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This page was generated on 2025-09-22 12:03 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 527/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 3.5.0  (landing page)
Erik Wright
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 Sep 2025)
git_url: https://git.bioconductor.org/packages/DECIPHER
git_branch: devel
git_last_commit: f5796e8
git_last_commit_date: 2025-04-15 10:10:51 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for DECIPHER on nebbiolo2

To the developers/maintainers of the DECIPHER package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: DECIPHER
Version: 3.5.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DECIPHER_3.5.0.tar.gz
StartedAt: 2025-09-21 22:54:55 -0400 (Sun, 21 Sep 2025)
EndedAt: 2025-09-21 23:34:56 -0400 (Sun, 21 Sep 2025)
EllapsedTime: 2400.8 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: DECIPHER.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DECIPHER_3.5.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DECIPHER.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘3.5.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    data      7.5Mb
    extdata   2.8Mb
    libs      1.6Mb
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AlignSeqs: no visible binding for global variable ‘deltaGrulesRNA’
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 ‘deltaGrulesRNA’
Treeline: multiple local function definitions for ‘.NNI’ with different
  formal arguments
Treeline: multiple local function definitions for ‘.minimize’ with
  different formal arguments
Undefined global functions or variables:
  deltaGrulesRNA 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
AlignSeqs          250.960  2.588 304.003
LearnNonCoding     124.725  5.684 134.829
FindNonCoding       62.370  0.611  63.732
Treeline            60.929  0.320  62.395
InferSelection      47.742  0.195  57.173
ExtractGenes        39.950  0.599  41.906
FindGenes           39.838  0.235  40.311
Genes-class         39.847  0.050  40.280
BrowseSeqs          34.717  0.201  44.378
WriteGenes          34.155  0.438  34.593
InferRecombination  26.258  0.116  27.608
DistanceMatrix      24.905  0.456  26.166
CorrectFrameshifts  21.002  0.352  29.399
AlignTranslation    14.836  0.117  16.717
DetectRepeats       12.450  0.317  15.073
StaggerAlignment    11.437  0.078  11.518
IdTaxa              10.322  0.025  10.539
Taxa-class          10.001  0.061  10.063
TrimDNA              9.708  0.097   9.806
Clusterize           9.415  0.058  10.616
InferDemography      8.758  0.022   8.782
LearnTaxa            7.237  0.707   7.945
Array2Matrix         7.349  0.091  12.091
DesignArray          6.858  0.152   8.763
AlignPairs           6.469  0.198   7.325
ScoreAlignment       5.783  0.091   5.875
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ...

Installation output

DECIPHER.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘DECIPHER’ ...
** this is package ‘DECIPHER’ version ‘3.5.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’:
AlignProfiles.c:438:37: warning: ‘lGs’ may be used uninitialized [-Wmaybe-uninitialized]
  438 |                                 lGs *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:62:51: note: ‘lGs’ was declared here
   62 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
      |                                                   ^~~
AlignProfiles.c:436:37: warning: ‘lGp’ may be used uninitialized [-Wmaybe-uninitialized]
  436 |                                 lGp *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:62:46: note: ‘lGp’ was declared here
   62 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
      |                                              ^~~
AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’:
AlignProfiles.c:1291:37: warning: ‘lGs’ may be used uninitialized [-Wmaybe-uninitialized]
 1291 |                                 lGs *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:820:51: note: ‘lGs’ was declared here
  820 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
      |                                                   ^~~
AlignProfiles.c:1289:37: warning: ‘lGp’ may be used uninitialized [-Wmaybe-uninitialized]
 1289 |                                 lGp *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:820:46: note: ‘lGp’ was declared here
  820 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
      |                                              ^~~
AlignProfiles.c: In function ‘alignProfiles’:
AlignProfiles.c:389:25: warning: ‘subM’ may be used uninitialized [-Wmaybe-uninitialized]
  389 |                 #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:82:17: note: ‘subM’ was declared here
   82 |         double *subM;
      |                 ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c AssignIndels.c -o AssignIndels.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function ‘calculateHairpinDeltaG’:
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;
      |                             ^~
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;
      |                                 ^~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c ChainSegments.c -o ChainSegments.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c Cluster.c -o Cluster.o
Cluster.c: In function ‘cluster._omp_fn.0’:
Cluster.c:439:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized]
  439 |                                                 minCols[rowIndices[i]] = minC;
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:57: note: ‘minC’ was declared here
  246 |         int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                         ^~~~
Cluster.c: In function ‘cluster._omp_fn.1’:
Cluster.c:469:50: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized]
  469 |                                         minCs[i] = minC;
      |                                         ~~~~~~~~~^~~~~~
Cluster.c:246:57: note: ‘minC’ was declared here
  246 |         int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                         ^~~~
Cluster.c: In function ‘cluster._omp_fn.2’:
Cluster.c:493:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized]
  493 |                                                 minCols[rowIndices[i]] = minC;
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:57: note: ‘minC’ was declared here
  246 |         int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                         ^~~~
Cluster.c: In function ‘cluster’:
Cluster.c:848:44: warning: ‘minCols’ may be used uninitialized [-Wmaybe-uninitialized]
  848 |                                 if (minCols[rowIndices[i]] == (minRow + 1)) {
      |                                            ^
Cluster.c:277:14: note: ‘minCols’ was declared here
  277 |         int *minCols;
      |              ^~~~~~~
Cluster.c:459:41: warning: ‘nDiv’ may be used uninitialized [-Wmaybe-uninitialized]
  459 |                                 #pragma omp parallel for private(i,j,minC,minH) schedule(guided) num_threads(nthreads)
      |                                         ^~~
Cluster.c:283:17: note: ‘nDiv’ was declared here
  283 |         double *nDiv;
      |                 ^~~~
Cluster.c:413:72: warning: ‘minC’ may be used uninitialized [-Wmaybe-uninitialized]
  413 |                                                 minCols[rowIndices[i]] = minC;
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:57: note: ‘minC’ was declared here
  246 |         int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                         ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c ClusterME.c -o ClusterME.o
ClusterME.c: In function ‘clusterME’:
ClusterME.c:322:101: warning: ‘LLRL’ may be used uninitialized [-Wmaybe-uninitialized]
  322 |                                                         subDists[C[i + j*n] + 3*(n - 1) - 1] = LLRL + LRRL; // ac
      |                                                                                                ~~~~~^~~~~~
ClusterME.c:284:24: note: ‘LLRL’ was declared here
