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This page was generated on 2023-01-02 09:00:26 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for DECIPHER on palomino5


To the developers/maintainers of the DECIPHER package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 477/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 2.27.0  (landing page)
Erik Wright
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/DECIPHER
git_branch: master
git_last_commit: ffdccd0
git_last_commit_date: 2022-11-01 11:06:21 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: DECIPHER
Version: 2.27.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DECIPHER.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DECIPHER_2.27.0.tar.gz
StartedAt: 2022-12-28 23:02:17 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 23:15:16 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 778.6 seconds
RetCode: 0
Status:   OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DECIPHER.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DECIPHER_2.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/DECIPHER.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DECIPHER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DECIPHER' version '2.27.0'
* 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
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* checking installed package size ... NOTE
  installed size is 12.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    data      7.3Mb
    extdata   2.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DesignSignatures: no visible binding for global variable 'deltaHrules'
FindGenes: no visible binding for global variable 'deltaHrulesRNA'
FindNonCoding: no visible binding for global variable 'deltaHrulesRNA'
LearnNonCoding: no visible binding for global variable 'deltaHrulesRNA'
PredictDBN: no visible binding for global variable 'deltaHrulesRNA'
TreeLine: multiple local function definitions for '.minimize' with
  different formal arguments
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 x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/DECIPHER/libs/x64/DECIPHER.dll':
  Found '_assert', possibly from 'assert' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
PredictDBN         94.79   0.38   96.47
MapCharacters      73.65   1.88   75.51
BrowseSeqs         47.25   1.44   49.22
ExtractGenes       44.58   0.84   45.80
Genes-class        42.62   0.95   43.59
WriteGenes         42.50   0.66   43.15
FindNonCoding      39.94   2.98   42.92
FindGenes          40.67   0.80   41.52
LearnNonCoding     37.19   2.43   39.66
AlignSeqs          22.87   4.36   27.24
CorrectFrameshifts 15.33   3.66   19.02
StaggerAlignment   11.19   2.01   13.22
AlignTranslation   11.03   1.11   12.18
Taxa-class         10.47   0.17   10.64
IdTaxa              9.84   0.29   10.14
DetectRepeats       8.68   0.55    9.24
TreeLine            7.39   0.45    7.84
LearnTaxa           5.92   0.82    6.75
DesignArray         5.64   0.00    5.64
Array2Matrix        5.39   0.01    5.41
ScoreAlignment      4.75   0.51    5.27
* 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/DECIPHER.Rcheck/00check.log'
for details.

Installation output

DECIPHER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'DECIPHER' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/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:424:37: warning: 'lGp' may be used uninitialized [-Wmaybe-uninitialized]
  424 |                                 lGp *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:61:46: note: 'lGp' was declared here
   61 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
      |                                              ^~~
AlignProfiles.c:426:37: warning: 'lGs' may be used uninitialized [-Wmaybe-uninitialized]
  426 |                                 lGs *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:61:51: note: 'lGs' was declared here
   61 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
      |                                                   ^~~
AlignProfiles.c: In function 'alignProfilesAA._omp_fn.0':
AlignProfiles.c:1266:37: warning: 'lGp' may be used uninitialized [-Wmaybe-uninitialized]
 1266 |                                 lGp *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:808:46: note: 'lGp' was declared here
  808 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
      |                                              ^~~
AlignProfiles.c:1268:37: warning: 'lGs' may be used uninitialized [-Wmaybe-uninitialized]
 1268 |                                 lGs *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:808:51: note: 'lGs' was declared here
  808 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
      |                                                   ^~~
AlignProfiles.c: In function 'alignProfiles':
AlignProfiles.c:378:25: warning: 'subM' may be used uninitialized [-Wmaybe-uninitialized]
  378 |                 #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(nthreads)
      |                         ^~~
AlignProfiles.c:81:17: note: 'subM' was declared here
   81 |         double *subM;
      |                 ^~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c AssignIndels.c -o AssignIndels.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateHairpinDeltaG':
CalculateDeltaG.c:463:49: warning: 's2' may be used uninitialized [-Wmaybe-uninitialized]
  463 |                         if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
      |                                             ~~~~^~~~~
CalculateDeltaG.c:375:33: note: 's2' was declared here
  375 |         int i, j, k, count, s1, s2;
      |                                 ^~
CalculateDeltaG.c:463:36: warning: 's1' may be used uninitialized [-Wmaybe-uninitialized]
  463 |                         if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
      |                                ~~~~^~~~~
CalculateDeltaG.c:375:29: note: 's1' was declared here
  375 |         int i, j, k, count, s1, s2;
      |                             ^~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function 'calculateFISH':
CalculateFISH.c:25:30: warning: missing braces around initializer [-Wmissing-braces]
   25 |         double dH_DR[4][4] = {
      |                              ^
   26 |                 -11.5, -7.8, -7, -8.3,
      |                 {                    }
   27 |                 -10.4, -12.8, -16.3, -9.1,
      |                 {                        }
   28 |                 -8.6, -8, -9.3, -5.9,
      |                 {                   }
   29 |                 -7.8, -5.5, -9, -7.8
      |                 {
   30 |         };
      |         }
CalculateFISH.c:31:30: warning: missing braces around initializer [-Wmissing-braces]
