   }{
   ,0.85,0.68,0.65,0.76
   }{
   ,0.798628781,0.239520858,0.503209827,0.766581547
   -
   }},{{
   ,0,0,0,0
   }{
   ,1.141098246,0.258195131,1.0651638,0.856582783
   }{
   ,0.976725675,0.565895968,0.755889609,1.150635633
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,1.125403302,0.88611252,0.911428974,1.496720812
   -
   }},{{
   ,1.68169282,0.968040559,1.099899195,1.822113278
   }{
   ,0,0,0,0
   }{
   ,1.566899704,1.100661785,1.295827995,1.545032445
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,1.35948517,1.048553951,1.242135174,1.478009492
   -
   }},{{
   ,1.125403302,0.584083861,1.07531714,1.231861002
   }{
   ,0.798628781,0.468913405,0.843147406,0.630005348
   }{
   ,0,0,0,0
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,0.85,0.68,0.65,0.75
   -
   }},{{
   ,0.85,0.68,0.65,0.75
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,0,0,0,0
   }{
  };
  }}}
DesignProbes.c: In function 'designProbes._omp_fn.0':
DesignProbes.c:834:29: warning: 'lastCycle' may be used uninitialized in this function [-Wmaybe-uninitialized]
         cycles += lastCycle - thisCycle;
                   ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:37: note: 'lastCycle' was declared here
    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
                                     ^~~~~~~~~
DesignProbes.c:834:29: warning: 'thisCycle' may be used uninitialized in this function [-Wmaybe-uninitialized]
         cycles += lastCycle - thisCycle;
                   ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:48: note: 'thisCycle' was declared here
    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
                                                ^~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Diff.c -o Diff.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'firstSeqsPosEqual':
DistanceMatrix.c:625:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if (!ci)
   ^~
DistanceMatrix.c:628:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    while (i < ex) {
    ^~~~~
DistanceMatrix.c:647:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if (!cj)
   ^~
DistanceMatrix.c:650:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    while (j < ey) {
    ^~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function 'pop':
EnumerateSequence.c:315:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
  x = x + (x >> 4) & 0xF0F0F0F;
      ~~^~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ExpandAmbiguities.c -o ExpandAmbiguities.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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:320:13: warning: 'I' may be used uninitialized in this function [-Wmaybe-uninitialized]
      pos = i*3 + k + 1;
            ~^~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function 'scoreCodonModel':
GeneFinding.c:388:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c:432:29: warning: 'lastVal' may be used uninitialized in this function [-Wmaybe-uninitialized]
      score += codons[lastVal*64 + val];
                      ~~~~~~~^~~
GeneFinding.c: In function 'startCodonModel':
GeneFinding.c:793:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
    val += 16*getBaseRC(x_i.ptr[j]);
                               ^
GeneFinding.c: In function 'scoreStartCodonModel':
GeneFinding.c:894:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
    val += 16*getBaseRC(x_i.ptr[j]);
                               ^
GeneFinding.c: In function 'initialCodonModel':
GeneFinding.c:928:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'scoreInitialCodonModel':
GeneFinding.c:1031:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'terminationCodonModel':
GeneFinding.c:1092:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'scoreTerminationCodonModel':
GeneFinding.c:1188:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'getRegion':
GeneFinding.c:1286:21: warning: 'x_i.length' may be used uninitialized in this function [-Wmaybe-uninitialized]
     (s==0 && j >= 0 && j + w <= x_i.length)) {
     ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1252:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'autocorrelationModel':
GeneFinding.c:1350:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'scoreAutocorrelationModel':
GeneFinding.c:1461:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'couplingModel':
GeneFinding.c:1573:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'scoreCouplingModel':
GeneFinding.c:1681:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'nucleotideBiasModel':
GeneFinding.c:1788:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'scoreNucleotideBiasModel':
GeneFinding.c:1882:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'upstreamMotifModel':