  284 |                 double LLRL, LRRL, LLRR, LRRR;
      |                        ^~~~
ClusterME.c:322:101: warning: ‘LRRL’ may be used uninitialized [-Wmaybe-uninitialized]
  322 |                                                         subDists[C[i + j*n] + 3*(n - 1) - 1] = LLRL + LRRL; // ac
      |                                                                                                ~~~~~^~~~~~
ClusterME.c:284:30: note: ‘LRRL’ was declared here
  284 |                 double LLRL, LRRL, LLRR, LRRR;
      |                              ^~~~
ClusterME.c:323:101: warning: ‘LLRR’ may be used uninitialized [-Wmaybe-uninitialized]
  323 |                                                         subDists[C[i + j*n] + 4*(n - 1) - 1] = LLRR + LRRR; // bc
      |                                                                                                ~~~~~^~~~~~
ClusterME.c:284:36: note: ‘LLRR’ was declared here
  284 |                 double LLRL, LRRL, LLRR, LRRR;
      |                                    ^~~~
ClusterME.c:323:101: warning: ‘LRRR’ may be used uninitialized [-Wmaybe-uninitialized]
  323 |                                                         subDists[C[i + j*n] + 4*(n - 1) - 1] = LLRR + LRRR; // bc
      |                                                                                                ~~~~~^~~~~~
ClusterME.c:284:42: note: ‘LRRR’ was declared here
  284 |                 double LLRL, LRRL, LLRR, LRRR;
      |                                          ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c ClusterML.c -o ClusterML.o
ClusterML.c: In function ‘clusterML’:
ClusterML.c:2045:17: warning: ‘node’ may be used uninitialized [-Wmaybe-uninitialized]
 2045 |         #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
      |                 ^~~
ClusterML.c:1913:17: note: ‘node’ was declared here
 1913 |         double *node;
      |                 ^~~~
ClusterML.c:2045:17: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized]
 2045 |         #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
      |                 ^~~
ClusterML.c:1959:14: note: ‘Up’ was declared here
 1959 |         int *Up;
      |              ^~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c ClusterMP.c -o ClusterMP.o
ClusterMP.c: In function ‘clusterMP._omp_fn.0’:
ClusterMP.c:190:71: warning: ‘temp_nodes’ may be used uninitialized [-Wmaybe-uninitialized]
  190 |                                                         temp_nodes[j] = 0;
      |                                                         ~~~~~~~~~~~~~~^~~
ClusterMP.c:163:34: note: ‘temp_nodes’ was declared here
  163 |                 int *temp_subM, *temp_nodes;
      |                                  ^~~~~~~~~~
ClusterMP.c:465:49: warning: ‘temp_lengths’ may be used uninitialized [-Wmaybe-uninitialized]
  465 |                                                 *(temp_lengths + j) += *(S + w*c + m)*weight;
      |                                                 ^~~~~~~~~~~~~~~~~~~
ClusterMP.c:162:38: note: ‘temp_lengths’ was declared here
  162 |                 double *temp_score, *temp_lengths;
      |                                      ^~~~~~~~~~~~
ClusterMP.c:485:73: warning: ‘temp_subM’ may be used uninitialized [-Wmaybe-uninitialized]
  485 |                                                                         *(temp_subM + c*m + w - 1) += weight;
      |                                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~
ClusterMP.c:163:22: note: ‘temp_subM’ was declared here
  163 |                 int *temp_subM, *temp_nodes;
      |                      ^~~~~~~~~
ClusterMP.c:202:49: warning: ‘P’ may be used uninitialized [-Wmaybe-uninitialized]
  202 |                                                 allStates(R, P, S, c, j, 0, k - 1, 0, k - 1, c, only);
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ClusterMP.c:185:38: note: ‘P’ was declared here
  185 |                                 int *P;
      |                                      ^
ClusterMP.c:385:61: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized]
  385 |                                                 *(R + 3*c*n + m) = 0;
      |                                                             ^
ClusterMP.c:105:22: note: ‘m’ was declared here
  105 |         int i, j, k, m, w;
      |                      ^
ClusterMP.c: In function ‘clusterMP’:
ClusterMP.c:159:17: warning: ‘lengths’ may be used uninitialized [-Wmaybe-uninitialized]
  159 |         #pragma omp parallel num_threads(nthreads)
      |                 ^~~
ClusterMP.c:128:17: note: ‘lengths’ was declared here
  128 |         double *lengths, *score;
      |                 ^~~~~~~
ClusterMP.c:159:17: warning: ‘nodes’ may be used uninitialized [-Wmaybe-uninitialized]
  159 |         #pragma omp parallel num_threads(nthreads)
      |                 ^~~
ClusterMP.c:129:20: note: ‘nodes’ was declared here
  129 |         int size, *nodes, *subM;
      |                    ^~~~~
ClusterMP.c:159:17: warning: ‘subM’ may be used uninitialized [-Wmaybe-uninitialized]
  159 |         #pragma omp parallel num_threads(nthreads)
      |                 ^~~
ClusterMP.c:129:28: note: ‘subM’ was declared here
  129 |         int size, *nodes, *subM;
      |                            ^~~~
ClusterMP.c:159:17: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized]
  159 |         #pragma omp parallel num_threads(nthreads)
      |                 ^~~
ClusterMP.c:145:14: note: ‘Up’ was declared here
  145 |         int *Up;
      |              ^~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c Compositions.c -o Compositions.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c Compression.c -o Compression.o
Compression.c: In function ‘nbit._omp_fn.0’:
Compression.c:1328:25: warning: ‘dict’ may be used uninitialized [-Wmaybe-uninitialized]
 1328 |                         free(dict);
      |                         ^~~~~~~~~~
Compression.c:545:31: note: ‘dict’ was declared here
  545 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                               ^~~~
Compression.c:1242:71: warning: ‘lastTriplet’ may be used uninitialized [-Wmaybe-uninitialized]
 1242 |                                 if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
      |                                                                    ~~~^~~~~~~~~~~~~~
Compression.c:632:26: note: ‘lastTriplet’ was declared here
  632 |                 int run, lastTriplet, lastCase;
      |                          ^~~~~~~~~~~
Compression.c:1012:62: warning: ‘word’ may be used uninitialized [-Wmaybe-uninitialized]
 1012 |                                                 word = (word << 8) | (unsigned int)reorder(byte);
      |                                                        ~~~~~~^~~~~
Compression.c:545:37: note: ‘word’ was declared here
  545 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                                     ^~~~
Compression.c:1013:54: warning: ‘count’ may be used uninitialized [-Wmaybe-uninitialized]
 1013 |                                                 count++;
      |                                                 ~~~~~^~
Compression.c:545:43: note: ‘count’ was declared here
  545 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                                           ^~~~~
Compression.c:546:41: warning: ‘rev’ may be used uninitialized [-Wmaybe-uninitialized]
  546 |                 int lastTemp, currTemp, rev, len, len2, thresh = 1;
      |                                         ^~~
Compression.c:1216:58: warning: ‘lastHit’ may be used uninitialized [-Wmaybe-uninitialized]
 1216 |                                                 p[c++] = (unsigned char)lastHit;
      |                                                          ^~~~~~~~~~~~~~~~~~~~~~
Compression.c:545:50: note: ‘lastHit’ was declared here
  545 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                                                  ^~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c ConsensusSequence.c -o ConsensusSequence.o