   31 |         double dS_DR[4][4] = {
      |                              ^
   32 |                 -36.4, -21.6, -19.7, -23.9,
      |                 {                         }
   33 |                 -28.4, -31.9, -47.1, -23.5,
      |                 {                         }
   34 |                 -22.9, -17.1, -23.2, -12.3,
      |                 {                         }
   35 |                 -23.2, -13.5, -26.1, -21.9
      |                 {
   36 |         };
      |         }
CalculateFISH.c:37:30: warning: missing braces around initializer [-Wmissing-braces]
   37 |         double dH_DD[4][4] = {
      |                              ^
   38 |                 -7.9, -8.4, -7.8, -7.2,
      |                 {                     }
   39 |                 -8.5, -8, -10.6, -7.8,
      |                 {                    }
   40 |                 -8.2, -9.8, -8, -8.4,
      |                 {                   }
   41 |                 -7.2, -8.2, -8.5, -7.9
      |                 {
   42 |         };
      |         }
CalculateFISH.c:43:30: warning: missing braces around initializer [-Wmissing-braces]
   43 |         double dS_DD[4][4] = {
      |                              ^
   44 |                 -22.2, -22.4, -21, -20.4,
      |                 {                       }
   45 |                 -22.7, -19.9, -27.2, -21,
      |                 {                       }
   46 |                 -22.2, -24.4, -19.9, -22.4,
      |                 {                         }
   47 |                 -21.3, -22.2, -22.7, -22.2
      |                 {
   48 |         };
      |         }
CalculateFISH.c:49:30: warning: missing braces around initializer [-Wmissing-braces]
   49 |         double dH_RR[4][4] = {
      |                              ^
   50 |                 -6.6, -10.17, -7.65, -5.76,
      |                 {                         }
   51 |                 -10.56, -12.21, -7.95, -7.65,
      |                 {                           }
   52 |                 -13.37, -14.21, -12.21, -10.17,
      |                 {                             }
   53 |                 -8.11, -13.37, -10.56, -6.6
      |                 {
   54 |         };
      |         }
CalculateFISH.c:55:30: warning: missing braces around initializer [-Wmissing-braces]
   55 |         double dS_RR[4][4] = {
      |                              ^
   56 |                 -18.38, -26.03, -19.18, -15.67,
      |                 {                             }
   57 |                 -28.25, -30.02, -19.18, -19.18,
      |                 {                             }
   58 |                 -35.68, -34.85, -30.02, -26.03,
      |                 {                             }
   59 |                 -22.59, -35.68, -28.25, -18.38
      |                 {
   60 |         };
      |         }
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function 'chainSegments':
ChainSegments.c:500:49: warning: 'upY' may be used uninitialized [-Wmaybe-uninitialized]
  500 |                         if (minX == minY && upX == upY) {
      |                                             ~~~~^~~~~~
ChainSegments.c:466:93: note: 'upY' was declared here
  466 |                         int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
      |                                                                                             ^~~
ChainSegments.c:500:49: warning: 'upX' may be used uninitialized [-Wmaybe-uninitialized]
  500 |                         if (minX == minY && upX == upY) {
      |                                             ~~~~^~~~~~
ChainSegments.c:466:88: note: 'upX' was declared here
  466 |                         int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
      |                                                                                        ^~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/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:403:50: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized]
  403 |                                         minCs[i] = minC;
      |                                         ~~~~~~~~~^~~~~~
Cluster.c:231:57: note: 'minC' was declared here
  231 |         int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                         ^~~~
Cluster.c: In function 'cluster._omp_fn.1':
Cluster.c:427:72: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized]
  427 |                                                 minCols[rowIndices[i]] = minC;
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:231:57: note: 'minC' was declared here
  231 |         int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                         ^~~~
Cluster.c: In function 'cluster':
Cluster.c:449:66: warning: 'minC' may be used uninitialized [-Wmaybe-uninitialized]
  449 |                 rans[1*(length - 1) + k] = *(colNums + colIndices[minCol]); // column merged
      |                                                                  ^
Cluster.c:231:57: note: 'minC' was declared here
  231 |         int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                         ^~~~
Cluster.c:739:47: warning: 'nDiv' may be used uninitialized [-Wmaybe-uninitialized]
  739 |                                 nDiv[i] = nDiv[i + 1];
      |                                           ~~~~^~~~~~~
Cluster.c:268:17: note: 'nDiv' was declared here
  268 |         double *nDiv;
      |                 ^~~~
In file included from F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41,
                 from Cluster.c:11:
F:/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:897:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized]
  897 | #define eval                    Rf_eval
      |                                 ^~~~~~~
Cluster.c:235:36: note: 'utilsPackage' was declared here
  235 |         SEXP ans, percentComplete, utilsPackage;
      |                                    ^~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:897:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized]
  897 | #define eval                    Rf_eval
      |                                 ^~~~~~~
Cluster.c:235:19: note: 'percentComplete' was declared here
  235 |         SEXP ans, percentComplete, utilsPackage;
      |                   ^~~~~~~~~~~~~~~
Cluster.c:801:43: warning: 'total' may be used uninitialized [-Wmaybe-uninitialized]
  801 |                         *rPercentComplete = floor(100*soFar/total);
      |                         ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
Cluster.c:234:23: note: 'total' was declared here
  234 |         double soFar, total, minHeight, *cut, *rans, *distanceMatrix, minH;
      |                       ^~~~~
Cluster.c:806:40: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized]
