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This page was generated on 2024-05-04 11:40:26 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 521/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 3.0.0  (landing page)
Erik Wright
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/DECIPHER
git_branch: RELEASE_3_19
git_last_commit: 1b13c4e
git_last_commit_date: 2024-04-30 10:25:51 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 3.0.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings DECIPHER_3.0.0.tar.gz
StartedAt: 2024-05-04 06:40:26 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 07:02:24 -0000 (Sat, 04 May 2024)
EllapsedTime: 1318.2 seconds
RetCode: 0
Status:   OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings DECIPHER_3.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DECIPHER.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘3.0.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    data      7.5Mb
    extdata   2.5Mb
    libs      1.9Mb
* 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 ‘.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          241.358  0.551 242.392
LearnNonCoding     143.521  1.433 145.173
MapCharacters      140.725  0.515 141.486
FindNonCoding      111.160  0.655 115.815
ExtractGenes        65.302  0.184  65.598
WriteGenes          64.721  0.140  65.668
Genes-class         63.013  0.196  63.325
FindGenes           62.870  0.183  63.164
BrowseSeqs          29.927  0.103  30.075
DetectRepeats       24.838  0.112  24.995
CorrectFrameshifts  22.076  0.072  22.192
LearnTaxa           16.863  0.311  17.445
StaggerAlignment    16.680  0.096  16.815
AlignTranslation    15.883  0.096  16.006
TreeLine            13.388  0.099  13.518
Taxa-class          13.325  0.016  13.368
IdTaxa              12.482  0.024  12.528
Clusterize           8.579  0.032   8.628
ScoreAlignment       7.237  0.012   7.266
Array2Matrix         5.405  0.020   5.431
TileSeqs             5.409  0.000   5.421
DesignArray          5.302  0.004   5.314
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.


Installation output

DECIPHER.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’:
AlignProfiles.c:426:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  426 |     lGp *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:61:39: note: ‘lGp’ was declared here
   61 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
      |                                       ^~~
AlignProfiles.c:428:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  428 |     lGs *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:61:44: note: ‘lGs’ was declared here
   61 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
      |                                            ^~~
AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’:
AlignProfiles.c:1270:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1270 |     lGp *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:810:39: note: ‘lGp’ was declared here
  810 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
      |                                       ^~~
AlignProfiles.c:1272:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1272 |     lGs *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:810:44: note: ‘lGs’ was declared here
  810 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
      |                                            ^~~
AlignProfiles.c: In function ‘alignProfiles’:
AlignProfiles.c:379:11: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  379 |   #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(nthreads)
      |           ^~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function ‘calculateHairpinDeltaG’:
CalculateDeltaG.c:463:28: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  463 |    if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
      |                        ~~~~^~~~~
CalculateDeltaG.c:463:15: warning: ‘s1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  463 |    if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
      |           ~~~~^~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function ‘calculateFISH’:
CalculateFISH.c:25:23: 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:31:23: 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:37:23: 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:43:23: 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:49:23: 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:55:23: warning: missing braces around initializer [-Wmissing-braces]
   55 |  double dS_RR[4][4] = {
      |                       ^