In function ‘runsAA’,
    inlined from ‘consensusProfileAA’ at ConsensusSequence.c:1836:3:
ConsensusSequence.c:454:50: warning: ‘lastPos’ may be used uninitialized [-Wmaybe-uninitialized]
  454 |                                 if (lastGap < (s - 2)) // ensure continuity before the run
      |                                               ~~~^~~~
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: In function ‘colScores’:
ConsensusSequence.c:1940:17: warning: ‘DBN’ may be used uninitialized [-Wmaybe-uninitialized]
 1940 |         double *DBN, *s;
      |                 ^~~
ConsensusSequence.c:1941:27: warning: ‘d’ may be used uninitialized [-Wmaybe-uninitialized]
 1941 |         int do_DBN, n, l, d;
      |                           ^
ConsensusSequence.c:2043:19: warning: ‘curr’ may be used uninitialized [-Wmaybe-uninitialized]
 2043 |         if (tGaps && curr > 0) {
      |             ~~~~~~^~~~~~~~~~~
ConsensusSequence.c:1930:37: note: ‘curr’ was declared here
 1930 |         double weight, total, prev, curr;
      |                                     ^~~~
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2083:17: warning: ‘HEC’ may be used uninitialized [-Wmaybe-uninitialized]
 2083 |         double *HEC, *s;
      |                 ^~~
ConsensusSequence.c:2084:27: warning: ‘d’ may be used uninitialized [-Wmaybe-uninitialized]
 2084 |         int do_HEC, n, l, d;
      |                           ^
ConsensusSequence.c:2186:19: warning: ‘curr’ may be used uninitialized [-Wmaybe-uninitialized]
 2186 |         if (tGaps && curr > 0) {
      |             ~~~~~~^~~~~~~~~~~
ConsensusSequence.c:2073:37: note: ‘curr’ was declared here
 2073 |         double weight, total, prev, curr;
      |                                     ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:71:27: warning: missing braces around initializer [-Wmissing-braces]
   71 |         double NN[4][4] = {
      |                           ^
   72 |                 -0.816507461,-2.5401714,-1.647430026,-1.184658548
      |                 {
   73 |                 ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
      |                 }{
   74 |                 ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
      |                 }{
   75 |                 ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
      |                 }{
   76 |         };
      |         }
DesignProbes.c:78:27: warning: missing braces around initializer [-Wmissing-braces]
   78 |         double PM[4][4] = {
      |                           ^
   79 |                 -0.141370102,-0.439805276,-0.285236035,-0.205111781
      |                 {
   80 |                 ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
      |                 }{
   81 |                 ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
      |                 }{
   82 |                 ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
      |                 }{
   83 |         };
      |         }
DesignProbes.c:85:34: warning: missing braces around initializer [-Wmissing-braces]
   85 |         double sMM[4][5][5][4] = {
      |                                  ^
   86 |                 0,0,0,0
      |                 {{{
   87 |                 ,1.545032445,1.254355018,1.491691514,1.329138183
      |                 }{
   88 |                 ,1.150635633,0.582415494,1.075877275,1.187937642
      |                 }{
   89 |                 ,1.203555051,1.001540513,0.864287715,0.717125848
      |                 }{
   90 |                 ,0.75,0.65,0.69,0.78
      |                 }{
   91 |                 ,0.630005348,0.18553379,0.730763505,0.709272397
      |                 -
      |                 }},{{
   92 |                 ,0,0,0,0
      |                 }{
   93 |                 ,0.856582783,-0.143236405,0.716721488,0.603652831
      |                 }{
   94 |                 ,0.851622883,0.653168672,0.676545316,1.187937642
      |                 }{
   95 |                 ,0.75,0.65,0.69,0.78
      |                 }{
   96 |                 ,1.231861002,0.746214538,1.087821916,0.989140748
      |                 -
      |                 }},{{
   97 |                 ,1.822113278,1.270687029,1.336192565,1.364584949
      |                 }{
   98 |                 ,0,0,0,0
      |                 }{
   99 |                 ,1.443665704,1.385046493,1.256013166,1.329138183
      |                 }{
  100 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  101 |                 ,1.478009492,0.882097231,1.20450984,1.061002478
      |                 -
      |                 }},{{
  102 |                 ,1.496720812,0.846496194,0.967868114,0.989140748
      |                 }{
  103 |                 ,0.766581547,-0.024857805,0.50754303,0.709272397
      |                 }{
  104 |                 ,0,0,0,0
      |                 }{
  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 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  109 |                 ,0.76,0.65,0.69,0.78
      |                 }{
  110 |                 ,0,0,0,0
      |                 }{
  111 |                 ,0,0,0,0
      |                 -
      |                 }}},{{{
  112 |                 ,1.295827995,0.84547091,0.91019099,1.256013166
      |                 }{
  113 |                 ,0.755889609,0.241428373,0.396379912,0.676545316
      |                 }{
  114 |                 ,0.99945386,0.740323132,0.435659206,0.864287715
      |                 }{
  115 |                 ,0.65,0.55,0.48,0.69
      |                 }{
  116 |                 ,0.843147406,0.101248351,0.49063599,0.50754303
      |                 -
      |                 }},{{
  117 |                 ,0,0,0,0
      |                 }{
  118 |                 ,1.0651638,0.249934344,0.699352949,0.716721488
      |                 }{
  119 |                 ,0.871921533,0.59458138,0.396379912,1.075877275
      |                 }{
  120 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  121 |                 ,1.07531714,0.318907854,0.653287717,0.967868114
      |                 -
      |                 }},{{
  122 |                 ,1.099899195,0.730184613,0.661798984,1.336192565
      |                 }{
  123 |                 ,0,0,0,0
      |                 }{
  124 |                 ,1.45897431,1.318532145,0.91019099,1.491691514
      |                 }{
  125 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  126 |                 ,1.242135174,0.894838095,1.108555445,1.20450984
      |                 -
      |                 }},{{
  127 |                 ,0.911428974,0.524430101,0.653287717,1.087821916
      |                 }{
  128 |                 ,0.503209827,0.274849491,0.49063599,0.730763505
      |                 }{
  129 |                 ,0,0,0,0
      |                 }{
  130 |                 ,0.65,0.55,0.48,0.69
      |                 }{
  131 |                 ,0.65,0.55,0.48,0.69
      |                 -
      |                 }},{{
  132 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  133 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  134 |                 ,0.65,0.55,0.48,0.69
      |                 }{
  135 |                 ,0,0,0,0
      |                 }{
  136 |                 ,0,0,0,0
      |                 -
      |                 }}},{{{
  137 |                 ,1.100661785,0.969784756,1.318532145,1.385046493
      |                 }{
  138 |                 ,0.565895968,-0.060347902,0.59458138,0.653168672
      |                 }{
  139 |                 ,0.782168488,0.788161238,0.740323132,1.001540513
      |                 }{
  140 |                 ,0.68,0.46,0.55,0.65
      |                 }{
  141 |                 ,0.468913405,-0.469855984,0.274849491,-0.024857805
      |                 -
      |                 }},{{
  142 |                 ,0,0,0,0
      |                 }{
  143 |                 ,0.258195131,-0.70438632,0.249934344,-0.143236405
      |                 }{