GeneFinding.c:1950:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'scoreUpstreamMotifModel':
GeneFinding.c:2057:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'scoreRunLengthModel':
GeneFinding.c:2276:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'stopCodonModel':
GeneFinding.c:2421:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
    val += 16*getBaseRC(x_i.ptr[j]);
                               ^
GeneFinding.c: In function 'scoreStopCodonModel':
GeneFinding.c:2522:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
    val += 16*getBaseRC(x_i.ptr[j]);
                               ^
GeneFinding.c: In function 'codonFrequencies':
GeneFinding.c:2554:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GetPools.c -o GetPools.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Import.c -o Import.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c InformationContent.c -o InformationContent.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c InsertGaps.c -o InsertGaps.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IntDist.c -o IntDist.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:79:20: warning: missing braces around initializer [-Wmissing-braces]
  double dH[4][4] = {
                    ^
   -7.9,-8.4,-7.8,-7.2
   {
   ,-8.5,-8.0,-10.6,-7.8
   }{
   ,-8.2,-9.8,-8.0,-8.4
   }{
   ,-7.2,-8.2,-8.5,-7.9
   }{
  };
  }
MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces]
  double dS[4][4] = {
                    ^
   -22.2,-22.4,-21.0,-20.4
   {
   ,-22.7,-19.9,-27.2,-21.0
   }{
   ,-22.2,-24.4,-19.9,-22.4
   }{
   ,-21.3,-22.2,-22.7,-22.2
   }{
  };
  }
MeltPolymer.c:54:10: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *rans;
          ^~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c MovingAverage.c -o MovingAverage.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function 'intMatchSelfOnce':
MultiMatch.c:866:21: warning: variable 'start' set but not used [-Wunused-but-set-variable]
  int i, j, k, temp, start = 0;
                     ^~~~~
In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:42,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rinternals.h:1557:16: 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-3~1.13-/R/include/Rdefines.h:42,
                 from MultiMatch.c:11:
C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rinternals.h:1557:16: 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;
     ~~~~~~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c NNLS.c -o NNLS.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Order.c -o Order.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function 'predictDBN':
PredictDBN.c:869:29: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
         range2[0] = nucs[pos[prev]];// + 1;
                             ^
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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:231:16: warning: 'states' may be used uninitialized in this function [-Wmaybe-uninitialized]
      states[j] = 'E';
      ~~~~~~~~~~^~~~~
PredictHEC.c:41:24: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double H, E, C, sum, *rans;
                        ^~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_decipher.c -o R_init_decipher.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RemoveGaps.c -o RemoveGaps.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ReplaceChars.c -o ReplaceChars.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c TerminalMismatch.c -o TerminalMismatch.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Translate.c -o Translate.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c VectorSums.c -o VectorSums.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"c:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
C:/rtools40/mingw32/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 GeneFinding.o GetPools.o Import.o InformationContent.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/DECIPHER.buildbin-libdir/00LOCK-DECIPHER/00new/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  
    Cophenetic                              html  
    CorrectFrameshifts                      html  
    CreateChimeras                          html  
    DB2Seqs                                 html  
    DECIPHER-package                        html  
    DesignArray                             html  
    DesignPrimers                           html  
    DesignProbes                            html  
    DesignSignatures                        html  
    DetectRepeats                           html  
    DigestDNA                               html  
    Disambiguate                            html  
    DistanceMatrix                          html  
