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This page was generated on 2021-09-22 15:04:49 -0400 (Wed, 22 Sep 2021).

CHECK results for DECIPHER on nebbiolo1

To the developers/maintainers of the DECIPHER package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 454/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 2.20.0  (landing page)
Erik Wright
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/DECIPHER
git_branch: RELEASE_3_13
git_last_commit: bcd35a8
git_last_commit_date: 2021-05-19 11:50:12 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DECIPHER
Version: 2.20.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DECIPHER_2.20.0.tar.gz
StartedAt: 2021-09-21 09:33:07 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 09:45:56 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 769.0 seconds
RetCode: 0
Status:   OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DECIPHER_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/DECIPHER.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘2.20.0’
* 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
* checking installed package size ... NOTE
  installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    data      7.4Mb
    extdata   1.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DesignSignatures: no visible binding for global variable ‘deltaHrules’
FindGenes: no visible binding for global variable ‘deltaHrulesRNA’
FindNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
LearnNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
PredictDBN: no visible binding for global variable ‘deltaHrulesRNA’
Undefined global functions or variables:
  deltaHrules deltaHrulesRNA
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
PredictDBN         113.410  0.420 113.901
DetectRepeats       86.375  0.082  86.468
LearnNonCoding      49.038  4.623  53.729
FindNonCoding       52.283  0.472  52.761
BrowseSeqs          44.155  0.164  44.361
ExtractGenes        41.935  0.336  44.140
Genes-class         35.631  0.096  35.730
FindGenes           32.765  0.308  33.076
WriteGenes          31.799  0.312  32.113
MapCharacters       27.954  0.160  28.210
AlignSeqs           21.362  0.668  22.034
CorrectFrameshifts  16.295  0.060  16.356
StaggerAlignment    11.753  0.084  11.837
Taxa-class          11.704  0.044  11.749
IdTaxa              11.372  0.052  11.424
AlignTranslation    11.202  0.072  11.276
LearnTaxa            6.848  0.496   7.344
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.



Installation output

DECIPHER.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:401:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  401 |     lGp *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:39:39: note: ‘lGp’ was declared here
   39 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
      |                                       ^~~
AlignProfiles.c:403:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  403 |     lGs *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:39:44: note: ‘lGs’ was declared here
   39 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS;
      |                                            ^~~
AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’:
AlignProfiles.c:1220:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1220 |     lGp *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:763:39: note: ‘lGp’ was declared here
  763 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
      |                                       ^~~
AlignProfiles.c:1222:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1222 |     lGs *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:763:44: note: ‘lGs’ was declared here
  763 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R;
      |                                            ^~~
AlignProfiles.c: In function ‘alignProfiles’:
AlignProfiles.c:355:11: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  355 |   #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs) num_threads(nthreads)
      |           ^~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:375:26: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  375 |  int i, j, k, count, s1, s2;
      |                          ^~
CalculateDeltaG.c:375:22: warning: ‘s1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  375 |  int i, j, k, count, s1, s2;
      |                      ^~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:422:72: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  422 |    int minDx = 2e9, minDy = 2e9, minX = -1, minY = -2, merge = 0, upX, upY;
      |                                                                        ^~~
ChainSegments.c:470:8: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  470 |     if (upX) { // new chain is last
      |        ^
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:403:15: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  403 |        minCol = minC;
      |        ~~~~~~~^~~~~~
Cluster.c:229:50: note: ‘minC’ was declared here
  229 |  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                  ^~~~
Cluster.c: In function ‘cluster._omp_fn.1’:
Cluster.c:418:30: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  418 |       minCols[rowIndices[i]] = minC;
      |       ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:229:50: note: ‘minC’ was declared here
  229 |  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                  ^~~~
Cluster.c: In function ‘cluster’:
Cluster.c:229:50: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Cluster.c:451:168: warning: ‘nDiv’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  451 |      rans[4*(length - 1) + k] = dMatrix2[length*colIndices[minCol] - colIndices[minCol]*(colIndices[minCol] + 1)/2 + rowIndices[minRow] - colIndices[minCol]]/2 + (nDiv[minCol] - nDiv[minRow + 1])/(2*(size-2)); // col
      |                                                                                                                                                                        ^