  144 |                 ,0.502914193,-0.060347902,0.241428373,0.582415494
      |                 }{
  145 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  146 |                 ,0.584083861,0.258975454,0.524430101,0.846496194
      |                 -
      |                 }},{{
  147 |                 ,0.968040559,0.797499702,0.730184613,1.270687029
      |                 }{
  148 |                 ,0,0,0,0
      |                 }{
  149 |                 ,1.081040749,0.969784756,0.84547091,1.254355018
      |                 }{
  150 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  151 |                 ,1.048553951,0.728354541,0.894838095,0.882097231
      |                 -
      |                 }},{{
  152 |                 ,0.88611252,0.258975454,0.318907854,0.746214538
      |                 }{
  153 |                 ,0.239520858,-0.469855984,0.101248351,0.18553379
      |                 }{
  154 |                 ,0,0,0,0
      |                 }{
  155 |                 ,0.68,0.46,0.55,0.65
      |                 }{
  156 |                 ,0.68,0.46,0.55,0.65
      |                 -
      |                 }},{{
  157 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  158 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  159 |                 ,0.68,0.46,0.55,0.65
      |                 }{
  160 |                 ,0,0,0,0
      |                 }{
  161 |                 ,0,0,0,0
      |                 -
      |                 }}},{{{
  162 |                 ,1.566899704,1.081040749,1.45897431,1.443665704
      |                 }{
  163 |                 ,0.976725675,0.502914193,0.871921533,0.851622883
      |                 }{
  164 |                 ,1.482046826,0.782168488,0.99945386,1.203555051
      |                 }{
  165 |                 ,0.85,0.68,0.65,0.76
      |                 }{
  166 |                 ,0.798628781,0.239520858,0.503209827,0.766581547
      |                 -
      |                 }},{{
  167 |                 ,0,0,0,0
      |                 }{
  168 |                 ,1.141098246,0.258195131,1.0651638,0.856582783
      |                 }{
  169 |                 ,0.976725675,0.565895968,0.755889609,1.150635633
      |                 }{
  170 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  171 |                 ,1.125403302,0.88611252,0.911428974,1.496720812
      |                 -
      |                 }},{{
  172 |                 ,1.68169282,0.968040559,1.099899195,1.822113278
      |                 }{
  173 |                 ,0,0,0,0
      |                 }{
  174 |                 ,1.566899704,1.100661785,1.295827995,1.545032445
      |                 }{
  175 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  176 |                 ,1.35948517,1.048553951,1.242135174,1.478009492
      |                 -
      |                 }},{{
  177 |                 ,1.125403302,0.584083861,1.07531714,1.231861002
      |                 }{
  178 |                 ,0.798628781,0.468913405,0.843147406,0.630005348
      |                 }{
  179 |                 ,0,0,0,0
      |                 }{
  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 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  185 |                 ,0,0,0,0
      |                 }{
  186 |         };
      |         }}}
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c:838:60: warning: ‘lastCycle’ may be used uninitialized [-Wmaybe-uninitialized]
  838 |                                                         if (thisCycle < lastCycle) {
      |                                                            ^
DesignProbes.c:270:58: note: ‘lastCycle’ was declared here
  270 |                         int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                                          ^~~~~~~~~
DesignProbes.c:838:60: warning: ‘thisCycle’ may be used uninitialized [-Wmaybe-uninitialized]
  838 |                                                         if (thisCycle < lastCycle) {
      |                                                            ^
DesignProbes.c:270:69: note: ‘thisCycle’ was declared here
  270 |                         int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                                                     ^~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c Diff.c -o Diff.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘firstSeqsPosEqual’:
DistanceMatrix.c:1009:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 1009 |                 if (!ci)
      |                 ^~
DistanceMatrix.c:1012:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 1012 |                         while (i < ex) {
      |                         ^~~~~
DistanceMatrix.c:1031:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 1031 |                 if (!cj)
      |                 ^~
DistanceMatrix.c:1034:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 1034 |                         while (j < ey) {
      |                         ^~~~~
DistanceMatrix.c: In function ‘computeOverlap._omp_fn.0’:
DistanceMatrix.c:1587:66: warning: ‘OV’ may be used uninitialized [-Wmaybe-uninitialized]
 1587 |                                         (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
      |                                                              ~~~~^~~~~~
DistanceMatrix.c:1096:92: note: ‘OV’ was declared here
 1096 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                                            ^~
DistanceMatrix.c:1587:66: warning: ‘off’ may be used uninitialized [-Wmaybe-uninitialized]
 1587 |                                         (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
      |                                                              ~~~~^~~~~~
DistanceMatrix.c:1096:96: note: ‘off’ was declared here
 1096 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                                                ^~~
DistanceMatrix.c:1266:53: warning: ‘one’ may be used uninitialized [-Wmaybe-uninitialized]
 1266 |                                                 two != one) {
      |                                                 ~~~~^~~~~~
DistanceMatrix.c:1241:29: note: ‘one’ was declared here
 1241 |                         int one, two;
      |                             ^~~
DistanceMatrix.c:1603:52: warning: ‘o’ may be used uninitialized [-Wmaybe-uninitialized]
 1603 |                                                 if (o == 1) {
      |                                                    ^
DistanceMatrix.c:1096:112: note: ‘o’ was declared here
 1096 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                                                                ^
DistanceMatrix.c:1606:91: warning: ‘ov’ may be used uninitialized [-Wmaybe-uninitialized]
 1606 |                                                         sim[i] = (double)pos/((double)(ov + count + g2));
      |                                                                                        ~~~^~~~~~~
DistanceMatrix.c:1096:88: note: ‘ov’ was declared here
 1096 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                                        ^~
In function ‘distance’,
    inlined from ‘distMatrix._omp_fn.0’ at DistanceMatrix.c:729:20:
DistanceMatrix.c:391:17: warning: ‘counts’ may be used uninitialized [-Wmaybe-uninitialized]
  391 |                 free(counts);
      |                 ^~~~~~~~~~~~
DistanceMatrix.c: In function ‘distMatrix._omp_fn.0’:
DistanceMatrix.c:137:30: note: ‘counts’ was declared here
  137 |         int i, j, I, J, m2, *counts;
      |                              ^~~~~~
DistanceMatrix.c: In function ‘distMatrix’:
DistanceMatrix.c:624:33: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized]
  624 |                         #pragma omp parallel for private(j,x_j,seqLength_j,start,end,index,width) schedule(guided) num_threads(nthreads)
      |                                 ^~~
DistanceMatrix.c:545:13: note: ‘m’ was declared here
  545 |         int m, *lkup_row, *lkup_col;
      |             ^