    ExtractGenes                            html  
    FindChimeras                            html  
    FindGenes                               html  
    FindNonCoding                           html  
    FindSynteny                             html  
    FormGroups                              html  
    Genes-class                             html  
    HEC_MI                                  html  
    IdClusters                              html  
    IdConsensus                             html  
    IdLengths                               html  
    IdTaxa                                  html  
    IdentifyByRank                          html  
    LearnNonCoding                          html  
    LearnTaxa                               html  
    MIQS                                    html  
    MODELS                                  html  
    MapCharacters                           html  
    MaskAlignment                           html  
    MeltDNA                                 html  
    NNLS                                    html  
    NonCoding-class                         html  
    NonCodingRNA                            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  
    WriteGenes                              html  
    deltaGrules                             html  
    deltaHrules                             html  
    deltaHrulesRNA                          html  
    deltaSrules                             html  
    deltaSrulesRNA                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'DECIPHER' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function 'alignProfiles._omp_fn.0':
AlignProfiles.c:401:9: warning: 'lGp' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGp *= tot;
     ~~~~^~~~~~
AlignProfiles.c:39:39: note: 'lGp' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
                                       ^~~
AlignProfiles.c:403:9: warning: 'lGs' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGs *= tot;
     ~~~~^~~~~~
AlignProfiles.c:39:44: note: 'lGs' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
                                            ^~~
AlignProfiles.c: In function 'alignProfilesAA._omp_fn.1':
AlignProfiles.c:1220:9: warning: 'lGp' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGp *= tot;
     ~~~~^~~~~~
AlignProfiles.c:763:39: note: 'lGp' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
                                       ^~~
AlignProfiles.c:1222:9: warning: 'lGs' may be used uninitialized in this function [-Wmaybe-uninitialized]
     lGs *= tot;
     ~~~~^~~~~~
AlignProfiles.c:763:44: note: 'lGs' was declared here
  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
                                            ^~~
AlignProfiles.c: In function 'alignProfiles':
AlignProfiles.c:355:11: warning: 'subM' may be used uninitialized in this function [-Wmaybe-uninitialized]
   #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs) num_threads(nthreads)
           ^~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c AssignIndels.c -o AssignIndels.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateHairpinDeltaG':
CalculateDeltaG.c:375:26: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, k, count, s1, s2;
                          ^~
CalculateDeltaG.c:375:22: warning: 's1' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, k, count, s1, s2;
                      ^~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:25:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_DR[4][4] = {
                       ^
   -11.5, -7.8, -7, -8.3,
   {                    }
   -10.4, -12.8, -16.3, -9.1,
   {                        }
   -8.6, -8, -9.3, -5.9,
   {                   }
   -7.8, -5.5, -9, -7.8
   {
  };
  }
CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_DR[4][4] = {
                       ^
   -36.4, -21.6, -19.7, -23.9,
   {                         }
   -28.4, -31.9, -47.1, -23.5,
   {                         }
   -22.9, -17.1, -23.2, -12.3,
   {                         }
   -23.2, -13.5, -26.1, -21.9
   {
  };
  }
CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_DD[4][4] = {
                       ^
   -7.9, -8.4, -7.8, -7.2,
   {                     }
   -8.5, -8, -10.6, -7.8,
   {                    }
   -8.2, -9.8, -8, -8.4,
   {                   }
   -7.2, -8.2, -8.5, -7.9
   {
  };
  }
CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_DD[4][4] = {
                       ^
   -22.2, -22.4, -21, -20.4,
   {                       }
   -22.7, -19.9, -27.2, -21,
   {                       }
   -22.2, -24.4, -19.9, -22.4,
   {                         }
   -21.3, -22.2, -22.7, -22.2
   {
  };
  }
CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces]
  double dH_RR[4][4] = {
                       ^
   -6.6, -10.17, -7.65, -5.76,
   {                         }
   -10.56, -12.21, -7.95, -7.65,
   {                           }
   -13.37, -14.21, -12.21, -10.17,
   {                             }
   -8.11, -13.37, -10.56, -6.6
   {
  };
  }
CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces]
  double dS_RR[4][4] = {
                       ^
   -18.38, -26.03, -19.18, -15.67,
   {                             }
   -28.25, -30.02, -19.18, -19.18,
   {                             }
   -35.68, -34.85, -30.02, -26.03,
   {                             }
   -22.59, -35.68, -28.25, -18.38
   {
  };
  }
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:422:72: warning: 'upY' may be used uninitialized in this function [-Wmaybe-uninitialized]
    int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
                                                                        ^~~
ChainSegments.c:422:67: 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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Cluster.c -o Cluster.o
Cluster.c: In function 'cluster._omp_fn.0':
Cluster.c:403:15: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
        minCol = minC;
        ~~~~~~~^~~~~~
Cluster.c:229:50: note: 'minC' was declared here
  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
                                                  ^~~~
Cluster.c: In function 'cluster._omp_fn.1':
Cluster.c:418:30: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
       minCols[rowIndices[i]] = minC;
       ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:229:50: note: 'minC' was declared here
  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
                                                  ^~~~
Cluster.c: In function 'cluster':
Cluster.c:229:50: warning: 'minC' may be used uninitialized in this function [-Wmaybe-uninitialized]
Cluster.c:451:168: warning: 'nDiv' may be used uninitialized in this function [-Wmaybe-uninitialized]
      rans[4*(length - 1) + k] = dMatrix2[length*colIndices[minCol] - colIndices[minCol]*(colIndices[minCol] + 1)/2 + rowIndices[minRow] - colIndices[minCol]]/2 + (nDiv[minCol] - nDiv[minRow + 1])/(2*(size-2)); // col
                                                                                                                                                                        ^
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ClusterML.c -o ClusterML.o
ClusterML.c: In function 'clusterML._omp_fn.2':
ClusterML.c:556:40: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
       node[count*maxWidth*4 + i*4 + 0] += *(Ls + 0*length + j);
                                        ^~
ClusterML.c:420:6: note: 'count' was declared here
  int count;
      ^~~~~
ClusterML.c: In function 'clusterML':
ClusterML.c:441:11: warning: 'node' may be used uninitialized in this function [-Wmaybe-uninitialized]
   #pragma omp parallel for private(i,j,y_i,row,count) schedule(guided) num_threads(nthreads)
           ^~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CommonGaps.c -o CommonGaps.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Compositions.c -o Compositions.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Compression.c -o Compression.o
Compression.c: In function 'nbit._omp_fn.0':
Compression.c:966:8: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (k==1 && letter >= 11) {
        ^
Compression.c:516:12: note: 'k' was declared here
  int i, j, k, pos;
            ^
Compression.c:1010:12: warning: 'count' may be used uninitialized in this function [-Wmaybe-uninitialized]
       count++;
       ~~~~~^~
Compression.c:542:29: note: 'count' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                             ^~~~~
Compression.c:1009:20: warning: 'word' may be used uninitialized in this function [-Wmaybe-uninitialized]
       word = (word << 8) | (unsigned int)reorder(byte);
              ~~~~~~^~~~~
Compression.c:542:23: note: 'word' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                       ^~~~
Compression.c:1212:14: warning: 'rev' may be used uninitialized in this function [-Wmaybe-uninitialized]
       p[c++] = rev==0 ? 254 : 255;
       ~~~~~~~^~~~~~~~~~~~~~~~~~~~
Compression.c:543:27: note: 'rev' was declared here
   int lastTemp, currTemp, rev, len, len2, thresh = 1;
                           ^~~
Compression.c:556:7: warning: 'lower' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int lower = 0;
       ^~~~~
Compression.c:1239:43: warning: 'lastTriplet' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
                                        ~~~^~~~~~~~~~~~~~
Compression.c:629:12: note: 'lastTriplet' was declared here
