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This page was generated on 2025-09-01 12:03 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 523/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 3.5.0  (landing page)
Erik Wright
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 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    OK  UNNEEDED, same version is already published
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: 2025-08-31 21:52:39 -0400 (Sun, 31 Aug 2025)
EndedAt: 2025-08-31 22:26:54 -0400 (Sun, 31 Aug 2025)
EllapsedTime: 2054.9 seconds
RetCode: 0
Status:   OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

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
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DECIPHER.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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          171.968  1.006 172.983
LearnNonCoding     118.021  4.811 123.650
FindNonCoding       61.329  0.786  62.118
Treeline            58.805  0.268  59.081
ExtractGenes        39.141  0.228  39.370
InferSelection      36.998  0.383  37.381
Genes-class         37.068  0.153  37.224
FindGenes           36.435  0.261  36.698
WriteGenes          34.584  0.421  35.009
BrowseSeqs          23.783  0.176  23.960
DistanceMatrix      23.086  0.118  23.205
InferRecombination  19.491  0.340  19.834
CorrectFrameshifts  16.556  0.087  16.644
StaggerAlignment    11.424  0.130  11.555
AlignTranslation    11.131  0.062  11.194
DetectRepeats       10.551  0.045  10.596
TrimDNA              9.951  0.115  10.066
Taxa-class          10.029  0.016  10.044
IdTaxa               9.802  0.010   9.812
InferDemography      8.546  0.006   8.552
Clusterize           7.806  0.050   7.856
LearnTaxa            6.654  0.600   7.254
ScoreAlignment       5.789  0.027   5.890
Array2Matrix         5.153  0.016   5.169
AlignPairs           4.909  0.170   5.081
DesignArray          5.012  0.048   5.060
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.


Installation output

DECIPHER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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_REDUCED0.0390.0010.042
Add2DB0.5980.0570.657
AdjustAlignment0.1890.0030.191
AlignDB1.1880.0501.238
AlignPairs4.9090.1705.081
AlignProfiles1.0060.0201.027
AlignSeqs171.968 1.006172.983
AlignSynteny2.6960.0052.702
AlignTranslation11.131 0.06211.194
AmplifyDNA0.0020.0010.003
Array2Matrix5.1530.0165.169
BLOSUM0.0170.0010.017
BrowseDB0.0350.0010.037
BrowseSeqs23.783 0.17623.960
CalculateEfficiencyArray0.2860.0020.287
CalculateEfficiencyFISH0.0040.0000.004
CalculateEfficiencyPCR0.0030.0000.004
Clusterize7.8060.0507.856
Codec1.2330.0001.234
ConsensusSequence0.1570.0010.159
Cophenetic2.6420.0042.646
CorrectFrameshifts16.556 0.08716.644
CreateChimeras0.6630.0030.666
DB2Seqs0.0240.0030.028
DesignArray5.0120.0485.060
DesignPrimers0.0090.0000.009
DesignProbes0.0060.0010.007
DesignSignatures0.0070.0000.007
DetectRepeats10.551 0.04510.596
DigestDNA0.140.000.14
Disambiguate0.0450.0000.044
DistanceMatrix23.086 0.11823.205
ExtractGenes39.141 0.22839.370
FindChimeras0.0680.0000.069
FindGenes36.435 0.26136.698
FindNonCoding61.329 0.78662.118
FindSynteny1.5660.0031.569
FormGroups0.0450.0010.046
Genes-class37.068 0.15337.224
HEC_MI0.2600.0030.264
IdConsensus0.4070.0030.411
IdLengths0.0330.0000.034
IdTaxa9.8020.0109.812
IdentifyByRank0.0340.0000.035
IndexSeqs1.0300.0021.032
InferDemography8.5460.0068.552
InferRecombination19.491 0.34019.834
InferSelection36.998 0.38337.381
InvertedIndex-class0.5780.0140.592
LearnNonCoding118.021 4.811123.650
LearnTaxa6.6540.6007.254
MIQS0.0400.0040.043
MMLSUM0.0080.0010.009
MODELS0.0010.0000.002
MapCharacters3.9120.0093.922
MaskAlignment0.7270.0080.838
MeltDNA0.1010.0010.205
NNLS0.0040.0000.004
NonCoding-class0.0810.0000.160
NonCodingRNA0.1640.0030.305
OrientNucleotides1.6400.0592.189
PAM0.0110.0020.014
PFASUM0.0170.0000.016
PredictDBN0.0160.0000.017
PredictHEC0.4380.0040.447
RESTRICTION_ENZYMES0.0020.0020.012
ReadDendrogram0.0330.0010.068
RemoveGaps0.020.000.02
ScoreAlignment5.7890.0275.890
SearchDB0.0640.0010.064
SearchIndex1.3920.0041.405
Seqs2DB0.1040.0020.106
StaggerAlignment11.424 0.13011.555
Synteny-class1.9050.0101.916
Taxa-class10.029 0.01610.044
TerminalChar0.0070.0010.007
TileSeqs3.4930.0003.494
TrainingSet_16S1.8650.0021.868
Treeline58.805 0.26859.081
TrimDNA 9.951 0.11510.066
WriteDendrogram0.0040.0000.004
WriteGenes34.584 0.42135.009
deltaGrules0.0080.0010.008
deltaGrulesRNA0.0210.0000.022
deltaHrules0.0180.0000.019
deltaHrulesRNA0.0170.0000.018
deltaSrules0.0520.0000.052
deltaSrulesRNA0.0160.0000.016