DistanceMatrix.c:624:33: warning: ‘lkup_row’ may be used uninitialized [-Wmaybe-uninitialized]
  624 |                         #pragma omp parallel for private(j,x_j,seqLength_j,start,end,index,width) schedule(guided) num_threads(nthreads)
      |                                 ^~~
DistanceMatrix.c:545:17: note: ‘lkup_row’ was declared here
  545 |         int m, *lkup_row, *lkup_col;
      |                 ^~~~~~~~
DistanceMatrix.c:624:33: warning: ‘lkup_col’ may be used uninitialized [-Wmaybe-uninitialized]
  624 |                         #pragma omp parallel for private(j,x_j,seqLength_j,start,end,index,width) schedule(guided) num_threads(nthreads)
      |                                 ^~~
DistanceMatrix.c:545:28: note: ‘lkup_col’ was declared here
  545 |         int m, *lkup_row, *lkup_col;
      |                            ^~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function ‘pop’:
EnumerateSequence.c:546:15: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  546 |         x = x + (x >> 4) & 0xF0F0F0F;
      |             ~~^~~~~~~~~~
EnumerateSequence.c: In function ‘enumerateSequence’:
EnumerateSequence.c:359:17: warning: ‘mN’ may be used uninitialized [-Wmaybe-uninitialized]
  359 |         #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
      |                 ^~~
EnumerateSequence.c:318:14: note: ‘mN’ was declared here
  318 |         int *mN;
      |              ^~
EnumerateSequence.c:359:17: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized]
  359 |         #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
      |                 ^~~
EnumerateSequence.c:319:13: note: ‘tot’ was declared here
  319 |         int tot; // total number of k-mers
      |             ^~~
EnumerateSequence.c: In function ‘enumerateSequenceReducedAA’:
EnumerateSequence.c:956:17: warning: ‘mN’ may be used uninitialized [-Wmaybe-uninitialized]
  956 |         #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
      |                 ^~~
EnumerateSequence.c:908:14: note: ‘mN’ was declared here
  908 |         int *mN;
      |              ^~
EnumerateSequence.c:956:17: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized]
  956 |         #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
      |                 ^~~
EnumerateSequence.c:909:13: note: ‘tot’ was declared here
  909 |         int tot; // total number of k-mers
      |             ^~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function ‘findFrameshifts’:
FindFrameshifts.c:464:43: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  464 |                         *rPercentComplete = floor(100*(double)(s + 1)/f_length);
      |                         ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FindFrameshifts.c:160:25: note: ‘rPercentComplete’ was declared here
  160 |         int before, v, *rPercentComplete;
      |                         ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/include/Rdefines.h:41,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.22-bioc/R/include/Rinternals.h:934:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  934 | #define eval                    Rf_eval
FindFrameshifts.c:467:33: note: in expansion of macro ‘eval’
  467 |                                 eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                 ^~~~
FindFrameshifts.c:162:14: note: ‘percentComplete’ was declared here
  162 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/include/Rinternals.h:934:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
  934 | #define eval                    Rf_eval
FindFrameshifts.c:467:33: note: in expansion of macro ‘eval’
  467 |                                 eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                 ^~~~
FindFrameshifts.c:162:31: note: ‘utilsPackage’ was declared here
  162 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
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;
      |                            ^
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:376:28: warning: ‘K’ may be used uninitialized [-Wmaybe-uninitialized]
  376 |                         if (k == 1) {
      |                            ^
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;
      |                                  ^
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function ‘scoreCodonModel’:
GeneFinding.c:422:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
  422 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:389:22: note: ‘x_i.ptr’ was declared here
  389 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c:432:57: warning: ‘lastVal’ may be used uninitialized [-Wmaybe-uninitialized]
  432 |                                 if (val < 64 && lastVal < 64)
      |                                                 ~~~~~~~~^~~~
GeneFinding.c:372:32: note: ‘lastVal’ was declared here
  372 |         int i, j, s, fin, val, lastVal, dicodon;
      |                                ^~~~~~~
GeneFinding.c: In function ‘startCodonModel’:
GeneFinding.c:798:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
  798 |                         val += 16*getBase(x_i.ptr[j]);
      |                                                  ^
GeneFinding.c:772:22: note: ‘x_i.ptr’ was declared here
  772 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘scoreStartCodonModel’:
GeneFinding.c:899:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
  899 |                         val += 16*getBase(x_i.ptr[j]);
      |                                                  ^
GeneFinding.c:869:22: note: ‘x_i.ptr’ was declared here
  869 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘initialCodonModel’:
GeneFinding.c:952:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
  952 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:929:22: note: ‘x_i.ptr’ was declared here
  929 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘scoreInitialCodonModel’:
GeneFinding.c:1059:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 1059 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1032:22: note: ‘x_i.ptr’ was declared here
 1032 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘terminationCodonModel’:
GeneFinding.c:1116:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 1116 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1093:22: note: ‘x_i.ptr’ was declared here
 1093 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘scoreTerminationCodonModel’:
GeneFinding.c:1216:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 1216 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1189:22: note: ‘x_i.ptr’ was declared here
 1189 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘getRegion’:
GeneFinding.c:1317:81: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 1317 |                                                 seq[k] = getBaseLetterRC(x_i.ptr[j--]);
      |                                                                                 ^
GeneFinding.c:1253:22: note: ‘x_i.ptr’ was declared here
 1253 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c:1314:51: warning: ‘x_i.length’ may be used uninitialized [-Wmaybe-uninitialized]
 1314 |                                 (s == 0 && j >= 0 && j + w <= x_i.length)) {
      |                                 ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1253:22: note: ‘x_i.length’ was declared here
 1253 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘autocorrelationModel’:
GeneFinding.c:1379:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 1379 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1351:22: note: ‘x_i.ptr’ was declared here
 1351 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘scoreAutocorrelationModel’:
GeneFinding.c:1496:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 1496 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1462:22: note: ‘x_i.ptr’ was declared here
 1462 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘couplingModel’:
GeneFinding.c:1598:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 1598 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1574:22: note: ‘x_i.ptr’ was declared here