   int run, lastTriplet, lastCase;
            ^~~~~~~~~~~
Compression.c:1029:23: warning: 'dict' may be used uninitialized in this function [-Wmaybe-uninitialized]
         lastHit = dict[(word >> k) & 0xFF];
                       ^
Compression.c:542:17: note: 'dict' was declared here
   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
                 ^~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function 'consensusProfile':
ConsensusSequence.c:1578:10: warning: 'DBN' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *DBN, *s;
          ^~~
ConsensusSequence.c: In function 'consensusProfileAA':
ConsensusSequence.c:455:18: warning: 'lastPos' may be used uninitialized in this function [-Wmaybe-uninitialized]
      *(runs + s) += weight;
                  ^~
ConsensusSequence.c:397:23: note: 'lastPos' was declared here
  int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
                       ^~~~~~~
ConsensusSequence.c:1771:10: warning: 'HEC' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *HEC, *s;
          ^~~
ConsensusSequence.c: In function 'colScores':
ConsensusSequence.c:1938:20: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_DBN, n, l, d;
                    ^
ConsensusSequence.c:1937:10: warning: 'DBN' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *DBN, *s;
          ^~~
ConsensusSequence.c: In function 'colScoresAA':
ConsensusSequence.c:2063:20: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int do_HEC, n, l, d;
                    ^
ConsensusSequence.c:2062:10: warning: 'HEC' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *HEC, *s;
          ^~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ConsolidateGaps.c -o ConsolidateGaps.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:70:20: warning: missing braces around initializer [-Wmissing-braces]
  double NN[4][4] = {
                    ^
   -0.816507461,-2.5401714,-1.647430026,-1.184658548
   {
   ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
   }{
   ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
   }{
   ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
   }{
  };
  }
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
  double PM[4][4] = {
                    ^
   -0.141370102,-0.439805276,-0.285236035,-0.205111781
   {
   ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
   }{
   ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
   }{
   ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
   }{
  };
  }
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
  double sMM[4][5][5][4] = {
                           ^
   0,0,0,0
   {{{
   ,1.545032445,1.254355018,1.491691514,1.329138183
   }{
   ,1.150635633,0.582415494,1.075877275,1.187937642
   }{
   ,1.203555051,1.001540513,0.864287715,0.717125848
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.630005348,0.18553379,0.730763505,0.709272397
   -
   }},{{
   ,0,0,0,0
   }{
   ,0.856582783,-0.143236405,0.716721488,0.603652831
   }{
   ,0.851622883,0.653168672,0.676545316,1.187937642
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,1.231861002,0.746214538,1.087821916,0.989140748
   -
   }},{{
   ,1.822113278,1.270687029,1.336192565,1.364584949
   }{
   ,0,0,0,0
   }{
   ,1.443665704,1.385046493,1.256013166,1.329138183
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,1.478009492,0.882097231,1.20450984,1.061002478
   -
   }},{{
   ,1.496720812,0.846496194,0.967868114,0.989140748
   }{
   ,0.766581547,-0.024857805,0.50754303,0.709272397
   }{
   ,0,0,0,0
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.75,0.65,0.69,0.78
   -
   }},{{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.75,0.65,0.69,0.78
   }{
   ,0.76,0.65,0.69,0.78
   }{
   ,0,0,0,0
   }{
   ,0,0,0,0
   -
   }}},{{{
   ,1.295827995,0.84547091,0.91019099,1.256013166
   }{
   ,0.755889609,0.241428373,0.396379912,0.676545316
   }{
   ,0.99945386,0.740323132,0.435659206,0.864287715
   }{
   ,0.65,0.55,0.48,0.69
   }{
   ,0.843147406,0.101248351,0.49063599,0.50754303
   -
   }},{{
   ,0,0,0,0
   }{
   ,1.0651638,0.249934344,0.699352949,0.716721488
   }{
   ,0.871921533,0.59458138,0.396379912,1.075877275
   }{
   ,0.65,0.56,0.49,0.69
   }{
   ,1.07531714,0.318907854,0.653287717,0.967868114
   -
   }},{{
   ,1.099899195,0.730184613,0.661798984,1.336192565
   }{
   ,0,0,0,0
   }{
   ,1.45897431,1.318532145,0.91019099,1.491691514
   }{
   ,0.65,0.56,0.49,0.69
   }{
   ,1.242135174,0.894838095,1.108555445,1.20450984
   -
   }},{{
   ,0.911428974,0.524430101,0.653287717,1.087821916
   }{
   ,0.503209827,0.274849491,0.49063599,0.730763505
   }{
   ,0,0,0,0
   }{
   ,0.65,0.55,0.48,0.69
   }{
   ,0.65,0.55,0.48,0.69
   -
   }},{{
   ,0.65,0.56,0.49,0.69
   }{