  806 |                                 before = *rPercentComplete;
      |                                 ~~~~~~~^~~~~~~~~~~~~~~~~~~
Cluster.c:233:25: note: 'rPercentComplete' was declared here
  233 |         int before, v, *rPercentComplete;
      |                         ^~~~~~~~~~~~~~~~
Cluster.c:787:52: warning: 'minCols' may be used uninitialized [-Wmaybe-uninitialized]
  787 |                                         if (minCols[rowIndices[j]] >= 0) {
      |                                                    ^
Cluster.c:262:14: note: 'minCols' was declared here
  262 |         int *minCols;
      |              ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ClusterML.c -o ClusterML.o
ClusterML.c:5666:13: warning: 'L_unknown_5_SIMD' defined but not used [-Wunused-function]
 5666 | static void L_unknown_5_SIMD(double *__restrict Ls, const int i3, const int i1, const int i2, const double *P1, const double *P2, const double epsilon, const double inv_epsilon, const int root)
      |             ^~~~~~~~~~~~~~~~
ClusterML.c:5064:13: warning: 'L_unknown_SIMD' defined but not used [-Wunused-function]
 5064 | static void L_unknown_SIMD(double *__restrict Ls, const int i3, const int i1, const int i2, const double *P1, const double *P2, const double epsilon, const double inv_epsilon, const int root)
      |             ^~~~~~~~~~~~~~
ClusterML.c: In function 'clusterML':
ClusterML.c:6905:17: warning: 'node' may be used uninitialized [-Wmaybe-uninitialized]
 6905 |         #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
      |                 ^~~
ClusterML.c:6775:17: note: 'node' was declared here
 6775 |         double *node;
      |                 ^~~~
In file included from F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:38,
                 from ClusterML.c:11:
F:/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:55:25: warning: 'I' may be used uninitialized [-Wmaybe-uninitialized]
   55 | #define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
      |                         ^~~~~~~~~~
ClusterML.c:6737:17: note: 'I' was declared here
 6737 |         double *I;
      |                 ^
F:/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:55:25: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized]
   55 | #define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
      |                         ^~~~~~~~~~
ClusterML.c:6736:14: note: 'Up' was declared here
 6736 |         int *Up;
      |              ^~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ClusterMP.c -o ClusterMP.o
ClusterMP.c: In function 'clusterMP._omp_fn.0':
ClusterMP.c:72:22: warning: 'm' may be used uninitialized [-Wmaybe-uninitialized]
   72 |         int i, j, k, m, w;
      |                      ^
ClusterMP.c:245:57: warning: 'P' may be used uninitialized [-Wmaybe-uninitialized]
  245 |                                                         allStates(R, P, S, c, n, c, k - 1, c, n, 0, 1);
      |                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ClusterMP.c:125:30: note: 'P' was declared here
  125 |                         int *P;
      |                              ^
ClusterMP.c: In function 'clusterMP':
ClusterMP.c:113:17: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized]
  113 |         #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
      |                 ^~~
ClusterMP.c:100:14: note: 'Up' was declared here
  100 |         int *Up;
      |              ^~
ClusterMP.c:113:17: warning: 'subM' may be used uninitialized [-Wmaybe-uninitialized]
  113 |         #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
      |                 ^~~
ClusterMP.c:86:22: note: 'subM' was declared here
   86 |         int *nodes, *subM;
      |                      ^~~~
ClusterMP.c:113:17: warning: 'nodes' may be used uninitialized [-Wmaybe-uninitialized]
  113 |         #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
      |                 ^~~
ClusterMP.c:86:14: note: 'nodes' was declared here
   86 |         int *nodes, *subM;
      |              ^~~~~
ClusterMP.c:113:17: warning: 'lengths' may be used uninitialized [-Wmaybe-uninitialized]
  113 |         #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
      |                 ^~~
ClusterMP.c:85:17: note: 'lengths' was declared here
   85 |         double *lengths, *score;
      |                 ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CommonGaps.c -o CommonGaps.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Compositions.c -o Compositions.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/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:993:35: warning: 'k' may be used uninitialized [-Wmaybe-uninitialized]
  993 |                                 j += k;
      |                                 ~~^~~~
Compression.c:516:19: note: 'k' was declared here
  516 |         int i, j, k, pos;
      |                   ^
Compression.c:1010:54: warning: 'count' may be used uninitialized [-Wmaybe-uninitialized]
 1010 |                                                 count++;
      |                                                 ~~~~~^~
Compression.c:542:43: note: 'count' was declared here
  542 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                                           ^~~~~
Compression.c:1009:62: warning: 'word' may be used uninitialized [-Wmaybe-uninitialized]
 1009 |                                                 word = (word << 8) | (unsigned int)reorder(byte);
      |                                                        ~~~~~~^~~~~
Compression.c:542:37: note: 'word' was declared here
  542 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                                     ^~~~
Compression.c:543:41: warning: 'rev' may be used uninitialized [-Wmaybe-uninitialized]
  543 |                 int lastTemp, currTemp, rev, len, len2, thresh = 1;
      |                                         ^~~
Compression.c:688:36: warning: 'lower' may be used uninitialized [-Wmaybe-uninitialized]
  688 |                                 if (lower==1)
      |                                    ^
Compression.c:556:21: note: 'lower' was declared here
  556 |                 int lower = 0;
      |                     ^~~~~
Compression.c:1239:71: warning: 'lastTriplet' may be used uninitialized [-Wmaybe-uninitialized]
 1239 |                                 if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
      |                                                                    ~~~^~~~~~~~~~~~~~
Compression.c:629:26: note: 'lastTriplet' was declared here
  629 |                 int run, lastTriplet, lastCase;
      |                          ^~~~~~~~~~~
Compression.c:1086:61: warning: 'dict' may be used uninitialized [-Wmaybe-uninitialized]