 1574 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘scoreCouplingModel’:
GeneFinding.c:1712:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 1712 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1682:22: note: ‘x_i.ptr’ was declared here
 1682 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1827:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 1827 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1789:22: note: ‘x_i.ptr’ was declared here
 1789 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘scoreNucleotideBiasModel’:
GeneFinding.c:1914:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 1914 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:1883:22: note: ‘x_i.ptr’ was declared here
 1883 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘upstreamMotifModel’:
GeneFinding.c:1993:75: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 1993 |                                         val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]);
      |                                                                           ^
GeneFinding.c:1951:22: note: ‘x_i.ptr’ was declared here
 1951 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘scoreUpstreamMotifModel’:
GeneFinding.c:2093:75: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 2093 |                                         val += mult[k - 1]*getBase(x_i.ptr[j - k + 1]);
      |                                                                           ^
GeneFinding.c:2058:22: note: ‘x_i.ptr’ was declared here
 2058 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘scoreRunLengthModel’:
GeneFinding.c:2308:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 2308 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:2277:22: note: ‘x_i.ptr’ was declared here
 2277 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘stopCodonModel’:
GeneFinding.c:2426:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 2426 |                         val += 16*getBase(x_i.ptr[j]);
      |                                                  ^
GeneFinding.c:2400:22: note: ‘x_i.ptr’ was declared here
 2400 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘scoreStopCodonModel’:
GeneFinding.c:2527:50: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 2527 |                         val += 16*getBase(x_i.ptr[j]);
      |                                                  ^
GeneFinding.c:2497:22: note: ‘x_i.ptr’ was declared here
 2497 |         Chars_holder x_i;
      |                      ^~~
GeneFinding.c: In function ‘codonFrequencies’:
GeneFinding.c:2578:56: warning: ‘x_i.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 2578 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:2555:22: note: ‘x_i.ptr’ was declared here
 2555 |         Chars_holder x_i;
      |                      ^~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c GetPools.c -o GetPools.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c Import.c -o Import.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c InformationContent.c -o InformationContent.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c IntDist.c -o IntDist.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c ManipulateXStringSet.c -o ManipulateXStringSet.o
ManipulateXStringSet.c: In function ‘mergePairs._omp_fn.0’:
ManipulateXStringSet.c:1106:58: warning: ‘l2’ may be used uninitialized [-Wmaybe-uninitialized]
 1106 |                                                 p2 = (l2 + pow(10, ((double)q2_i.ptr[s2 + 1] - 33)/-10))/2;
      |                                                      ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ManipulateXStringSet.c:1087:36: note: ‘l2’ was declared here
 1087 |                         double l1, l2; // last probability
      |                                    ^~
ManipulateXStringSet.c:1096:58: warning: ‘l1’ may be used uninitialized [-Wmaybe-uninitialized]
 1096 |                                                 p1 = (l1 + pow(10, ((double)q1_i.ptr[s1 + 1] - 33)/-10))/2;
      |                                                      ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ManipulateXStringSet.c:1087:32: note: ‘l1’ was declared here
 1087 |                         double l1, l2; // last probability
      |                                ^~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -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:406:25: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized]
  406 |                         SET_VECTOR_ELT(ret, s, ans);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
MeltPolymer.c:53:19: note: ‘ans’ was declared here
   53 |         SEXP ret, ans;
      |                   ^~~
MeltPolymer.c:358:41: warning: ‘rans’ may be used uninitialized [-Wmaybe-uninitialized]
  358 |                                         *(rans + k + l*s) += 1;
      |                                         ^~~~~~~~~~~~~~~~~
MeltPolymer.c:54:17: note: ‘rans’ was declared here
   54 |         double *rans;
      |                 ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c MovingAverage.c -o MovingAverage.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c NNLS.c -o NNLS.o
NNLS.c: In function ‘NNLS’:
NNLS.c:78:51: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
   78 |                                 *rPercentComplete = floor(100*((double)i + 1)/(double)l);
      |                                 ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NNLS.c:40:34: note: ‘rPercentComplete’ was declared here
   40 |         int i, j, k, before, v, *rPercentComplete;
      |                                  ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/include/Rdefines.h:41,
                 from NNLS.c:17:
/home/biocbuild/bbs-3.22-bioc/R/include/Rinternals.h:934:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  934 | #define eval                    Rf_eval
NNLS.c:82:41: note: in expansion of macro ‘eval’
   82 |                                         eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                         ^~~~
NNLS.c:48:14: note: ‘percentComplete’ was declared here
   48 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/include/Rinternals.h:934:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
  934 | #define eval                    Rf_eval
NNLS.c:82:41: note: in expansion of macro ‘eval’
   82 |                                         eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                         ^~~~
NNLS.c:48:31: note: ‘utilsPackage’ was declared here
   48 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c Order.c -o Order.o
Order.c: In function ‘radixOrder’:
Order.c:169:41: warning: ‘bounds’ may be used uninitialized [-Wmaybe-uninitialized]
  169 |                                 #pragma omp parallel num_threads(NTHREADS)
      |                                         ^~~
Order.c:99:19: note: ‘bounds’ was declared here
   99 |         R_xlen_t *bounds;
      |                   ^~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’:
PairwiseAlignment.c:446:39: warning: ‘p3’ may be used uninitialized [-Wmaybe-uninitialized]
  446 |                                 p3[0] = l1;
      |                                 ~~~~~~^~~~
PairwiseAlignment.c:176:24: note: ‘p3’ was declared here
  176 |         int *p1, *p2, *p3, *p4;
      |                        ^~
PairwiseAlignment.c:447:39: warning: ‘p4’ may be used uninitialized [-Wmaybe-uninitialized]
  447 |                                 p4[0] = l2 - j1;
      |                                 ~~~~~~^~~~~~~~~
PairwiseAlignment.c:176:29: note: ‘p4’ was declared here
  176 |         int *p1, *p2, *p3, *p4;
      |                             ^~
PairwiseAlignment.c:450:39: warning: ‘p1’ may be used uninitialized [-Wmaybe-uninitialized]
  450 |                                 p1[0] = l2;
      |                                 ~~~~~~^~~~
PairwiseAlignment.c:176:14: note: ‘p1’ was declared here
  176 |         int *p1, *p2, *p3, *p4;
      |              ^~