   56 |   -18.38, -26.03, -19.18, -15.67,
      |   {                             }
   57 |   -28.25, -30.02, -19.18, -19.18,
      |   {                             }
   58 |   -35.68, -34.85, -30.02, -26.03,
      |   {                             }
   59 |   -22.59, -35.68, -28.25, -18.38
      |   {
   60 |  };
      |  }
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function ‘chainSegments’:
ChainSegments.c:524:28: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  524 |    if (minX == minY && upX == upY) {
      |                        ~~~~^~~~~~
ChainSegments.c:524:28: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Cluster.c -o Cluster.o
Cluster.c: In function ‘cluster._omp_fn.0’:
Cluster.c:418:15: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  418 |      minCs[i] = minC;
      |      ~~~~~~~~~^~~~~~
Cluster.c:246:50: 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:442:30: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  442 |       minCols[rowIndices[i]] = minC;
      |       ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:50: note: ‘minC’ was declared here
  246 |  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                  ^~~~
Cluster.c: In function ‘cluster’:
Cluster.c:464:52: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  464 |   rans[1*(length - 1) + k] = *(colNums + colIndices[minCol]); // column merged
      |                                                    ^
Cluster.c:781:13: warning: ‘nDiv’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  781 |     nDiv[j] -= dMatrix2[length*colIndices[j] - colIndices[j]*(colIndices[j] + 1)/2 + rowIndices[i] - colIndices[j]]; // col sums
      |             ^~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ClusterML.c -o ClusterML.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rdefines.h:38,
                 from ClusterML.c:16:
ClusterML.c: In function ‘clusterML’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/include/R_ext/RS.h:55:25: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   55 | #define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
      |                         ^~~~~~~~~~
ClusterML.c:1206:7: note: ‘Up’ was declared here
 1206 |  int *Up;
      |       ^~
ClusterML.c:1293:10: warning: ‘node’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1293 |  #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
      |          ^~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ClusterMP.c -o ClusterMP.o
ClusterMP.c: In function ‘clusterMP._omp_fn.0’:
ClusterMP.c:98:15: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   98 |  int i, j, k, m, w;
      |               ^
ClusterMP.c:153:9: warning: ‘P’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  153 |    int *P;
      |         ^
ClusterMP.c: In function ‘clusterMP’:
ClusterMP.c:640:3: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  640 |   free(Up);
      |   ^~~~~~~~
ClusterMP.c:140:10: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  140 |  #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
      |          ^~~
ClusterMP.c:140:10: warning: ‘nodes’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ClusterMP.c:140:10: warning: ‘lengths’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Compositions.c -o Compositions.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Compression.c -o Compression.o
Compression.c: In function ‘nbit._omp_fn.0’:
Compression.c:978:17: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  978 |      p[c] = ((k - 1) >> 8) & 0xFF; // length of run
      |              ~~~^~~~
Compression.c:516:12: note: ‘k’ was declared here
  516 |  int i, j, k, pos;
      |            ^
Compression.c:1012:12: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1012 |       count++;
      |       ~~~~~^~
Compression.c:544:29: note: ‘count’ was declared here
  544 |   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                             ^~~~~
Compression.c:1011:20: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1011 |       word = (word << 8) | (unsigned int)reorder(byte);
      |              ~~~~~~^~~~~
Compression.c:544:23: note: ‘word’ was declared here
  544 |   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                       ^~~~
Compression.c:1214:14: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1214 |       p[c++] = rev == 0 ? 254 : 255;
      |       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
Compression.c:545:27: note: ‘rev’ was declared here
  545 |   int lastTemp, currTemp, rev, len, len2, thresh = 1;
      |                           ^~~