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ClusterML.c -o ClusterML.o
ClusterML.c: In function ‘clusterML._omp_fn.2’:
ClusterML.c:556:40: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  556 |       node[count*maxWidth*4 + i*4 + 0] += *(Ls + 0*length + j);
      |                                        ^~
ClusterML.c:420:6: note: ‘count’ was declared here
  420 |  int count;
      |      ^~~~~
ClusterML.c: In function ‘clusterML’:
ClusterML.c:441:11: warning: ‘node’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  441 |   #pragma omp parallel for private(i,j,y_i,row,count) schedule(guided) num_threads(nthreads)
      |           ^~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c CommonGaps.c -o CommonGaps.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Compositions.c -o Compositions.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:976:17: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  976 |      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:1010:12: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1010 |       count++;
      |       ~~~~~^~
Compression.c:542:29: note: ‘count’ was declared here
  542 |   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                             ^~~~~
Compression.c:1009:20: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1009 |       word = (word << 8) | (unsigned int)reorder(byte);
      |              ~~~~~~^~~~~
Compression.c:542:23: note: ‘word’ was declared here
  542 |   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                       ^~~~
Compression.c:1212:14: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1212 |       p[c++] = rev==0 ? 254 : 255;
      |       ~~~~~~~^~~~~~~~~~~~~~~~~~~~
Compression.c:543:27: note: ‘rev’ was declared here
  543 |   int lastTemp, currTemp, rev, len, len2, thresh = 1;
      |                           ^~~
Compression.c:556:7: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  556 |   int lower = 0;
      |       ^~~~~
Compression.c:1239:43: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1239 |     if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
      |                                        ~~~^~~~~~~~~~~~~~
Compression.c:629:12: note: ‘lastTriplet’ was declared here
  629 |   int run, lastTriplet, lastCase;
      |            ^~~~~~~~~~~
Compression.c:1325:4: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1325 |    free(dict);
      |    ^~~~~~~~~~
Compression.c:542:17: note: ‘dict’ was declared here
  542 |   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                 ^~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:456:14: warning: ‘length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  456 |    } else if (length==2) { // run of length 3
      |              ^
ConsensusSequence.c:397:15: note: ‘length’ was declared here
  397 |  int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
      |               ^~~~~~
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:1938:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1938 |  int do_DBN, n, l, d;
      |                    ^
ConsensusSequence.c:1937:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1937 |  double *DBN, *s;
      |          ^~~
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2063:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2063 |  int do_HEC, n, l, d;
      |                    ^
ConsensusSequence.c:2062:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2062 |  double *HEC, *s;
      |          ^~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:834:29: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  834 |         cycles += lastCycle - thisCycle;
      |                   ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:37: note: ‘lastCycle’ was declared here
  267 |    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                     ^~~~~~~~~
DesignProbes.c:834:29: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  834 |         cycles += lastCycle - thisCycle;
      |                   ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:267:48: note: ‘thisCycle’ was declared here
  267 |    int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                                ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Diff.c -o Diff.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:625:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  625 |   if (!ci)
      |   ^~
DistanceMatrix.c:628:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  628 |    while (i < ex) {
      |    ^~~~~
DistanceMatrix.c:647:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  647 |   if (!cj)
      |   ^~
DistanceMatrix.c:650:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  650 |    while (j < ey) {
      |    ^~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:315:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  315 |  x = x + (x >> 4) & 0xF0F0F0F;
      |      ~~^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:320:13: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  320 |      pos = i*3 + k + 1;
      |            ~^~
In file included from /home/biocbuild/bbs-3.13-bioc/R/include/Rdefines.h:42,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.13-bioc/R/include/Rinternals.h:1557:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1557 | #define eval   Rf_eval
      |                ^~~~~~~
FindFrameshifts.c:162:24: note: ‘utilsPackage’ was declared here
  162 |  SEXP percentComplete, utilsPackage;
      |                        ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/include/Rdefines.h:42,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.13-bioc/R/include/Rinternals.h:1557:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1557 | #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/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:388:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  388 |  Chars_holder x_i;
      |               ^~~