PairwiseAlignment.c:451:39: warning: ‘p2’ may be used uninitialized [-Wmaybe-uninitialized]
  451 |                                 p2[0] = l1 - i1;
      |                                 ~~~~~~^~~~~~~~~
PairwiseAlignment.c:176:19: note: ‘p2’ was declared here
  176 |         int *p1, *p2, *p3, *p4;
      |                   ^~
PairwiseAlignment.c: In function ‘alignPairs’:
PairwiseAlignment.c:1108:17: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
 1108 |         #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
PairwiseAlignment.c:1036:25: note: ‘rPercentComplete’ was declared here
 1036 |         int before, v, *rPercentComplete;
      |                         ^~~~~~~~~~~~~~~~
PairwiseAlignment.c:1108:17: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
 1108 |         #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
PairwiseAlignment.c:1038:14: note: ‘percentComplete’ was declared here
 1038 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
PairwiseAlignment.c:1108:17: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
 1108 |         #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
PairwiseAlignment.c:1038:31: note: ‘utilsPackage’ was declared here
 1038 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c PopulationGenetics.c -o PopulationGenetics.o
PopulationGenetics.c: In function ‘correlationProfile’:
PopulationGenetics.c:140:51: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  140 |                                 *rPercentComplete = floor(100*soFar/tot);
      |                                 ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
PopulationGenetics.c:40:68: note: ‘rPercentComplete’ was declared here
   40 |         int i, j, k, p, I, J, minL, warn = NA_INTEGER, v, before, *rPercentComplete;
      |                                                                    ^~~~~~~~~~~~~~~~
PopulationGenetics.c:140:53: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized]
  140 |                                 *rPercentComplete = floor(100*soFar/tot);
      |                                                     ^~~~~~~~~~~~~~~~~~~~
PopulationGenetics.c:41:31: note: ‘tot’ was declared here
   41 |         double weight, soFar, tot;
      |                               ^~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/include/Rdefines.h:41,
                 from PopulationGenetics.c:11:
/home/biocbuild/bbs-3.22-bioc/R/include/Rinternals.h:934:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  934 | #define eval                    Rf_eval
PopulationGenetics.c:143:41: note: in expansion of macro ‘eval’
  143 |                                         eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                         ^~~~
PopulationGenetics.c:50:14: note: ‘percentComplete’ was declared here
   50 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/R/include/Rinternals.h:934:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
  934 | #define eval                    Rf_eval
PopulationGenetics.c:143:41: note: in expansion of macro ‘eval’
  143 |                                         eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                         ^~~~
PopulationGenetics.c:50:31: note: ‘utilsPackage’ was declared here
   50 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function ‘predictDBN’:
PredictDBN.c:601:25: warning: ‘leftSymbol’ may be used uninitialized [-Wmaybe-uninitialized]
  601 |                         Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictDBN.c:489:14: note: ‘leftSymbol’ was declared here
  489 |         char leftSymbol, rightSymbol;
      |              ^~~~~~~~~~
PredictDBN.c:601:25: warning: ‘rightSymbol’ may be used uninitialized [-Wmaybe-uninitialized]
  601 |                         Traceback(MI, tot, unpaired, pos, states, leftSymbol, rightSymbol, 0, l - 1);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictDBN.c:489:26: note: ‘rightSymbol’ was declared here
  489 |         char leftSymbol, rightSymbol;
      |                          ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function ‘predictHEC’:
PredictHEC.c:51:31: warning: ‘rans’ may be used uninitialized [-Wmaybe-uninitialized]
   51 |         double HEC[N], temp, *rans;
      |                               ^~~~
PredictHEC.c:247:43: warning: ‘states’ may be used uninitialized [-Wmaybe-uninitialized]
  247 |                                 states[j] = nms[0];
      |                                 ~~~~~~~~~~^~~~~~~~
PredictHEC.c:52:15: note: ‘states’ was declared here
   52 |         char *states;
      |               ^~~~~~
PredictHEC.c:273:25: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized]
  273 |                         SET_VECTOR_ELT(ret, i, ans);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:59:19: note: ‘ans’ was declared here
   59 |         SEXP ret, ans;
      |                   ^~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c R_init_decipher.c -o R_init_decipher.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c Search.c -o Search.o
Search.c: In function ‘searchIndex._omp_fn.0’:
Search.c:578:92: warning: ‘subScores’ may be used uninitialized [-Wmaybe-uninitialized]
  578 |                                                         if (lkup != NA_INTEGER && subScores[p1*l_i.length + lkup] != NA_REAL)
      |                                                                                            ^
Search.c:317:33: note: ‘subScores’ was declared here
  317 |                         double *subScores; // substitution scores (if maxIt > 0)
      |                                 ^~~~~~~~~
Search.c:449:66: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized]
  449 |                                                 score2[j] = score[o1[j]];
      |                                                                  ^
Search.c:282:33: note: ‘score’ was declared here
  282 |                         double *score, *addScore, *score2, *addScore2;
      |                                 ^~~~~
Search.c:450:72: warning: ‘addScore’ may be used uninitialized [-Wmaybe-uninitialized]
  450 |                                                 addScore2[j] = addScore[o1[j]];
      |                                                                        ^
Search.c:282:41: note: ‘addScore’ was declared here
  282 |                         double *score, *addScore, *score2, *addScore2;
      |                                         ^~~~~~~~
Search.c:587:83: warning: ‘maxLen’ may be used uninitialized [-Wmaybe-uninitialized]
  587 |                                                         if (deltaTarget >= maxSep + maxLen) {
      |                                                                            ~~~~~~~^~~~~~~~
Search.c:560:45: note: ‘maxLen’ was declared here
  560 |                                         int maxLen; // maximum observed length
      |                                             ^~~~~~
Search.c:555:59: warning: ‘s_j.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
  555 |                                         Chars_holder p_i, s_j;
      |                                                           ^~~
Search.c:626:55: warning: ‘s_j.length’ may be used uninitialized [-Wmaybe-uninitialized]
  626 |                                                 bound = s_j.length - 1; // right bound
      |                                                 ~~~~~~^~~~~~~~~~~~~~~~
Search.c:555:59: note: ‘s_j.length’ was declared here
  555 |                                         Chars_holder p_i, s_j;
      |                                                           ^~~
Search.c:882:59: warning: ‘s_j.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
  882 |                                         Chars_holder p_i, s_j;
      |                                                           ^~~
Search.c:1150:72: warning: ‘len’ may be used uninitialized [-Wmaybe-uninitialized]
 1150 |                                         anchor[k++] = posQuery[p] + len[p] - 1;
      |                                                                        ^