Compression.c:558:7: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  558 |   int lower = 0;
      |       ^~~~~
Compression.c:1241:43: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1241 |     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
      |                                        ~~~^~~~~~~~~~~~~~
Compression.c:631:12: note: ‘lastTriplet’ was declared here
  631 |   int run, lastTriplet, lastCase;
      |            ^~~~~~~~~~~
Compression.c:1031:23: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1031 |         lastHit = dict[(word >> k) & 0xFF];
      |                       ^
Compression.c:544:17: note: ‘dict’ was declared here
  544 |   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                 ^~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function ‘consensusProfile’:
ConsensusSequence.c:1578:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1578 |  double *DBN, *s;
      |          ^~~
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:455:18: warning: ‘lastPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  455 |      *(runs + s) += weight;
      |                  ^~
ConsensusSequence.c:397:23: note: ‘lastPos’ was declared here
  397 |  int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
      |                       ^~~~~~~
ConsensusSequence.c:1771:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1771 |  double *HEC, *s;
      |          ^~~
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:2046:27: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2046 |    *(rans + k) += GO*(curr*total);
      |                      ~~~~~^~~~~~~
ConsensusSequence.c:2046:27: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:1941:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1941 |  int do_DBN, n, l, d;
      |                    ^
ConsensusSequence.c:1940:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1940 |  double *DBN, *s;
      |          ^~~
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2189:27: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2189 |    *(rans + k) += GO*(curr*total);
      |                      ~~~~~^~~~~~~
ConsensusSequence.c:2189:27: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:2084:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2084 |  int do_HEC, n, l, d;
      |                    ^
ConsensusSequence.c:2083:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2083 |  double *HEC, *s;
      |          ^~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:70:20: warning: missing braces around initializer [-Wmissing-braces]
   70 |  double NN[4][4] = {
      |                    ^
   71 |   -0.816507461,-2.5401714,-1.647430026,-1.184658548
      |   {
   72 |   ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
      |   }{
   73 |   ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
      |   }{
   74 |   ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
      |   }{
   75 |  };
      |  }
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
   77 |  double PM[4][4] = {
      |                    ^
   78 |   -0.141370102,-0.439805276,-0.285236035,-0.205111781
      |   {
   79 |   ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
      |   }{
   80 |   ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
      |   }{
   81 |   ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
      |   }{
   82 |  };
      |  }
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
   84 |  double sMM[4][5][5][4] = {
      |                           ^
   85 |   0,0,0,0
      |   {{{
   86 |   ,1.545032445,1.254355018,1.491691514,1.329138183
      |   }{
   87 |   ,1.150635633,0.582415494,1.075877275,1.187937642
      |   }{
   88 |   ,1.203555051,1.001540513,0.864287715,0.717125848
      |   }{
   89 |   ,0.75,0.65,0.69,0.78
      |   }{
   90 |   ,0.630005348,0.18553379,0.730763505,0.709272397
      |   -
      |   }},{{
   91 |   ,0,0,0,0
      |   }{
   92 |   ,0.856582783,-0.143236405,0.716721488,0.603652831
      |   }{
   93 |   ,0.851622883,0.653168672,0.676545316,1.187937642
      |   }{
   94 |   ,0.75,0.65,0.69,0.78
      |   }{
   95 |   ,1.231861002,0.746214538,1.087821916,0.989140748
      |   -
      |   }},{{
   96 |   ,1.822113278,1.270687029,1.336192565,1.364584949
      |   }{
   97 |   ,0,0,0,0
      |   }{
   98 |   ,1.443665704,1.385046493,1.256013166,1.329138183
      |   }{
   99 |   ,0.75,0.65,0.69,0.78
      |   }{
  100 |   ,1.478009492,0.882097231,1.20450984,1.061002478
      |   -
      |   }},{{
  101 |   ,1.496720812,0.846496194,0.967868114,0.989140748
      |   }{