   ,0.65,0.56,0.49,0.69
   }{
   ,0.65,0.55,0.48,0.69
   }{
   ,0,0,0,0
   }{
   ,0,0,0,0
   -
   }}},{{{
   ,1.100661785,0.969784756,1.318532145,1.385046493
   }{
   ,0.565895968,-0.060347902,0.59458138,0.653168672
   }{
   ,0.782168488,0.788161238,0.740323132,1.001540513
   }{
   ,0.68,0.46,0.55,0.65
   }{
   ,0.468913405,-0.469855984,0.274849491,-0.024857805
   -
   }},{{
   ,0,0,0,0
   }{
   ,0.258195131,-0.70438632,0.249934344,-0.143236405
   }{
   ,0.502914193,-0.060347902,0.241428373,0.582415494
   }{
   ,0.68,0.47,0.56,0.65
   }{
   ,0.584083861,0.258975454,0.524430101,0.846496194
   -
   }},{{
   ,0.968040559,0.797499702,0.730184613,1.270687029
   }{
   ,0,0,0,0
   }{
   ,1.081040749,0.969784756,0.84547091,1.254355018
   }{
   ,0.68,0.47,0.56,0.65
   }{
   ,1.048553951,0.728354541,0.894838095,0.882097231
   -
   }},{{
   ,0.88611252,0.258975454,0.318907854,0.746214538
   }{
   ,0.239520858,-0.469855984,0.101248351,0.18553379
   }{
   ,0,0,0,0
   }{
   ,0.68,0.46,0.55,0.65
   }{
   ,0.68,0.46,0.55,0.65
   -
   }},{{
   ,0.68,0.47,0.56,0.65
   }{
   ,0.68,0.47,0.56,0.65
   }{
   ,0.68,0.46,0.55,0.65
   }{
   ,0,0,0,0
   }{
   ,0,0,0,0
   -
   }}},{{{
   ,1.566899704,1.081040749,1.45897431,1.443665704
   }{
   ,0.976725675,0.502914193,0.871921533,0.851622883
   }{
   ,1.482046826,0.782168488,0.99945386,1.203555051
   }{
   ,0.85,0.68,0.65,0.76
   }{
   ,0.798628781,0.239520858,0.503209827,0.766581547
   -
   }},{{
   ,0,0,0,0
   }{
   ,1.141098246,0.258195131,1.0651638,0.856582783
   }{
   ,0.976725675,0.565895968,0.755889609,1.150635633
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,1.125403302,0.88611252,0.911428974,1.496720812
   -
   }},{{
   ,1.68169282,0.968040559,1.099899195,1.822113278
   }{
   ,0,0,0,0
   }{
   ,1.566899704,1.100661785,1.295827995,1.545032445
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,1.35948517,1.048553951,1.242135174,1.478009492
   -
   }},{{
   ,1.125403302,0.584083861,1.07531714,1.231861002
   }{
   ,0.798628781,0.468913405,0.843147406,0.630005348
   }{
   ,0,0,0,0
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,0.85,0.68,0.65,0.75
   -
   }},{{
   ,0.85,0.68,0.65,0.75
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,0.85,0.68,0.65,0.75
   }{
   ,0,0,0,0
   }{
  };
  }}}
DesignProbes.c: In function 'designProbes._omp_fn.0':
DesignProbes.c:834:29: warning: 'lastCycle' may be used uninitialized in this function [-Wmaybe-uninitialized]
         cycles += lastCycle - thisCycle;
                   ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:37: note: 'lastCycle' was declared here
    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
                                     ^~~~~~~~~
DesignProbes.c:834:29: warning: 'thisCycle' may be used uninitialized in this function [-Wmaybe-uninitialized]
         cycles += lastCycle - thisCycle;
                   ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:48: note: 'thisCycle' was declared here
    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
                                                ^~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Diff.c -o Diff.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'firstSeqsPosEqual':
DistanceMatrix.c:625:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if (!ci)
   ^~
DistanceMatrix.c:628:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    while (i < ex) {
    ^~~~~
DistanceMatrix.c:647:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if (!cj)
   ^~
DistanceMatrix.c:650:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
    while (j < ey) {
    ^~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function 'pop':
EnumerateSequence.c:315:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
  x = x + (x >> 4) & 0xF0F0F0F;
      ~~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ExpandAmbiguities.c -o ExpandAmbiguities.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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:320:13: warning: 'I' may be used uninitialized in this function [-Wmaybe-uninitialized]
      pos = i*3 + k + 1;
            ~^~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function 'scoreCodonModel':
GeneFinding.c:388:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c:432:29: warning: 'lastVal' may be used uninitialized in this function [-Wmaybe-uninitialized]
      score += codons[lastVal*64 + val];
                      ~~~~~~~^~~
GeneFinding.c: In function 'startCodonModel':
GeneFinding.c:793:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
    val += 16*getBaseRC(x_i.ptr[j]);
                               ^
GeneFinding.c: In function 'scoreStartCodonModel':
GeneFinding.c:894:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