Search.c:370:30: note: ‘len’ was declared here
  370 |                         int *len; // length of each hit
      |                              ^~~
Search.c:1139:58: warning: ‘chain’ may be used uninitialized [-Wmaybe-uninitialized]
 1139 |                                         while (p != chain[p]) {
      |                                                          ^
Search.c:369:30: note: ‘chain’ was declared here
  369 |                         int *chain; // set of joined hits per match
      |                              ^~~~~
Search.c:371:30: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized]
  371 |                         int *res; // indices of results
      |                              ^~~
Search.c: In function ‘searchIndex’:
Search.c:224:17: warning: ‘sM’ may be used uninitialized [-Wmaybe-uninitialized]
  224 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:111:17: note: ‘sM’ was declared here
  111 |         double *sM, dS;
      |                 ^~
Search.c:224:17: warning: ‘dS’ may be used uninitialized [-Wmaybe-uninitialized]
  224 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:111:21: note: ‘dS’ was declared here
  111 |         double *sM, dS;
      |                     ^~
Search.c:224:17: warning: ‘lkup_row’ may be used uninitialized [-Wmaybe-uninitialized]
  224 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:112:14: note: ‘lkup_row’ was declared here
  112 |         int *lkup_row, *lkup_col, *pwv;
      |              ^~~~~~~~
Search.c:224:17: warning: ‘lkup_col’ may be used uninitialized [-Wmaybe-uninitialized]
  224 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:112:25: note: ‘lkup_col’ was declared here
  112 |         int *lkup_row, *lkup_col, *pwv;
      |                         ^~~~~~~~
Search.c:224:17: warning: ‘pwv’ may be used uninitialized [-Wmaybe-uninitialized]
  224 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:112:36: note: ‘pwv’ was declared here
  112 |         int *lkup_row, *lkup_col, *pwv;
      |                                    ^~~
Search.c:224:17: warning: ‘scores’ may be used uninitialized [-Wmaybe-uninitialized]
  224 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:113:17: note: ‘scores’ was declared here
  113 |         double *scores, *addScores;
      |                 ^~~~~~
Search.c:224:17: warning: ‘addScores’ may be used uninitialized [-Wmaybe-uninitialized]
  224 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:113:26: note: ‘addScores’ was declared here
  113 |         double *scores, *addScores;
      |                          ^~~~~~~~~
Search.c:224:17: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  224 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:174:25: note: ‘rPercentComplete’ was declared here
  174 |         int before, v, *rPercentComplete;
      |                         ^~~~~~~~~~~~~~~~
Search.c:224:17: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  224 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:176:14: note: ‘percentComplete’ was declared here
  176 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
Search.c:224:17: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
  224 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:176:31: note: ‘utilsPackage’ was declared here
  176 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
Search.c:224:17: warning: ‘matrices’ may be used uninitialized [-Wmaybe-uninitialized]
  224 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:217:16: note: ‘matrices’ was declared here
  217 |         int ***matrices;
      |                ^~~~~~~~
Search.c:1287:38: warning: ‘anchors’ may be used uninitialized [-Wmaybe-uninitialized]
 1287 |                                 int *anchor = anchors[j];
      |                                      ^~~~~~
Search.c:1232:15: note: ‘anchors’ was declared here
 1232 |         int **anchors; // pointers to anchor positions
      |               ^~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c TerminalMismatch.c -o TerminalMismatch.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c Translate.c -o Translate.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c Utils.c -o Utils.o
Utils.c: In function ‘splitPartitions’:
Utils.c:990:35: warning: ‘change’ may be used uninitialized [-Wmaybe-uninitialized]
  990 |                 } else if (change - j >= m && // large enough partition
      |                            ~~~~~~~^~~
Utils.c:984:13: note: ‘change’ was declared here
  984 |         int change; // index before start of partition
      |             ^~~~~~
Utils.c: In function ‘matchColumns’:
Utils.c:1198:55: warning: ‘lkup’ may be used uninitialized [-Wmaybe-uninitialized]
 1198 |                                         int val = lkup[(unsigned char)x_i.ptr[o[j]]];
      |                                                       ^
Utils.c:1130:14: note: ‘lkup’ was declared here
 1130 |         int *lkup;
      |              ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c VectorSums.c -o VectorSums.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterME.o ClusterML.o ClusterMP.o Compositions.o Compression.o ConsensusSequence.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o IntDist.o ManipulateXStringSet.o MeltPolymer.o MovingAverage.o NNLS.o Order.o PairwiseAlignment.o PopulationGenetics.o PredictDBN.o PredictHEC.o R_init_decipher.o S4Vectors_stubs.o Search.o TerminalMismatch.o Translate.o Utils.o VectorSums.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-DECIPHER/00new/DECIPHER/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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_REDUCED0.0680.0020.100
Add2DB0.8750.0680.986
AdjustAlignment0.3180.0090.331
AlignDB1.8770.1672.066
AlignPairs6.4690.1987.325
AlignProfiles1.5190.0901.667
AlignSeqs250.960 2.588304.003
AlignSynteny3.5010.0023.834
AlignTranslation14.836 0.11716.717
AmplifyDNA0.0020.0010.003
Array2Matrix 7.349 0.09112.091
BLOSUM0.0250.0010.041
BrowseDB0.0680.0000.123
BrowseSeqs34.717 0.20144.378
CalculateEfficiencyArray0.0190.0030.022
CalculateEfficiencyFISH0.0050.0000.005
CalculateEfficiencyPCR0.0050.0000.005
Clusterize 9.415 0.05810.616
Codec1.2160.0011.295
ConsensusSequence0.1940.0010.348
Cophenetic3.7610.0054.487
CorrectFrameshifts21.002 0.35229.399
CreateChimeras1.0170.0431.234
DB2Seqs0.0380.0040.049
DesignArray6.8580.1528.763
DesignPrimers0.0110.0000.011
DesignProbes0.0090.0000.009
DesignSignatures0.0090.0000.010
DetectRepeats12.450 0.31715.073
DigestDNA0.1350.0050.140
Disambiguate0.0440.0000.044
DistanceMatrix24.905 0.45626.166
ExtractGenes39.950 0.59941.906
FindChimeras0.0730.0010.073
FindGenes39.838 0.23540.311
FindNonCoding62.370 0.61163.732
FindSynteny1.6960.0091.705
FormGroups0.0530.0000.053
Genes-class39.847 0.05040.280
HEC_MI0.2890.0030.292
IdConsensus0.4780.0050.517
IdLengths0.0390.0000.039
IdTaxa10.322 0.02510.539
IdentifyByRank0.0280.0090.037
IndexSeqs0.9620.0030.965
InferDemography8.7580.0228.782
InferRecombination26.258 0.11627.608
InferSelection47.742 0.19557.173
InvertedIndex-class0.7580.0060.818
LearnNonCoding124.725 5.684134.829
LearnTaxa7.2370.7077.945
MIQS0.0410.0040.045
MMLSUM0.0080.0010.010
MODELS0.0010.0000.001
MapCharacters4.0150.0194.036
MaskAlignment0.4650.0040.469
MeltDNA0.0720.0000.072
NNLS0.0020.0000.003
NonCoding-class0.0590.0000.059
NonCodingRNA0.1170.0000.117
OrientNucleotides0.6160.0050.621
PAM0.0070.0020.009
PFASUM0.0090.0010.011
PredictDBN0.0070.0010.009
PredictHEC0.2970.0010.298
RESTRICTION_ENZYMES0.0010.0010.002
ReadDendrogram0.0240.0010.026
RemoveGaps0.0140.0000.014
ScoreAlignment5.7830.0915.875
SearchDB0.0510.0020.053
SearchIndex1.3400.0021.342
Seqs2DB0.1060.0000.107
StaggerAlignment11.437 0.07811.518
Synteny-class1.9510.0111.962
Taxa-class10.001 0.06110.063
TerminalChar0.0060.0020.007
TileSeqs3.5330.0003.532
TrainingSet_16S1.8680.0031.872
Treeline60.929 0.32062.395
TrimDNA9.7080.0979.806
WriteDendrogram0.0030.0000.003
WriteGenes34.155 0.43834.593
deltaGrules0.0080.0010.009
deltaGrulesRNA0.0190.0020.022
deltaHrules0.0180.0000.019
deltaHrulesRNA0.0160.0010.018
deltaSrules0.0500.0000.051
deltaSrulesRNA0.0150.0010.016