  102 |   ,0.766581547,-0.024857805,0.50754303,0.709272397
      |   }{
  103 |   ,0,0,0,0
      |   }{
  104 |   ,0.75,0.65,0.69,0.78
      |   }{
  105 |   ,0.75,0.65,0.69,0.78
      |   -
      |   }},{{
  106 |   ,0.75,0.65,0.69,0.78
      |   }{
  107 |   ,0.75,0.65,0.69,0.78
      |   }{
  108 |   ,0.76,0.65,0.69,0.78
      |   }{
  109 |   ,0,0,0,0
      |   }{
  110 |   ,0,0,0,0
      |   -
      |   }}},{{{
  111 |   ,1.295827995,0.84547091,0.91019099,1.256013166
      |   }{
  112 |   ,0.755889609,0.241428373,0.396379912,0.676545316
      |   }{
  113 |   ,0.99945386,0.740323132,0.435659206,0.864287715
      |   }{
  114 |   ,0.65,0.55,0.48,0.69
      |   }{
  115 |   ,0.843147406,0.101248351,0.49063599,0.50754303
      |   -
      |   }},{{
  116 |   ,0,0,0,0
      |   }{
  117 |   ,1.0651638,0.249934344,0.699352949,0.716721488
      |   }{
  118 |   ,0.871921533,0.59458138,0.396379912,1.075877275
      |   }{
  119 |   ,0.65,0.56,0.49,0.69
      |   }{
  120 |   ,1.07531714,0.318907854,0.653287717,0.967868114
      |   -
      |   }},{{
  121 |   ,1.099899195,0.730184613,0.661798984,1.336192565
      |   }{
  122 |   ,0,0,0,0
      |   }{
  123 |   ,1.45897431,1.318532145,0.91019099,1.491691514
      |   }{
  124 |   ,0.65,0.56,0.49,0.69
      |   }{
  125 |   ,1.242135174,0.894838095,1.108555445,1.20450984
      |   -
      |   }},{{
  126 |   ,0.911428974,0.524430101,0.653287717,1.087821916
      |   }{
  127 |   ,0.503209827,0.274849491,0.49063599,0.730763505
      |   }{
  128 |   ,0,0,0,0
      |   }{
  129 |   ,0.65,0.55,0.48,0.69
      |   }{
  130 |   ,0.65,0.55,0.48,0.69
      |   -
      |   }},{{
  131 |   ,0.65,0.56,0.49,0.69
      |   }{
  132 |   ,0.65,0.56,0.49,0.69
      |   }{
  133 |   ,0.65,0.55,0.48,0.69
      |   }{
  134 |   ,0,0,0,0
      |   }{
  135 |   ,0,0,0,0
      |   -
      |   }}},{{{
  136 |   ,1.100661785,0.969784756,1.318532145,1.385046493
      |   }{
  137 |   ,0.565895968,-0.060347902,0.59458138,0.653168672
      |   }{
  138 |   ,0.782168488,0.788161238,0.740323132,1.001540513
      |   }{
  139 |   ,0.68,0.46,0.55,0.65
      |   }{
  140 |   ,0.468913405,-0.469855984,0.274849491,-0.024857805
      |   -
      |   }},{{
  141 |   ,0,0,0,0
      |   }{
  142 |   ,0.258195131,-0.70438632,0.249934344,-0.143236405
      |   }{
  143 |   ,0.502914193,-0.060347902,0.241428373,0.582415494
      |   }{
  144 |   ,0.68,0.47,0.56,0.65
      |   }{
  145 |   ,0.584083861,0.258975454,0.524430101,0.846496194
      |   -
      |   }},{{
  146 |   ,0.968040559,0.797499702,0.730184613,1.270687029
      |   }{
  147 |   ,0,0,0,0
      |   }{
  148 |   ,1.081040749,0.969784756,0.84547091,1.254355018
      |   }{
  149 |   ,0.68,0.47,0.56,0.65
      |   }{
  150 |   ,1.048553951,0.728354541,0.894838095,0.882097231
      |   -
      |   }},{{
  151 |   ,0.88611252,0.258975454,0.318907854,0.746214538
      |   }{
  152 |   ,0.239520858,-0.469855984,0.101248351,0.18553379
      |   }{
  153 |   ,0,0,0,0
      |   }{
  154 |   ,0.68,0.46,0.55,0.65
      |   }{
  155 |   ,0.68,0.46,0.55,0.65
      |   -
      |   }},{{
  156 |   ,0.68,0.47,0.56,0.65
      |   }{
  157 |   ,0.68,0.47,0.56,0.65
      |   }{
  158 |   ,0.68,0.46,0.55,0.65
      |   }{
  159 |   ,0,0,0,0
      |   }{
  160 |   ,0,0,0,0
      |   -
      |   }}},{{{
  161 |   ,1.566899704,1.081040749,1.45897431,1.443665704
      |   }{
  162 |   ,0.976725675,0.502914193,0.871921533,0.851622883
      |   }{
  163 |   ,1.482046826,0.782168488,0.99945386,1.203555051
      |   }{
  164 |   ,0.85,0.68,0.65,0.76
      |   }{
  165 |   ,0.798628781,0.239520858,0.503209827,0.766581547
      |   -
      |   }},{{
  166 |   ,0,0,0,0
      |   }{
  167 |   ,1.141098246,0.258195131,1.0651638,0.856582783
      |   }{
  168 |   ,0.976725675,0.565895968,0.755889609,1.150635633
      |   }{
  169 |   ,0.85,0.68,0.65,0.75
      |   }{
  170 |   ,1.125403302,0.88611252,0.911428974,1.496720812
      |   -
      |   }},{{
  171 |   ,1.68169282,0.968040559,1.099899195,1.822113278
      |   }{
  172 |   ,0,0,0,0
      |   }{
  173 |   ,1.566899704,1.100661785,1.295827995,1.545032445
      |   }{
  174 |   ,0.85,0.68,0.65,0.75
      |   }{
  175 |   ,1.35948517,1.048553951,1.242135174,1.478009492
      |   -
      |   }},{{
  176 |   ,1.125403302,0.584083861,1.07531714,1.231861002
      |   }{
  177 |   ,0.798628781,0.468913405,0.843147406,0.630005348
      |   }{
  178 |   ,0,0,0,0
      |   }{
  179 |   ,0.85,0.68,0.65,0.75
      |   }{
  180 |   ,0.85,0.68,0.65,0.75
      |   -
      |   }},{{
  181 |   ,0.85,0.68,0.65,0.75
      |   }{
  182 |   ,0.85,0.68,0.65,0.75
      |   }{
  183 |   ,0.85,0.68,0.65,0.75