 1086 |                                                         dict[word] = j;
      |                                                             ^
Compression.c:542:31: note: 'dict' was declared here
  542 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                               ^~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function 'consensusProfile':
ConsensusSequence.c:1578:17: warning: 'DBN' may be used uninitialized [-Wmaybe-uninitialized]
 1578 |         double *DBN, *s;
      |                 ^~~
In function 'runsAA',
    inlined from 'consensusProfileAA' at ConsensusSequence.c:1836:3:
ConsensusSequence.c:455:41: warning: 'lastPos' may be used uninitialized [-Wmaybe-uninitialized]
  455 |                                         *(runs + s) += weight;
      |                                         ^~~~~~~~~~~
ConsensusSequence.c: In function 'consensusProfileAA':
ConsensusSequence.c:397:30: note: 'lastPos' was declared here
  397 |         int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
      |                              ^~~~~~~
ConsensusSequence.c:1771:17: warning: 'HEC' may be used uninitialized [-Wmaybe-uninitialized]
 1771 |         double *HEC, *s;
      |                 ^~~
ConsensusSequence.c: In function 'colScores':
ConsensusSequence.c:1939:27: warning: 'd' may be used uninitialized [-Wmaybe-uninitialized]
 1939 |         int do_DBN, n, l, d;
      |                           ^
ConsensusSequence.c:1938:17: warning: 'DBN' may be used uninitialized [-Wmaybe-uninitialized]
 1938 |         double *DBN, *s;
      |                 ^~~
ConsensusSequence.c: In function 'colScoresAA':
ConsensusSequence.c:2076:27: warning: 'd' may be used uninitialized [-Wmaybe-uninitialized]
 2076 |         int do_HEC, n, l, d;
      |                           ^
ConsensusSequence.c:2075:17: warning: 'HEC' may be used uninitialized [-Wmaybe-uninitialized]
 2075 |         double *HEC, *s;
      |                 ^~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function 'designProbes':
DesignProbes.c:70:27: warning: missing braces around initializer [-Wmissing-braces]
   70 |         double NN[4][4] = {
      |                           ^
   71 |                 -0.816507461,-2.5401714,-1.647430026,-1.184658548
      |                 {
   72 |                 ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
      |                 }{
   73 |                 ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
      |                 }{
   74 |                 ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
      |                 }{
   75 |         };
      |         }
DesignProbes.c:77:27: warning: missing braces around initializer [-Wmissing-braces]
   77 |         double PM[4][4] = {
      |                           ^
   78 |                 -0.141370102,-0.439805276,-0.285236035,-0.205111781
      |                 {
   79 |                 ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
      |                 }{
   80 |                 ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
      |                 }{
   81 |                 ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
      |                 }{
   82 |         };
      |         }
DesignProbes.c:84:34: warning: missing braces around initializer [-Wmissing-braces]
   84 |         double sMM[4][5][5][4] = {
      |                                  ^
   85 |                 0,0,0,0
      |                 {{{
   86 |                 ,1.545032445,1.254355018,1.491691514,1.329138183
      |                 }{
   87 |                 ,1.150635633,0.582415494,1.075877275,1.187937642
      |                 }{
   88 |                 ,1.203555051,1.001540513,0.864287715,0.717125848
      |                 }{
   89 |                 ,0.75,0.65,0.69,0.78
      |                 }{
   90 |                 ,0.630005348,0.18553379,0.730763505,0.709272397
      |                 -
      |                 }},{{
   91 |                 ,0,0,0,0
      |                 }{
   92 |                 ,0.856582783,-0.143236405,0.716721488,0.603652831
      |                 }{
   93 |                 ,0.851622883,0.653168672,0.676545316,1.187937642
      |                 }{
   94 |                 ,0.75,0.65,0.69,0.78
      |                 }{
   95 |                 ,1.231861002,0.746214538,1.087821916,0.989140748
      |                 -
      |                 }},{{
   96 |                 ,1.822113278,1.270687029,1.336192565,1.364584949
      |                 }{
   97 |                 ,0,0,0,0
      |                 }{
   98 |                 ,1.443665704,1.385046493,1.256013166,1.329138183
      |                 }{
   99 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  100 |                 ,1.478009492,0.882097231,1.20450984,1.061002478
      |                 -
      |                 }},{{
  101 |                 ,1.496720812,0.846496194,0.967868114,0.989140748
      |                 }{
  102 |                 ,0.766581547,-0.024857805,0.50754303,0.709272397
      |                 }{
  103 |                 ,0,0,0,0
      |                 }{
  104 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  105 |                 ,0.75,0.65,0.69,0.78
      |                 -
      |                 }},{{
  106 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  107 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  108 |                 ,0.76,0.65,0.69,0.78
      |                 }{
  109 |                 ,0,0,0,0
      |                 }{
  110 |                 ,0,0,0,0
      |                 -
      |                 }}},{{{
  111 |                 ,1.295827995,0.84547091,0.91019099,1.256013166
      |                 }{
  112 |                 ,0.755889609,0.241428373,0.396379912,0.676545316
      |                 }{
  113 |                 ,0.99945386,0.740323132,0.435659206,0.864287715
      |                 }{
  114 |                 ,0.65,0.55,0.48,0.69
      |                 }{
  115 |                 ,0.843147406,0.101248351,0.49063599,0.50754303
      |                 -
      |                 }},{{
  116 |                 ,0,0,0,0
      |                 }{
  117 |                 ,1.0651638,0.249934344,0.699352949,0.716721488
      |                 }{
  118 |                 ,0.871921533,0.59458138,0.396379912,1.075877275
      |                 }{
  119 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  120 |                 ,1.07531714,0.318907854,0.653287717,0.967868114
      |                 -
      |                 }},{{
  121 |                 ,1.099899195,0.730184613,0.661798984,1.336192565
      |                 }{
  122 |                 ,0,0,0,0
      |                 }{