    val += 16*getBaseRC(x_i.ptr[j]);
                               ^
GeneFinding.c: In function 'initialCodonModel':
GeneFinding.c:928:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'scoreInitialCodonModel':
GeneFinding.c:1031:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'terminationCodonModel':
GeneFinding.c:1092:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'scoreTerminationCodonModel':
GeneFinding.c:1188:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'getRegion':
GeneFinding.c:1286:21: warning: 'x_i.length' may be used uninitialized in this function [-Wmaybe-uninitialized]
     (s==0 && j >= 0 && j + w <= x_i.length)) {
     ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1252:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'autocorrelationModel':
GeneFinding.c:1350:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'scoreAutocorrelationModel':
GeneFinding.c:1461:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'couplingModel':
GeneFinding.c:1573:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'scoreCouplingModel':
GeneFinding.c:1681:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'nucleotideBiasModel':
GeneFinding.c:1788:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'scoreNucleotideBiasModel':
GeneFinding.c:1882:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'upstreamMotifModel':
GeneFinding.c:1990:42: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
      val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
                                          ^
GeneFinding.c: In function 'scoreUpstreamMotifModel':
GeneFinding.c:2090:42: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
      val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
                                          ^
GeneFinding.c: In function 'scoreRunLengthModel':
GeneFinding.c:2276:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
GeneFinding.c: In function 'stopCodonModel':
GeneFinding.c:2421:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
    val += 16*getBaseRC(x_i.ptr[j]);
                               ^
GeneFinding.c: In function 'scoreStopCodonModel':
GeneFinding.c:2522:31: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
    val += 16*getBaseRC(x_i.ptr[j]);
                               ^
GeneFinding.c: In function 'codonFrequencies':
GeneFinding.c:2554:15: warning: 'x_i.ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
  Chars_holder x_i;
               ^~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GetPools.c -o GetPools.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Import.c -o Import.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c InformationContent.c -o InformationContent.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c InsertGaps.c -o InsertGaps.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IntDist.c -o IntDist.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:79:20: warning: missing braces around initializer [-Wmissing-braces]
  double dH[4][4] = {
                    ^
   -7.9,-8.4,-7.8,-7.2
   {
   ,-8.5,-8.0,-10.6,-7.8
   }{
   ,-8.2,-9.8,-8.0,-8.4
   }{
   ,-7.2,-8.2,-8.5,-7.9
   }{
  };
  }
MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces]
  double dS[4][4] = {
                    ^
   -22.2,-22.4,-21.0,-20.4
   {
   ,-22.7,-19.9,-27.2,-21.0
   }{
   ,-22.2,-24.4,-19.9,-22.4
   }{
   ,-21.3,-22.2,-22.7,-22.2
   }{
  };
  }
MeltPolymer.c:54:10: warning: 'rans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  double *rans;
          ^~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c MovingAverage.c -o MovingAverage.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function 'intMatchSelfOnce':
MultiMatch.c:866:21: warning: variable 'start' set but not used [-Wunused-but-set-variable]
  int i, j, k, temp, start = 0;
                     ^~~~~
In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:42,
                 from MultiMatch.c:11:
MultiMatch.c: In function 'matchLists':
C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rinternals.h:1557:16: 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-3~1.13-/R/include/Rdefines.h:42,
                 from MultiMatch.c:11:
C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rinternals.h:1557:16: 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;
     ~~~~~~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c NNLS.c -o NNLS.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Order.c -o Order.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function 'predictDBN':
PredictDBN.c:869:29: warning: 'prev' may be used uninitialized in this function [-Wmaybe-uninitialized]
         range2[0] = nucs[pos[prev]];// + 1;
                             ^