      |   }{
  184 |   ,0,0,0,0
      |   }{
  185 |  };
      |  }}}
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c:838:29: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  838 |         cycles += lastCycle - thisCycle;
      |                   ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:269:37: note: ‘lastCycle’ was declared here
  269 |    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                     ^~~~~~~~~
DesignProbes.c:838:29: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  838 |         cycles += lastCycle - thisCycle;
      |                   ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:269:48: note: ‘thisCycle’ was declared here
  269 |    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                                ^~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Diff.c -o Diff.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘firstSeqsPosEqual’:
DistanceMatrix.c:796:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  796 |   if (!ci)
      |   ^~
DistanceMatrix.c:799:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  799 |    while (i < ex) {
      |    ^~~~~
DistanceMatrix.c:818:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  818 |   if (!cj)
      |   ^~
DistanceMatrix.c:821:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  821 |    while (j < ey) {
      |    ^~~~~
DistanceMatrix.c: In function ‘computeOverlap._omp_fn.0’:
DistanceMatrix.c:1053:11: warning: ‘one’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1053 |       two != one) {
      |       ~~~~^~~~~~
DistanceMatrix.c:1028:8: note: ‘one’ was declared here
 1028 |    int one, two;
      |        ^~~
DistanceMatrix.c:1340:19: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1340 |       if (w1 - p1 + p2 > w2 - t2) {
      |           ~~~~~~~~^~~~
DistanceMatrix.c:883:69: note: ‘p2’ was declared here
  883 |  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:1340:14: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1340 |       if (w1 - p1 + p2 > w2 - t2) {
      |           ~~~^~~~
DistanceMatrix.c:883:65: note: ‘p1’ was declared here
  883 |  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:1374:31: warning: ‘off’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1374 |      (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
      |                           ~~~~^~~~~~
DistanceMatrix.c:883:89: note: ‘off’ was declared here
  883 |  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:1374:31: warning: ‘OV’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1374 |      (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
      |                           ~~~~^~~~~~
DistanceMatrix.c:883:85: note: ‘OV’ was declared here
  883 |  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:1379:42: warning: ‘ov’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1379 |        sim[i] = (double)pos/((double)(ov - g2));
      |                                      ~~~~^~~~~
DistanceMatrix.c:883:81: note: ‘ov’ was declared here
  883 |  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:1378:10: warning: ‘o’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1378 |       if (o == 1) {
      |          ^
DistanceMatrix.c:883:105: note: ‘o’ was declared here
  883 |  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;
      |                                                                                                         ^
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function ‘pop’:
EnumerateSequence.c:545:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  545 |  x = x + (x >> 4) & 0xF0F0F0F;
      |      ~~^~~~~~~~~~
EnumerateSequence.c: In function ‘enumerateSequence’:
EnumerateSequence.c:358:10: warning: ‘tot’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  358 |  #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
      |          ^~~
EnumerateSequence.c:358:10: warning: ‘mN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
EnumerateSequence.c: In function ‘enumerateSequenceReducedAA’:
EnumerateSequence.c:955:10: warning: ‘tot’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  955 |  #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
      |          ^~~
EnumerateSequence.c:955:10: warning: ‘mN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function ‘findFrameshifts’:
FindFrameshifts.c:381:14: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  381 |    } else if (k == 2) {
      |              ^
FindFrameshifts.c:318:19: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  318 |     if (C[k*rc + j*r + i] >= 0) {