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:1286:21: 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:1252:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1252 |  Chars_holder x_i;
      |               ^~~
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:1681:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1681 |  Chars_holder x_i;
      |               ^~~
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1788:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1788 |  Chars_holder x_i;
      |               ^~~
GeneFinding.c: In function ‘scoreNucleotideBiasModel’:
GeneFinding.c:1882:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1882 |  Chars_holder x_i;
      |               ^~~
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:2276:15: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2276 |  Chars_holder x_i;
      |               ^~~
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/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c GetPools.c -o GetPools.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Import.c -o Import.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c InformationContent.c -o InformationContent.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c InsertGaps.c -o InsertGaps.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c IntDist.c -o IntDist.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:54:10: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   54 |  double *rans;
      |          ^~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function ‘intMatchSelfOnce’:
MultiMatch.c:866:21: warning: variable ‘start’ set but not used [-Wunused-but-set-variable]
  866 |  int i, j, k, temp, start = 0;
      |                     ^~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/include/Rdefines.h:42,
                 from MultiMatch.c:11:
MultiMatch.c: In function ‘matchLists’:
/home/biocbuild/bbs-3.13-bioc/R/include/Rinternals.h:1557:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1557 | #define eval   Rf_eval
      |                ^~~~~~~
MultiMatch.c:244:24: note: ‘utilsPackage’ was declared here
  244 |  SEXP percentComplete, utilsPackage;
      |                        ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/include/Rdefines.h:42,
                 from MultiMatch.c:11:
/home/biocbuild/bbs-3.13-bioc/R/include/Rinternals.h:1557:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1557 | #define eval   Rf_eval
      |                ^~~~~~~
MultiMatch.c:244:7: note: ‘percentComplete’ was declared here
  244 |  SEXP percentComplete, utilsPackage;
      |       ^~~~~~~~~~~~~~~
MultiMatch.c:327:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  327 |     before = *rPercentComplete;
      |     ~~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c NNLS.c -o NNLS.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Order.c -o Order.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:869:29: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  869 |         range2[0] = nucs[pos[prev]];// + 1;
      |                             ^
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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:42:8: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   42 |  char *states;
      |        ^~~~~~
PredictHEC.c:41:24: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   41 |  double H, E, C, sum, *rans;
      |                        ^~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c RemoveGaps.c -o RemoveGaps.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ReplaceChars.c -o ReplaceChars.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Translate.c -o Translate.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c VectorSums.c -o VectorSums.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.o CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PredictDBN.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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_REDUCED0.0440.0080.052
Add2DB0.2360.0150.253
AdjustAlignment0.1750.0040.180
AlignDB0.8380.0680.908
AlignProfiles0.7520.0160.768
AlignSeqs21.362 0.66822.034
AlignSynteny2.4240.0042.430
AlignTranslation11.202 0.07211.276
AmplifyDNA0.0000.0040.003
Array2Matrix4.6900.0324.722
BrowseDB0.0240.0040.028
BrowseSeqs44.155 0.16444.361
CalculateEfficiencyArray0.0120.0040.016
CalculateEfficiencyFISH0.0050.0000.005
CalculateEfficiencyPCR0.0040.0000.004
Codec1.1250.0001.125
ConsensusSequence0.1490.0040.152
Cophenetic0.9820.0070.990
CorrectFrameshifts16.295 0.06016.356
CreateChimeras0.6870.0000.687
DB2Seqs0.0100.0080.018
DesignArray4.5920.0284.619
DesignPrimers0.0010.0000.001
DesignProbes0.0010.0000.001
DesignSignatures0.0010.0000.001
DetectRepeats86.375 0.08286.468
DigestDNA0.1330.0090.142
Disambiguate0.0400.0070.048
DistanceMatrix0.0280.0040.032
ExtractGenes41.935 0.33644.140
FindChimeras0.0540.0000.054
FindGenes32.765 0.30833.076
FindNonCoding52.283 0.47252.761
FindSynteny1.2110.0041.215
FormGroups0.0410.0000.041
Genes-class35.631 0.09635.730
HEC_MI0.2620.0040.266
IdClusters0.4920.0120.504
IdConsensus0.710.020.73
IdLengths0.0150.0040.019
IdTaxa11.372 0.05211.424
IdentifyByRank0.0220.0000.023
LearnNonCoding49.038 4.62353.729
LearnTaxa6.8480.4967.344
MIQS0.0450.0000.046
MODELS0.0010.0000.001
MapCharacters27.954 0.16028.210
MaskAlignment0.4710.0040.475
MeltDNA0.0350.0040.040
NNLS0.0000.0040.004
NonCoding-class0.0580.0040.063
NonCodingRNA0.1120.0000.113
OrientNucleotides0.9110.0000.911
PFASUM0.0260.0040.031
PredictDBN113.410 0.420113.901
PredictHEC0.2380.0040.243
RESTRICTION_ENZYMES0.0020.0040.005
ReadDendrogram0.0600.0000.059
RemoveGaps0.0130.0000.012
SearchDB0.0560.0030.059
Seqs2DB0.0840.0030.087
StaggerAlignment11.753 0.08411.837
Synteny-class1.8830.0121.895
Taxa-class11.704 0.04411.749
TerminalChar0.0100.0040.014
TileSeqs4.1180.0004.118
TrainingSet_16S1.9460.0001.945
TrimDNA0.0460.0080.054
WriteDendrogram0.0030.0000.004
WriteGenes31.799 0.31232.113
deltaGrules0.0070.0040.011
deltaHrules0.020.000.02
deltaHrulesRNA0.0430.0000.043
deltaSrules0.0560.0000.056
deltaSrulesRNA0.0170.0000.017