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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 509/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 3.3.2  (landing page)
Erik Wright
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/DECIPHER
git_branch: devel
git_last_commit: c3647f8
git_last_commit_date: 2024-12-19 19:27:29 -0500 (Thu, 19 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for DECIPHER on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: DECIPHER
Version: 3.3.2
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DECIPHER_3.3.2.tar.gz
StartedAt: 2024-12-24 05:56:27 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 06:17:55 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 1288.1 seconds
RetCode: 0
Status:   OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DECIPHER_3.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DECIPHER.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘3.3.2’
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is 13.4Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    data      7.5Mb
    extdata   2.5Mb
    libs      1.5Mb
* 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          241.122  0.717 242.400
LearnNonCoding     136.327  1.751 138.367
FindNonCoding      108.245  0.448 110.413
Treeline            87.927  0.848  89.132
ExtractGenes        62.203  0.211  62.567
Genes-class         61.361  0.180  61.706
FindGenes           61.354  0.120  63.876
WriteGenes          58.402  0.514  59.049
InferRecombination  32.284  0.071  32.420
BrowseSeqs          29.763  0.140  29.959
DistanceMatrix      29.232  0.248  29.531
CorrectFrameshifts  20.634  0.032  20.709
DetectRepeats       18.067  0.096  18.204
LearnTaxa           16.862  0.406  17.319
StaggerAlignment    16.558  0.163  16.767
AlignTranslation    15.613  0.112  15.762
Taxa-class          11.891  0.136  12.057
IdTaxa              11.466  0.032  11.533
Clusterize           7.164  0.055   7.241
ScoreAlignment       6.958  0.060   7.037
MapCharacters        5.608  0.064   5.689
TileSeqs             5.439  0.012   5.466
Array2Matrix         5.368  0.008   5.386
DesignArray          5.271  0.036   5.318
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.


Installation output

DECIPHER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |                 ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c AssignIndels.c -o AssignIndels.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c CalculateDeltaG.c -o CalculateDeltaG.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 |         };
      |         }
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c ChainSegments.c -o ChainSegments.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |              ^~~~~~~
In file included from /home/biocbuild/R/R/include/Rdefines.h:41,
                 from Cluster.c:11:
/home/biocbuild/R/R/include/Rinternals.h:927:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
  927 | #define eval                    Rf_eval
Cluster.c:920:33: note: in expansion of macro ‘eval’
  920 |                                 eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                 ^~~~
Cluster.c:250:36: note: ‘utilsPackage’ was declared here
  250 |         SEXP ans, percentComplete, utilsPackage;
      |                                    ^~~~~~~~~~~~
Cluster.c:916:45: warning: ‘total’ may be used uninitialized [-Wmaybe-uninitialized]
  916 |                         *rPercentComplete = floor(100*soFar/total);
      |                                             ^~~~~~~~~~~~~~~~~~~~~~
Cluster.c:249:23: note: ‘total’ was declared here
  249 |         double soFar, total, minHeight, *cut, *rans, *distanceMatrix, minH;
      |                       ^~~~~
Cluster.c:916:43: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  916 |                         *rPercentComplete = floor(100*soFar/total);
      |                         ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
Cluster.c:248:25: note: ‘rPercentComplete’ was declared here
  248 |         int before, v, *rPercentComplete;
      |                         ^~~~~~~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:927:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  927 | #define eval                    Rf_eval
Cluster.c:920:33: note: in expansion of macro ‘eval’
  920 |                                 eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                 ^~~~
Cluster.c:250:19: note: ‘percentComplete’ was declared here
  250 |         SEXP ans, percentComplete, utilsPackage;
      |                   ^~~~~~~~~~~~~~~
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;
      |                                                         ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |                                          ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |              ^~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |              ^~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c Compositions.c -o Compositions.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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: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:1215:56: warning: ‘rev’ may be used uninitialized [-Wmaybe-uninitialized]
 1215 |                                                 p[c++] = rev == 0 ? 254 : 255;
      |                                                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
Compression.c:546:41: note: ‘rev’ was declared here
  546 |                 int lastTemp, currTemp, rev, len, len2, thresh = 1;
      |                                         ^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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: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: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;
      |                                     ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |                                                          ^~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c Diff.c -o Diff.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |                                                                                        ^~
DistanceMatrix.c: In function ‘distMatrix._omp_fn.0’:
DistanceMatrix.c:137:25: warning: ‘m2’ may be used uninitialized [-Wmaybe-uninitialized]
  137 |         int i, j, I, J, m2, *counts;
      |                         ^~
DistanceMatrix.c:137:30: warning: ‘counts’ may be used uninitialized [-Wmaybe-uninitialized]
  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;
      |                            ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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
      |             ^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c ExpandAmbiguities.c -o ExpandAmbiguities.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/R/R/include/Rdefines.h:41,
                 from FindFrameshifts.c:11:
/home/biocbuild/R/R/include/Rinternals.h:927:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  927 | #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/R/R/include/Rinternals.h:927:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
  927 | #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;
      |                                  ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |                      ^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c GetPools.c -o GetPools.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c Import.c -o Import.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c InformationContent.c -o InformationContent.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c IntDist.c -o IntDist.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c ManipulateXStringSet.c -o ManipulateXStringSet.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |                 ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c MovingAverage.c -o MovingAverage.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/R/R/include/Rdefines.h:41,
                 from NNLS.c:17:
/home/biocbuild/R/R/include/Rinternals.h:927:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  927 | #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/R/R/include/Rinternals.h:927:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
  927 | #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;
      |                               ^~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |                   ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |                               ^~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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:136:51: warning: ‘rPercentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  136 |                                 *rPercentComplete = floor(100*soFar/tot);
      |                                 ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
PopulationGenetics.c:43:43: note: ‘rPercentComplete’ was declared here
   43 |         int i, j, k, p, I, J, v, before, *rPercentComplete;
      |                                           ^~~~~~~~~~~~~~~~
PopulationGenetics.c:136:53: warning: ‘tot’ may be used uninitialized [-Wmaybe-uninitialized]
  136 |                                 *rPercentComplete = floor(100*soFar/tot);
      |                                                     ^~~~~~~~~~~~~~~~~~~~
PopulationGenetics.c:44:31: note: ‘tot’ was declared here
   44 |         double weight, soFar, tot;
      |                               ^~~
In file included from /home/biocbuild/R/R/include/Rdefines.h:41,
                 from PopulationGenetics.c:17:
/home/biocbuild/R/R/include/Rinternals.h:927:33: warning: ‘percentComplete’ may be used uninitialized [-Wmaybe-uninitialized]
  927 | #define eval                    Rf_eval
PopulationGenetics.c:139:41: note: in expansion of macro ‘eval’
  139 |                                         eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                         ^~~~
PopulationGenetics.c:53:14: note: ‘percentComplete’ was declared here
   53 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:927:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized]
  927 | #define eval                    Rf_eval
PopulationGenetics.c:139:41: note: in expansion of macro ‘eval’
  139 |                                         eval(lang4(install("setTxtProgressBar"), pBar, percentComplete, R_NilValue), utilsPackage);
      |                                         ^~~~
PopulationGenetics.c:53:31: note: ‘utilsPackage’ was declared here
   53 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c PredictDBN.c -o PredictDBN.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |                   ^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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:371:30: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized]
  371 |                         int *res; // indices of results
      |                              ^~~
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: 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;
      |                ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c TerminalMismatch.c -o TerminalMismatch.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c Translate.c -o Translate.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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;
      |              ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c VectorSums.c -o VectorSums.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/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/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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_REDUCED0.3250.0000.325
Add2DB0.8160.0520.876
AdjustAlignment0.2570.0040.267
AlignDB1.5010.0481.556
AlignPairs4.3780.0924.487
AlignProfiles1.1210.0201.143
AlignSeqs241.122 0.717242.400
AlignSynteny3.7160.0443.773
AlignTranslation15.613 0.11215.762
AmplifyDNA0.0030.0000.005
Array2Matrix5.3680.0085.386
BLOSUM0.0180.0000.018
BrowseDB0.0520.0000.056
BrowseSeqs29.763 0.14029.959
CalculateEfficiencyArray0.0170.0040.020
CalculateEfficiencyFISH0.0060.0000.006
CalculateEfficiencyPCR0.0060.0000.007
Clusterize7.1640.0557.241
Codec1.3960.0001.399
ConsensusSequence0.2370.0000.238
Cophenetic3.7790.0123.799
CorrectFrameshifts20.634 0.03220.709
CreateChimeras1.0390.0001.041
DB2Seqs0.0440.0000.060
DesignArray5.2710.0365.318
DesignPrimers0.0050.0080.013
DesignProbes0.0120.0000.012
DesignSignatures0.0130.0000.013
DetectRepeats18.067 0.09618.204
DigestDNA0.2030.0000.203
Disambiguate0.0760.0000.076
DistanceMatrix29.232 0.24829.531
ExtractGenes62.203 0.21162.567
FindChimeras0.0950.0000.096
FindGenes61.354 0.12063.876
FindNonCoding108.245 0.448110.413
FindSynteny2.1750.0162.198
FormGroups0.0910.0040.095
Genes-class61.361 0.18061.706
HEC_MI0.2250.0040.230
IdConsensus0.5540.0120.567
IdLengths0.0410.0000.041
IdTaxa11.466 0.03211.533
IdentifyByRank0.0430.0000.044
IndexSeqs1.2340.0001.236
InferRecombination32.284 0.07132.420
InvertedIndex-class0.6540.0080.662
LearnNonCoding136.327 1.751138.367
LearnTaxa16.862 0.40617.319
MIQS0.0500.0010.050
MMLSUM0.0050.0030.009
MODELS0.0020.0000.002
MapCharacters5.6080.0645.689
MaskAlignment0.6290.0120.642
MeltDNA0.0870.0000.087
NNLS0.0040.0000.003
NonCoding-class0.0560.0000.057
NonCodingRNA0.1000.0000.101
OrientNucleotides0.4750.0000.476
PAM0.0040.0040.008
PFASUM0.010.000.01
PredictDBN0.0100.0000.009
PredictHEC0.3490.0040.355
RESTRICTION_ENZYMES0.0020.0000.003
ReadDendrogram0.0280.0000.028
RemoveGaps0.0160.0000.016
ScoreAlignment6.9580.0607.037
SearchDB0.0640.0000.065
SearchIndex1.9130.0001.918
Seqs2DB0.1280.0040.132
StaggerAlignment16.558 0.16316.767
Synteny-class2.7810.0042.792
Taxa-class11.891 0.13612.057
TerminalChar0.0080.0000.008
TileSeqs5.4390.0125.466
TrainingSet_16S2.7460.0122.764
Treeline87.927 0.84889.132
TrimDNA0.1740.0000.174
WriteDendrogram0.0050.0000.004
WriteGenes58.402 0.51459.049
deltaGrules0.0060.0040.010
deltaGrulesRNA0.0160.0040.021
deltaHrules0.0170.0000.017
deltaHrulesRNA0.0170.0000.017
deltaSrules0.070.000.07
deltaSrulesRNA0.0150.0000.015