      |                  ~^~
FindFrameshifts.c:370:8: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  370 |      i += B[k*rc + j*r + i];
      |      ~~^~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rdefines.h:41,
                 from FindFrameshifts.c:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rinternals.h:901:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  901 | #define eval   Rf_eval
      |                ^~~~~~~
FindFrameshifts.c:162:24: note: ‘utilsPackage’ was declared here
  162 |  SEXP percentComplete, utilsPackage;
      |                        ^~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rdefines.h:41,
                 from FindFrameshifts.c:11:
/home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rinternals.h:901:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  901 | #define eval   Rf_eval
      |                ^~~~~~~
FindFrameshifts.c:162:7: note: ‘percentComplete’ was declared here
  162 |  SEXP percentComplete, utilsPackage;
      |       ^~~~~~~~~~~~~~~
FindFrameshifts.c:468:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  468 |     before = *rPercentComplete;
      |     ~~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function ‘scoreCodonModel’:
GeneFinding.c:422:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  422 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c:432:29: warning: ‘lastVal’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  432 |      score += codons[lastVal*64 + val];
      |                      ~~~~~~~^~~
GeneFinding.c: In function ‘startCodonModel’:
GeneFinding.c:791:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  791 |    val = getBaseRC(x_i.ptr[j++]);
      |                           ^
GeneFinding.c: In function ‘scoreStartCodonModel’:
GeneFinding.c:892:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  892 |    val = getBaseRC(x_i.ptr[j++]);
      |                           ^
GeneFinding.c: In function ‘initialCodonModel’:
GeneFinding.c:973:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  973 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘scoreInitialCodonModel’:
GeneFinding.c:1059:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1059 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘terminationCodonModel’:
GeneFinding.c:1131:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1131 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘scoreTerminationCodonModel’:
GeneFinding.c:1216:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1216 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘getRegion’:
GeneFinding.c:1286:23: warning: ‘x_i.length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1286 |     (s == 0 && j >= 0 && j + w <= x_i.length)) {
      |     ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1289:39: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1289 |       seq[k] = getBaseLetterRC(x_i.ptr[j--]);
      |                                       ^
GeneFinding.c: In function ‘autocorrelationModel’:
GeneFinding.c:1379:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1379 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘scoreAutocorrelationModel’:
GeneFinding.c:1496:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1496 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘couplingModel’:
GeneFinding.c:1598:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1598 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘scoreCouplingModel’:
GeneFinding.c:1712:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1712 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1826:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1826 |     val = getBaseRC(x_i.ptr[j++]);
      |                            ^
GeneFinding.c: In function ‘scoreNucleotideBiasModel’:
GeneFinding.c:1913:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1913 |     val = getBaseRC(x_i.ptr[j++]);
      |                            ^
GeneFinding.c: In function ‘upstreamMotifModel’:
GeneFinding.c:1990:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1990 |      val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
      |                                          ^
GeneFinding.c: In function ‘scoreUpstreamMotifModel’:
GeneFinding.c:2090:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2090 |      val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
      |                                          ^
GeneFinding.c: In function ‘scoreRunLengthModel’:
GeneFinding.c:2307:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2307 |     val = getBaseRC(x_i.ptr[j++]);