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_decipher.c -o R_init_decipher.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RemoveGaps.c -o RemoveGaps.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ReplaceChars.c -o ReplaceChars.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c TerminalMismatch.c -o TerminalMismatch.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Translate.c -o Translate.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c VectorSums.c -o VectorSums.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include'   -I"C:/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
C:/rtools40/mingw64/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 GeneFinding.o GetPools.o Import.o InformationContent.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_2.20.0.zip
* DONE (DECIPHER)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'DECIPHER' successfully unpacked and MD5 sums checked

Tests output


Example timings

DECIPHER.Rcheck/examples_i386/DECIPHER-Ex.timings

nameusersystemelapsed
AA_REDUCED0.040.000.04
Add2DB0.500.020.88
AdjustAlignment0.360.000.51
AlignDB1.000.111.27
AlignProfiles1.190.121.76
AlignSeqs27.87 2.3030.17
AlignSynteny2.800.082.87
AlignTranslation14.19 0.3514.60
AmplifyDNA0.010.000.01
Array2Matrix7.560.017.58
BrowseDB0.020.000.02
BrowseSeqs57.87 0.6958.56
CalculateEfficiencyArray0.040.000.03
CalculateEfficiencyFISH000
CalculateEfficiencyPCR000
Codec0.960.000.97
ConsensusSequence0.190.000.19
Cophenetic0.970.000.97
CorrectFrameshifts21.28 0.6621.95
CreateChimeras0.770.000.77
DB2Seqs0.010.000.01
DesignArray7.440.007.44
DesignPrimers000
DesignProbes000
DesignSignatures000
DetectRepeats93.89 0.4594.37
DigestDNA0.140.000.14
Disambiguate0.050.000.05
DistanceMatrix0.030.000.03
ExtractGenes50.30 1.1451.46
FindChimeras0.060.000.06
FindGenes48.08 1.0049.09
FindNonCoding58.17 9.4267.60
FindSynteny1.410.001.40
FormGroups0.060.000.06
Genes-class54.76 1.3656.18
HEC_MI0.300.060.36
IdClusters0.550.000.54
IdConsensus0.680.020.71
IdLengths0.040.000.03
IdTaxa13.79 0.3014.09
IdentifyByRank0.050.000.05
LearnNonCoding50.09 6.9657.06
LearnTaxa 8.36 2.9411.30
MIQS0.070.000.06
MODELS000
MapCharacters35.02 1.1636.60
MaskAlignment0.620.000.62
MeltDNA0.050.000.05
NNLS000
NonCoding-class0.080.000.08
NonCodingRNA0.150.010.17
OrientNucleotides0.820.000.81
PFASUM0.070.000.08
PredictDBN126.02 0.23126.75
PredictHEC0.330.000.32
RESTRICTION_ENZYMES000
ReadDendrogram0.060.000.07
RemoveGaps0.020.000.01
SearchDB0.060.000.07
Seqs2DB0.080.000.07
StaggerAlignment13.65 1.5715.24
Synteny-class1.880.001.87
Taxa-class12.79 2.0714.88
TerminalChar0.020.000.01
TileSeqs4.140.004.14
TrainingSet_16S2.250.022.27
TrimDNA0.060.000.06
WriteDendrogram000
WriteGenes47.82 2.5650.41
deltaGrules0.010.000.01
deltaHrules0.030.020.06
deltaHrulesRNA0.040.000.05
deltaSrules0.100.000.09
deltaSrulesRNA0.030.010.05

DECIPHER.Rcheck/examples_x64/DECIPHER-Ex.timings

nameusersystemelapsed
AA_REDUCED0.040.010.07
Add2DB0.270.020.28
AdjustAlignment0.250.000.25
AlignDB1.080.061.14
AlignProfiles0.940.030.97
AlignSeqs21.55 2.2423.78
AlignSynteny2.470.092.57
AlignTranslation11.12 0.3911.53
AmplifyDNA0.000.020.01
Array2Matrix6.280.016.30
BrowseDB0.030.000.03
BrowseSeqs49.66 0.6050.25
CalculateEfficiencyArray0.010.000.02
CalculateEfficiencyFISH000
CalculateEfficiencyPCR000
Codec1.100.001.09
ConsensusSequence0.170.000.17
Cophenetic0.980.011.00
CorrectFrameshifts16.18 0.4716.99
CreateChimeras0.640.020.65
DB2Seqs0.010.000.02
DesignArray6.220.006.22
DesignPrimers000
DesignProbes000
DesignSignatures000
DetectRepeats 99.77 0.59100.37
DigestDNA0.230.020.25
Disambiguate0.080.000.08
DistanceMatrix0.050.000.05
ExtractGenes48.43 1.3149.76
FindChimeras0.070.000.07
FindGenes46.03 1.1747.21
FindNonCoding51.87 8.1460.04
FindSynteny1.300.001.29
FormGroups0.050.000.05
Genes-class48.87 0.9449.81
HEC_MI0.250.010.27
IdClusters0.520.000.51
IdConsensus0.720.000.72
IdLengths0.010.000.02
IdTaxa11.24 0.0211.25
IdentifyByRank0.010.000.01
LearnNonCoding45.81 5.7251.55
LearnTaxa7.321.849.16
MIQS0.040.020.06
MODELS000
MapCharacters29.14 1.4030.56
MaskAlignment0.570.020.58
MeltDNA0.030.000.03
NNLS0.010.000.02
NonCoding-class0.070.000.06
NonCodingRNA0.120.000.12
OrientNucleotides0.920.000.93
PFASUM0.050.020.06
PredictDBN116.19 0.14116.33
PredictHEC0.250.000.25
RESTRICTION_ENZYMES000
ReadDendrogram0.080.000.07
RemoveGaps0.010.000.02
SearchDB0.030.000.03
Seqs2DB0.080.000.08
StaggerAlignment12.94 1.9214.86
Synteny-class2.060.012.08
Taxa-class12.52 0.4412.95
TerminalChar000
TileSeqs5.50.05.5
TrainingSet_16S2.420.002.42
TrimDNA0.070.000.06
WriteDendrogram000
WriteGenes45.75 0.2245.97
deltaGrules0.010.000.01
deltaHrules0.020.020.04
deltaHrulesRNA0.010.000.01
deltaSrules0.070.000.06
deltaSrulesRNA0.030.000.03