Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 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: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 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: 2021-10-14 09:29:51 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:42:23 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 752.3 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         108.222  0.296 108.542
DetectRepeats       82.367  0.068  82.439
LearnNonCoding      47.639  3.600  51.358
FindNonCoding       49.461  0.348  49.813
BrowseSeqs          44.315  0.208  44.562
ExtractGenes        39.314  0.375  42.936
Genes-class         35.827  0.102  35.930
FindGenes           34.260  0.204  34.466
WriteGenes          31.059  0.092  31.152
MapCharacters       28.040  0.148  28.365
AlignSeqs           21.612  0.355  21.969
CorrectFrameshifts  15.865  0.064  15.929
StaggerAlignment    11.680  0.124  11.805
AlignTranslation    10.904  0.073  10.979
IdTaxa              10.905  0.044  10.948
Taxa-class          10.798  0.024  10.822
LearnTaxa            7.075  0.396   7.474
* 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_REDUCED0.0400.0120.052
Add2DB0.2380.0310.272
AdjustAlignment0.1950.0040.199
AlignDB0.8920.0450.938
AlignProfiles0.7900.0080.799
AlignSeqs21.612 0.35521.969
AlignSynteny2.7010.0282.730
AlignTranslation10.904 0.07310.979
AmplifyDNA0.0040.0000.003
Array2Matrix4.4720.0314.504
BrowseDB0.0220.0000.023
BrowseSeqs44.315 0.20844.562
CalculateEfficiencyArray0.0120.0040.015
CalculateEfficiencyFISH0.0050.0000.005
CalculateEfficiencyPCR0.0040.0000.005
Codec1.2050.0041.208
ConsensusSequence0.1500.0040.154
Cophenetic1.0350.0001.035
CorrectFrameshifts15.865 0.06415.929
CreateChimeras0.7030.0000.704
DB2Seqs0.0150.0050.021
DesignArray4.4590.0164.474
DesignPrimers0.0000.0000.001
DesignProbes0.0010.0000.000
DesignSignatures0.0020.0000.001
DetectRepeats82.367 0.06882.439
DigestDNA0.1310.0040.135
Disambiguate0.0420.0000.043
DistanceMatrix0.0280.0000.028
ExtractGenes39.314 0.37542.936
FindChimeras0.0480.0040.053
FindGenes34.260 0.20434.466
FindNonCoding49.461 0.34849.813
FindSynteny1.2450.0001.244
FormGroups0.0350.0040.040
Genes-class35.827 0.10235.930
HEC_MI0.2620.0040.266
IdClusters0.5160.0030.518
IdConsensus0.7460.0280.775
IdLengths0.0210.0000.021
IdTaxa10.905 0.04410.948
IdentifyByRank0.0210.0000.021
LearnNonCoding47.639 3.60051.358
LearnTaxa7.0750.3967.474
MIQS0.0420.0040.046
MODELS000
MapCharacters28.040 0.14828.365
MaskAlignment0.4670.0040.471
MeltDNA0.0390.0000.039
NNLS0.0040.0000.004
NonCoding-class0.0540.0080.062
NonCodingRNA0.1090.0040.113
OrientNucleotides0.8870.0060.894
PFASUM0.0240.0060.029
PredictDBN108.222 0.296108.542
PredictHEC0.2390.0040.243
RESTRICTION_ENZYMES0.0050.0000.005
ReadDendrogram0.0580.0000.058
RemoveGaps0.0110.0000.010
SearchDB0.0330.0000.033
Seqs2DB0.0980.0040.102
StaggerAlignment11.680 0.12411.805
Synteny-class1.6660.0081.674
Taxa-class10.798 0.02410.822
TerminalChar0.0130.0000.014
TileSeqs3.9840.0003.984
TrainingSet_16S1.790.001.79
TrimDNA0.0770.0000.078
WriteDendrogram0.0040.0000.004
WriteGenes31.059 0.09231.152
deltaGrules0.0090.0000.009
deltaHrules0.0190.0000.019
deltaHrulesRNA0.0180.0000.018
deltaSrules0.0520.0000.052
deltaSrulesRNA0.0160.0000.016