      |                            ^
GeneFinding.c: In function ‘stopCodonModel’:
GeneFinding.c:2419:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2419 |    val = getBaseRC(x_i.ptr[j++]);
      |                           ^
GeneFinding.c: In function ‘scoreStopCodonModel’:
GeneFinding.c:2520:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2520 |    val = getBaseRC(x_i.ptr[j++]);
      |                           ^
GeneFinding.c: In function ‘codonFrequencies’:
GeneFinding.c:2578:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2578 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c GetPools.c -o GetPools.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Import.c -o Import.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c InformationContent.c -o InformationContent.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c IntDist.c -o IntDist.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ManipulateXStringSet.c -o ManipulateXStringSet.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function ‘meltPolymer’:
MeltPolymer.c:79:20: 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:88:20: 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:358:24: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  358 |      *(rans + k + l*s) += 1;
      |                        ^~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c NNLS.c -o NNLS.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Order.c -o Order.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’:
PairwiseAlignment.c:472:11: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  472 |     P2[i] = p2;
      |     ~~~~~~^~~~
PairwiseAlignment.c:175:12: note: ‘p2’ was declared here
  175 |  int *p1, *p2, *p3, *p4;
      |            ^~
PairwiseAlignment.c:471:11: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  471 |     P1[i] = p1;
      |     ~~~~~~^~~~
PairwiseAlignment.c:175:7: note: ‘p1’ was declared here
  175 |  int *p1, *p2, *p3, *p4;
      |       ^~
PairwiseAlignment.c:476:11: warning: ‘p4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  476 |     P4[i] = p4;
      |     ~~~~~~^~~~
PairwiseAlignment.c:175:22: note: ‘p4’ was declared here
  175 |  int *p1, *p2, *p3, *p4;
      |                      ^~
PairwiseAlignment.c:475:11: warning: ‘p3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  475 |     P3[i] = p3;
      |     ~~~~~~^~~~
PairwiseAlignment.c:175:17: note: ‘p3’ was declared here
  175 |  int *p1, *p2, *p3, *p4;
      |                 ^~
PairwiseAlignment.c: In function ‘alignPairs’:
PairwiseAlignment.c:1107:10: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1107 |  #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
      |          ^~~
PairwiseAlignment.c:1107:10: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
PairwiseAlignment.c:1107:10: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function ‘predictDBN’:
PredictDBN.c:873:29: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  873 |         range2[0] = nucs[pos[prev]];// + 1;
      |                             ^
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function ‘predictHEC’:
PredictHEC.c:255:4: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  255 |    SET_VECTOR_ELT(ret, i, ans);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:233:16: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  233 |      states[j] = 'C';
      |      ~~~~~~~~~~^~~~~
PredictHEC.c:237:18: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  237 |     *(rans + 3*j + 1) = E;
      |      ~~~~~~~~~~~~^~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Search.c -o Search.o
Search.c: In function ‘searchIndex._omp_fn.0’:
Search.c:515:12: warning: ‘s_j.length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  515 |      bound = s_j.length - 1; // right bound
      |      ~~~~~~^~~~~~~~~~~~~~~~
Search.c:443:23: note: ‘s_j.length’ was declared here
  443 |     Chars_holder p_i, s_j;
      |                       ^~~
Search.c:443:23: warning: ‘s_j.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:449:9: warning: ‘maxLen’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  449 |     int maxLen; // maximum observed length
      |         ^~~~~~
Search.c: In function ‘searchIndex’:
Search.c:969:5: warning: ‘ans3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  969 |     SET_VECTOR_ELT(ans3, k, ans);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
Search.c:201:9: warning: ‘matrices’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  201 |  int ***matrices;
      |         ^~~~~~~~