  123 |                 ,1.45897431,1.318532145,0.91019099,1.491691514
      |                 }{
  124 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  125 |                 ,1.242135174,0.894838095,1.108555445,1.20450984
      |                 -
      |                 }},{{
  126 |                 ,0.911428974,0.524430101,0.653287717,1.087821916
      |                 }{
  127 |                 ,0.503209827,0.274849491,0.49063599,0.730763505
      |                 }{
  128 |                 ,0,0,0,0
      |                 }{
  129 |                 ,0.65,0.55,0.48,0.69
      |                 }{
  130 |                 ,0.65,0.55,0.48,0.69
      |                 -
      |                 }},{{
  131 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  132 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  133 |                 ,0.65,0.55,0.48,0.69
      |                 }{
  134 |                 ,0,0,0,0
      |                 }{
  135 |                 ,0,0,0,0
      |                 -
      |                 }}},{{{
  136 |                 ,1.100661785,0.969784756,1.318532145,1.385046493
      |                 }{
  137 |                 ,0.565895968,-0.060347902,0.59458138,0.653168672
      |                 }{
  138 |                 ,0.782168488,0.788161238,0.740323132,1.001540513
      |                 }{
  139 |                 ,0.68,0.46,0.55,0.65
      |                 }{
  140 |                 ,0.468913405,-0.469855984,0.274849491,-0.024857805
      |                 -
      |                 }},{{
  141 |                 ,0,0,0,0
      |                 }{
  142 |                 ,0.258195131,-0.70438632,0.249934344,-0.143236405
      |                 }{
  143 |                 ,0.502914193,-0.060347902,0.241428373,0.582415494
      |                 }{
  144 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  145 |                 ,0.584083861,0.258975454,0.524430101,0.846496194
      |                 -
      |                 }},{{
  146 |                 ,0.968040559,0.797499702,0.730184613,1.270687029
      |                 }{
  147 |                 ,0,0,0,0
      |                 }{
  148 |                 ,1.081040749,0.969784756,0.84547091,1.254355018
      |                 }{
  149 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  150 |                 ,1.048553951,0.728354541,0.894838095,0.882097231
      |                 -
      |                 }},{{
  151 |                 ,0.88611252,0.258975454,0.318907854,0.746214538
      |                 }{
  152 |                 ,0.239520858,-0.469855984,0.101248351,0.18553379
      |                 }{
  153 |                 ,0,0,0,0
      |                 }{
  154 |                 ,0.68,0.46,0.55,0.65
      |                 }{
  155 |                 ,0.68,0.46,0.55,0.65
      |                 -
      |                 }},{{
  156 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  157 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  158 |                 ,0.68,0.46,0.55,0.65
      |                 }{
  159 |                 ,0,0,0,0
      |                 }{
  160 |                 ,0,0,0,0
      |                 -
      |                 }}},{{{
  161 |                 ,1.566899704,1.081040749,1.45897431,1.443665704
      |                 }{
  162 |                 ,0.976725675,0.502914193,0.871921533,0.851622883
      |                 }{
  163 |                 ,1.482046826,0.782168488,0.99945386,1.203555051
      |                 }{
  164 |                 ,0.85,0.68,0.65,0.76
      |                 }{
  165 |                 ,0.798628781,0.239520858,0.503209827,0.766581547
      |                 -
      |                 }},{{
  166 |                 ,0,0,0,0
      |                 }{
  167 |                 ,1.141098246,0.258195131,1.0651638,0.856582783
      |                 }{
  168 |                 ,0.976725675,0.565895968,0.755889609,1.150635633
      |                 }{
  169 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  170 |                 ,1.125403302,0.88611252,0.911428974,1.496720812
      |                 -
      |                 }},{{
  171 |                 ,1.68169282,0.968040559,1.099899195,1.822113278
      |                 }{
  172 |                 ,0,0,0,0
      |                 }{
  173 |                 ,1.566899704,1.100661785,1.295827995,1.545032445
      |                 }{
  174 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  175 |                 ,1.35948517,1.048553951,1.242135174,1.478009492
      |                 -
      |                 }},{{
  176 |                 ,1.125403302,0.584083861,1.07531714,1.231861002
      |                 }{
  177 |                 ,0.798628781,0.468913405,0.843147406,0.630005348
      |                 }{
  178 |                 ,0,0,0,0
      |                 }{
  179 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  180 |                 ,0.85,0.68,0.65,0.75
      |                 -
      |                 }},{{
  181 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  182 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  183 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  184 |                 ,0,0,0,0
      |                 }{
  185 |         };
      |         }}}
DesignProbes.c: In function 'designProbes._omp_fn.0':
DesignProbes.c:836:77: warning: 'lastCycle' may be used uninitialized [-Wmaybe-uninitialized]
  836 |                                                                 cycles += 4 + lastCycle - thisCycle;
      |                                                                           ~~^~~~~~~~~~~
DesignProbes.c:267:58: note: 'lastCycle' was declared here
  267 |                         int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                                          ^~~~~~~~~
DesignProbes.c:834:85: warning: 'thisCycle' may be used uninitialized [-Wmaybe-uninitialized]
  834 |                                                                 cycles += lastCycle - thisCycle;
      |                                                                           ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:69: note: 'thisCycle' was declared here
  267 |                         int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                                                     ^~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Diff.c -o Diff.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'firstSeqsPosEqual':
DistanceMatrix.c:756:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  756 |                 if (!ci)
      |                 ^~
DistanceMatrix.c:759:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  759 |                         while (i < ex) {
      |                         ^~~~~
DistanceMatrix.c:778:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  778 |                 if (!cj)
      |                 ^~
DistanceMatrix.c:781:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  781 |                         while (j < ey) {
      |                         ^~~~~
DistanceMatrix.c: In function 'similarities._omp_fn.0':
DistanceMatrix.c:995:45: warning: 'OV' may be used uninitialized [-Wmaybe-uninitialized]
  995 |                                 (double)(OV + g)/(double)w1 < coverage &&
      |                                         ~~~~^~~~
DistanceMatrix.c:843:45: note: 'OV' was declared here
  843 |         int i, j, n, s, p1, p2, t1, t2, ov, OV, g1, g2, g, o, count, *r;
      |                                             ^~
DistanceMatrix.c:1015:82: warning: 'ov' may be used uninitialized [-Wmaybe-uninitialized]
 1015 |                                                 rans[i] = (double)s/((double)(ov + count + g2));
      |                                                                               ~~~^~~~~~~
DistanceMatrix.c:843:41: note: 'ov' was declared here
  843 |         int i, j, n, s, p1, p2, t1, t2, ov, OV, g1, g2, g, o, count, *r;
      |                                         ^~
DistanceMatrix.c:1000:44: warning: 'o' may be used uninitialized [-Wmaybe-uninitialized]
 1000 |                                         if (o == 1) {
      |                                            ^
DistanceMatrix.c:843:60: note: 'o' was declared here
  843 |         int i, j, n, s, p1, p2, t1, t2, ov, OV, g1, g2, g, o, count, *r;
      |                                                            ^
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function 'pop':
EnumerateSequence.c:315:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
  315 |         x = x + (x >> 4) & 0xF0F0F0F;
      |             ~~^~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function 'findFrameshifts':
FindFrameshifts.c:381:35: warning: 'K' may be used uninitialized [-Wmaybe-uninitialized]
  381 |                         } else if (k==2) {
      |                                   ^
FindFrameshifts.c:135:34: note: 'K' was declared here
  135 |         int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
      |                                  ^
FindFrameshifts.c:317:43: warning: 'J' may be used uninitialized [-Wmaybe-uninitialized]
  317 |                         while (i > 0 && j > 0) {
      |                                         ~~^~~
FindFrameshifts.c:135:31: note: 'J' was declared here
  135 |         int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
      |                               ^
FindFrameshifts.c:317:34: warning: 'I' may be used uninitialized [-Wmaybe-uninitialized]
  317 |                         while (i > 0 && j > 0) {
      |                                ~~^~~
FindFrameshifts.c:135:28: note: 'I' was declared here
  135 |         int s, o, i, j, k, I, J, K, n, m, w, r, c, rc;
      |                            ^
In file included from F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41,
                 from FindFrameshifts.c:11:
F:/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:897:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized]
  897 | #define eval                    Rf_eval
      |                                 ^~~~~~~
FindFrameshifts.c:162:31: note: 'utilsPackage' was declared here
  162 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:897:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized]
  897 | #define eval                    Rf_eval
      |                                 ^~~~~~~
FindFrameshifts.c:162:14: note: 'percentComplete' was declared here
  162 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
FindFrameshifts.c:468:40: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized]
  468 |                                 before = *rPercentComplete;
      |                                 ~~~~~~~^~~~~~~~~~~~~~~~~~~
FindFrameshifts.c:160:25: note: 'rPercentComplete' was declared here
  160 |         int before, v, *rPercentComplete;
      |                         ^~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function 'scoreCodonModel':
GeneFinding.c:431:57: warning: 'lastVal' may be used uninitialized [-Wmaybe-uninitialized]
  431 |                                 if (val < 64 && lastVal < 64)
      |                                                 ~~~~~~~~^~~~
GeneFinding.c:371:32: note: 'lastVal' was declared here
  371 |         int i, j, s, fin, val, lastVal, dicodon;
      |                                ^~~~~~~
GeneFinding.c:421:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
  421 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:388:22: note: 'x_i.ptr' was declared here
  388 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'startCodonModel':
GeneFinding.c:791:48: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
  791 |                         val = getBaseRC(x_i.ptr[j++]);
      |                                                ^
GeneFinding.c:771:22: note: 'x_i.ptr' was declared here
  771 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreStartCodonModel':
GeneFinding.c:892:48: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
  892 |                         val = getBaseRC(x_i.ptr[j++]);
      |                                                ^
GeneFinding.c:868:22: note: 'x_i.ptr' was declared here
  868 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'initialCodonModel':
GeneFinding.c:972:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
  972 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:928:22: note: 'x_i.ptr' was declared here
  928 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreInitialCodonModel':
GeneFinding.c:1058:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1058 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1031:22: note: 'x_i.ptr' was declared here
 1031 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'terminationCodonModel':
GeneFinding.c:1130:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1130 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1092:22: note: 'x_i.ptr' was declared here
 1092 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreTerminationCodonModel':
GeneFinding.c:1215:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1215 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1188:22: note: 'x_i.ptr' was declared here
 1188 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'getRegion':
GeneFinding.c:1285:35: warning: 'x_i.length' may be used uninitialized [-Wmaybe-uninitialized]
 1285 |                         if ((s==1 && j < x_i.length && j - w + 1 >= 0) ||
      |                              ~~~~~^~~~~~~~~~~~~~~~~
GeneFinding.c:1252:22: note: 'x_i.length' was declared here