Search.c:208:10: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  208 |  #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |          ^~~
Search.c:208:10: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:10: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:10: warning: ‘lkup_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:10: warning: ‘lkup_row’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:10: warning: ‘dS’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:10: warning: ‘sM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Translate.c -o Translate.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Utils.c -o Utils.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rdefines.h:41,
                 from Utils.c:16:
Utils.c: In function ‘matchOrder’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rinternals.h:901:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  901 | #define eval   Rf_eval
      |                ^~~~~~~
Utils.c:333:24: note: ‘utilsPackage’ was declared here
  333 |  SEXP percentComplete, utilsPackage;
      |                        ^~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rdefines.h:41,
                 from Utils.c:16:
/home/biocbuild/R/R-beta-2024-04-15_r86425/include/Rinternals.h:901:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  901 | #define eval   Rf_eval
      |                ^~~~~~~
Utils.c:333:7: note: ‘percentComplete’ was declared here
  333 |  SEXP percentComplete, utilsPackage;
      |       ^~~~~~~~~~~~~~~
Utils.c:431:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  431 |     before = *rPercentComplete;
      |     ~~~~~~~^~~~~~~~~~~~~~~~~~~
Utils.c: In function ‘splitPartitions’:
Utils.c:982:21: warning: ‘change’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  982 |   } else if (change - j >= m && // large enough partition
      |              ~~~~~~~^~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c VectorSums.c -o VectorSums.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Biostrings/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.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 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-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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_REDUCED0.0520.0080.060
Add2DB0.8580.0360.900
AdjustAlignment0.2930.0000.295
AlignDB1.5230.0241.552
AlignPairs4.1230.0404.174
AlignProfiles1.1470.0041.154
AlignSeqs241.358 0.551242.392
AlignSynteny4.2210.0044.233
AlignTranslation15.883 0.09616.006
AmplifyDNA0.0030.0000.003
Array2Matrix5.4050.0205.431
BLOSUM0.0130.0040.017
BrowseDB0.0570.0000.060
BrowseSeqs29.927 0.10330.075
CalculateEfficiencyArray0.0150.0040.019
CalculateEfficiencyFISH0.0060.0000.006
CalculateEfficiencyPCR0.0060.0000.005
Clusterize8.5790.0328.628
Codec1.4400.0001.442
ConsensusSequence0.2450.0000.246
Cophenetic0.2130.0000.213
CorrectFrameshifts22.076 0.07222.192
CreateChimeras1.1100.0001.111
DB2Seqs0.0490.0070.056
DesignArray5.3020.0045.314
DesignPrimers0.0130.0000.014
DesignProbes0.0140.0000.014
DesignSignatures0.0150.0000.015
DetectRepeats24.838 0.11224.995
DigestDNA0.2210.0000.221
Disambiguate0.0760.0000.076
DistanceMatrix0.0630.0040.067
ExtractGenes65.302 0.18465.598
FindChimeras0.1010.0040.105
FindGenes62.870 0.18363.164
FindNonCoding111.160 0.655115.815
FindSynteny2.2340.0042.242
FormGroups0.080.000.08
Genes-class63.013 0.19663.325
HEC_MI0.2050.0120.217
IdConsensus0.5920.0080.602
IdLengths0.0450.0000.045
IdTaxa12.482 0.02412.528
IdentifyByRank0.0470.0000.047
IndexSeqs1.2200.0041.226
InvertedIndex-class0.6880.0120.700
LearnNonCoding143.521 1.433145.173
LearnTaxa16.863 0.31117.445
MIQS0.0400.0040.044
MMLSUM0.0090.0000.009
MODELS0.0030.0000.003
MapCharacters140.725 0.515141.486
MaskAlignment0.5660.0040.572
MeltDNA0.0770.0000.078
NNLS0.0000.0040.004
NonCoding-class0.0500.0080.058
NonCodingRNA0.0910.0120.103
OrientNucleotides0.5540.0000.555
PAM0.0090.0000.009
PFASUM0.010.000.01
PredictDBN0.0110.0000.011
PredictHEC0.2700.0080.279
RESTRICTION_ENZYMES0.0010.0010.003
ReadDendrogram0.0240.0020.026
RemoveGaps0.0180.0000.018
ScoreAlignment7.2370.0127.266
SearchDB0.0690.0040.073
SearchIndex1.6340.1541.792
Seqs2DB0.1460.0050.150
StaggerAlignment16.680 0.09616.815
Synteny-class2.8240.0162.847
Taxa-class13.325 0.01613.368
TerminalChar0.0080.0000.009
TileSeqs5.4090.0005.421
TrainingSet_16S2.6940.0002.700
TreeLine13.388 0.09913.518
TrimDNA0.1700.0040.174
WriteDendrogram0.0040.0000.005
WriteGenes64.721 0.14065.668
deltaGrules0.0100.0000.011
deltaGrulesRNA0.0210.0000.022
deltaHrules0.0180.0000.018
deltaHrulesRNA0.0170.0000.017
deltaSrules0.0740.0000.074
deltaSrulesRNA0.0160.0000.016