 1252 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c:1289:81: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1289 |                                                 seq[k] = getBaseLetterRC(x_i.ptr[j--]);
      |                                                                                 ^
GeneFinding.c:1252:22: note: 'x_i.ptr' was declared here
 1252 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'autocorrelationModel':
GeneFinding.c:1378:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1378 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1350:22: note: 'x_i.ptr' was declared here
 1350 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreAutocorrelationModel':
GeneFinding.c:1495:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1495 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1461:22: note: 'x_i.ptr' was declared here
 1461 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'couplingModel':
GeneFinding.c:1597:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1597 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1573:22: note: 'x_i.ptr' was declared here
 1573 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreCouplingModel':
GeneFinding.c:1711:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1711 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1681:22: note: 'x_i.ptr' was declared here
 1681 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'nucleotideBiasModel':
GeneFinding.c:1826:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1826 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1788:22: note: 'x_i.ptr' was declared here
 1788 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreNucleotideBiasModel':
GeneFinding.c:1913:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1913 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1882:22: note: 'x_i.ptr' was declared here
 1882 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'upstreamMotifModel':
GeneFinding.c:1990:77: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 1990 |                                         val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
      |                                                                             ^
GeneFinding.c:1950:22: note: 'x_i.ptr' was declared here
 1950 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreUpstreamMotifModel':
GeneFinding.c:2090:77: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 2090 |                                         val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
      |                                                                             ^
GeneFinding.c:2057:22: note: 'x_i.ptr' was declared here
 2057 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreRunLengthModel':
GeneFinding.c:2307:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 2307 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:2276:22: note: 'x_i.ptr' was declared here
 2276 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'stopCodonModel':
GeneFinding.c:2419:48: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 2419 |                         val = getBaseRC(x_i.ptr[j++]);
      |                                                ^
GeneFinding.c:2399:22: note: 'x_i.ptr' was declared here
 2399 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'scoreStopCodonModel':
GeneFinding.c:2520:48: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 2520 |                         val = getBaseRC(x_i.ptr[j++]);
      |                                                ^
GeneFinding.c:2496:22: note: 'x_i.ptr' was declared here
 2496 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function 'codonFrequencies':
GeneFinding.c:2577:56: warning: 'x_i.ptr' may be used uninitialized [-Wmaybe-uninitialized]
 2577 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:2554:22: note: 'x_i.ptr' was declared here
 2554 |         Chars_holder x_i;
      |                      ^~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GetPools.c -o GetPools.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Import.c -o Import.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c InformationContent.c -o InformationContent.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c InsertGaps.c -o InsertGaps.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IntDist.c -o IntDist.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function 'meltPolymer':
MeltPolymer.c:79:27: warning: missing braces around initializer [-Wmissing-braces]
   79 |         double dH[4][4] = {
      |                           ^
   80 |                 -7.9,-8.4,-7.8,-7.2
      |                 {
   81 |                 ,-8.5,-8.0,-10.6,-7.8
      |                 }{
   82 |                 ,-8.2,-9.8,-8.0,-8.4
      |                 }{
   83 |                 ,-7.2,-8.2,-8.5,-7.9
      |                 }{
   84 |         };
      |         }
MeltPolymer.c:88:27: warning: missing braces around initializer [-Wmissing-braces]
   88 |         double dS[4][4] = {
      |                           ^
   89 |                 -22.2,-22.4,-21.0,-20.4
      |                 {
   90 |                 ,-22.7,-19.9,-27.2,-21.0
      |                 }{
   91 |                 ,-22.2,-24.4,-19.9,-22.4
      |                 }{
   92 |                 ,-21.3,-22.2,-22.7,-22.2
      |                 }{
   93 |         };
      |         }
MeltPolymer.c:54:17: warning: 'rans' may be used uninitialized [-Wmaybe-uninitialized]
   54 |         double *rans;
      |                 ^~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c MovingAverage.c -o MovingAverage.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function 'intMatchSelfOnce':
MultiMatch.c:871:28: warning: variable 'start' set but not used [-Wunused-but-set-variable]
  871 |         int i, j, k, temp, start = 0;
      |                            ^~~~~
MultiMatch.c: In function 'matchOverlap._omp_fn.0':
MultiMatch.c:1033:45: warning: 'one' may be used uninitialized [-Wmaybe-uninitialized]
 1033 |                                         two != one) {
      |                                         ~~~~^~~~~~
MultiMatch.c:1008:21: note: 'one' was declared here
 1008 |                 int one, two;
      |                     ^~~
In file included from F:/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41,
                 from MultiMatch.c:11:
F:/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h: In function 'matchLists':
F:/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:897:33: warning: 'utilsPackage' may be used uninitialized [-Wmaybe-uninitialized]
  897 | #define eval                    Rf_eval
      |                                 ^~~~~~~
MultiMatch.c:247:31: note: 'utilsPackage' was declared here
  247 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
F:/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:897:33: warning: 'percentComplete' may be used uninitialized [-Wmaybe-uninitialized]
  897 | #define eval                    Rf_eval
      |                                 ^~~~~~~
MultiMatch.c:247:14: note: 'percentComplete' was declared here
  247 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
MultiMatch.c:330:40: warning: 'rPercentComplete' may be used uninitialized [-Wmaybe-uninitialized]
  330 |                                 before = *rPercentComplete;
      |                                 ~~~~~~~^~~~~~~~~~~~~~~~~~~
MultiMatch.c:242:51: note: 'rPercentComplete' was declared here
  242 |         int i, j, size_x = length(x), before, v, *rPercentComplete;
      |                                                   ^~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c NNLS.c -o NNLS.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Order.c -o Order.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c: In function 'alignPair._omp_fn.0':
PairwiseAlignment.c:469:39: warning: 'p2' may be used uninitialized [-Wmaybe-uninitialized]
  469 |                                 P2[i] = p2;
      |                                 ~~~~~~^~~~
PairwiseAlignment.c:173:19: note: 'p2' was declared here
  173 |         int *p1, *p2, *p3, *p4;
      |                   ^~
PairwiseAlignment.c:468:39: warning: 'p1' may be used uninitialized [-Wmaybe-uninitialized]
  468 |                                 P1[i] = p1;
      |                                 ~~~~~~^~~~
PairwiseAlignment.c:173:14: note: 'p1' was declared here
  173 |         int *p1, *p2, *p3, *p4;
      |              ^~
PairwiseAlignment.c:473:39: warning: 'p4' may be used uninitialized [-Wmaybe-uninitialized]
  473 |                                 P4[i] = p4;
      |                                 ~~~~~~^~~~
PairwiseAlignment.c:173:29: note: 'p4' was declared here
  173 |         int *p1, *p2, *p3, *p4;
      |                             ^~
PairwiseAlignment.c:472:39: warning: 'p3' may be used uninitialized [-Wmaybe-uninitialized]
  472 |                                 P3[i] = p3;
      |                                 ~~~~~~^~~~
PairwiseAlignment.c:173:24: note: 'p3' was declared here
  173 |         int *p1, *p2, *p3, *p4;
      |                        ^~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c PredictDBN.c -o PredictDBN.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function 'predictHEC':
PredictHEC.c:255:25: warning: 'ans' may be used uninitialized [-Wmaybe-uninitialized]
  255 |                         SET_VECTOR_ELT(ret, i, ans);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:49:19: note: 'ans' was declared here
   49 |         SEXP ret, ans;
      |                   ^~~
PredictHEC.c:233:51: warning: 'states' may be used uninitialized [-Wmaybe-uninitialized]
  233 |                                         states[j] = 'C';
      |                                         ~~~~~~~~~~^~~~~
PredictHEC.c:42:15: note: 'states' was declared here
   42 |         char *states;
      |               ^~~~~~
PredictHEC.c:236:40: warning: 'rans' may be used uninitialized [-Wmaybe-uninitialized]
  236 |                                 *(rans + 3*j) = H;
      |                                  ~~~~~~^~~~~~
PredictHEC.c:41:31: note: 'rans' was declared here
   41 |         double H, E, C, sum, *rans;
      |                               ^~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_decipher.c -o R_init_decipher.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RemoveGaps.c -o RemoveGaps.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ReplaceChars.c -o ReplaceChars.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c SphericalKmeans.c -o SphericalKmeans.o
SphericalKmeans.c: In function 'sphericalKmeans':
SphericalKmeans.c:117:25: warning: 'b' may be used uninitialized [-Wmaybe-uninitialized]
  117 |                         free(b);
      |                         ^~~~~~~
SphericalKmeans.c:40:17: note: 'b' was declared here
   40 |         double *b, *c; // previous and current centers
      |                 ^
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c TerminalMismatch.c -o TerminalMismatch.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Translate.c -o Translate.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c VectorSums.c -o VectorSums.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/XVector/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
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 ClusterMP.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 PairwiseAlignment.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o SphericalKmeans.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-DECIPHER/00new/DECIPHER/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DECIPHER)

Tests output

Example timings

DECIPHER.Rcheck/DECIPHER-Ex.timings

nameusersystemelapsed
AA_REDUCED0.040.000.03
Add2DB0.320.000.33
AdjustAlignment0.170.000.17
AlignDB1.220.061.28
AlignProfiles0.690.060.75
AlignSeqs22.87 4.3627.24
AlignSynteny2.300.172.46
AlignTranslation11.03 1.1112.18
AmplifyDNA0.000.020.01
Array2Matrix5.390.015.41
BrowseDB0.020.000.01
BrowseSeqs47.25 1.4449.22
CalculateEfficiencyArray0.010.000.02
CalculateEfficiencyFISH000
CalculateEfficiencyPCR0.020.000.01
Clusterize4.610.114.72
Codec0.930.000.94
ConsensusSequence0.220.010.23
Cophenetic0.190.000.19
CorrectFrameshifts15.33 3.6619.02
CreateChimeras0.530.000.53
DB2Seqs0.020.000.01
DesignArray5.640.005.64
DesignPrimers000
DesignProbes000
DesignSignatures000
DetectRepeats8.680.559.24
DigestDNA0.130.000.13
Disambiguate0.030.000.03
DistanceMatrix0.030.000.03
ExtractGenes44.58 0.8445.80
FindChimeras0.050.000.04
FindGenes40.67 0.8041.52
FindNonCoding39.94 2.9842.92
FindSynteny101
FormGroups0.010.020.03
Genes-class42.62 0.9543.59
HEC_MI0.250.000.25
IdConsensus0.530.050.58
IdLengths0.020.000.01
IdTaxa 9.84 0.2910.14
IdentifyByRank0.030.000.03
LearnNonCoding37.19 2.4339.66
LearnTaxa5.920.826.75
MIQS0.030.010.05
MODELS000
MapCharacters73.65 1.8875.51
MaskAlignment0.480.000.49
MeltDNA0.030.000.03
NNLS000
NonCoding-class0.050.010.06
NonCodingRNA0.110.020.12
OrientNucleotides0.700.000.71
PFASUM0.020.010.03
PredictDBN94.79 0.3896.47
PredictHEC0.220.000.22
RESTRICTION_ENZYMES000
ReadDendrogram0.060.000.08
RemoveGaps000
ScoreAlignment4.750.515.27
SearchDB0.040.000.03
Seqs2DB0.070.020.09
StaggerAlignment11.19 2.0113.22
Synteny-class1.580.021.59
Taxa-class10.47 0.1710.64
TerminalChar000
TileSeqs3.000.033.04
TrainingSet_16S1.440.051.49
TreeLine7.390.457.84
TrimDNA0.130.000.13
WriteDendrogram000
WriteGenes42.50 0.6643.15
deltaGrules0.010.000.02
deltaHrules0.020.000.01
deltaHrulesRNA0.010.000.02
deltaSrules0.050.020.06
deltaSrulesRNA0.020.000.02