##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings DECIPHER_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DECIPHER.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘2.30.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is 13.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    data      7.5Mb
    extdata   2.3Mb
    libs      1.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AlignSeqs: no visible binding for global variable ‘deltaGrulesRNA’
DesignSignatures: no visible binding for global variable ‘deltaHrules’
FindGenes: no visible binding for global variable ‘deltaHrulesRNA’
FindNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
LearnNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
PredictDBN: no visible binding for global variable ‘deltaGrulesRNA’
TreeLine: multiple local function definitions for ‘.minimize’ with
  different formal arguments
Undefined global functions or variables:
  deltaGrulesRNA deltaHrules deltaHrulesRNA
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘DECIPHER-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LearnNonCoding
> ### Title: Learn a Non-Coding RNA Model
> ### Aliases: LearnNonCoding
> 
> ### ** Examples
> 
> # import a family of non-coding RNAs
> fas_path <- system.file("extdata",
+ 	"IhtA.fas",
+ 	package="DECIPHER")
> rna <- readRNAStringSet(fas_path)
> rna
RNAStringSet object of length 27:
     width seq                                              names               
 [1]   103 AAGAUGAUAUUCUGCGCCAUGGA...UGAUUGUUGUUUUCUUGGCUUU KE360988.1/6443-6...
 [2]   105 AAGAUGAUAUUCUCCGCCGUGGA...AACUUUAUGUUUUCUUGGCUUU AE002161.1/54676-...
 [3]   107 AAGUUGGUAUUCUAACGCCAUGG...UAUCUCCGGUUCUCUUGGCUUU AE001273.1/773281...
 [4]   107 AAGUUGGUAUUCUAACGCCAUGG...UGUCUCCAGUUCUCUUGGCUUU AE002160.2/53054-...
 [5]   103 AAGAUGAUAUUCUACGCCAUGGA...UGAUUGUUGUUUUCUUGGCUUU AE015925.1/52097-...
 ...   ... ...
[23]   107 AAGUUGGUAUUCUAACGCCAUGG...UAUCUCCGGUUCUCUUGGCUUU CP006674.1 Chlamy...
[24]   103 AAGAUGAUAUUCUGCGCCAUGGA...UGAUUGUUGUUUUCUUGGCUUU KE356008.1 Chlamy...
[25]   108 AAGUUGGUAUUCUAACGCCAUGG...UAUCUCCGGUUCUCUUGGCUUU CVNC01000001.1 Ch...
[26]   103 AAGAUGAUAUUCUGCGCCAUGGA...UGAUUGUUGUUUUCUUGGCUUU AP006861.1 Chlamy...
[27]   101 AAGAUGAUAUUCUACGCCAUGGA...AUGAUGUUGUUUUCUUGGCUUU CP015840.1 Chlamy...
> 
> # align the sequences
> RNA <- AlignSeqs(rna)
Predicting structures based on free energies:
================================================================================

Time difference of 0.83 secs

Determining distance matrix based on shared 7-mers:
================================================================================

Time difference of 0 secs

Clustering into groups by similarity:
================================================================================

Time difference of 0.01 secs

Aligning Sequences:
================================================================================

Time difference of 0.21 secs

Iteration 1 of 2:

Determining distance matrix based on alignment:
================================================================================

Time difference of 0 secs

Reclustering into groups by similarity:
================================================================================

Time difference of 0.01 secs

Realigning Sequences:
================================================================================

Time difference of 0.11 secs

Iteration 2 of 2:

Determining distance matrix based on alignment:
================================================================================

Time difference of 0 secs

Reclustering into groups by similarity:
================================================================================

Time difference of 0.01 secs

Realigning Sequences:
================================================================================

Time difference of 0.02 secs

> RNA
RNAStringSet object of length 27:
     width seq                                              names               
 [1]   113 AAGAUGAUAUUCUG-CGCCAUGG...GAUUGU-UGUUUUCUUGGCUUU KE360988.1/6443-6...
 [2]   113 AAGAUGAUAUUCUC-CGCCGUGG...AACUUUAUGUUUUCUUGGCUUU AE002161.1/54676-...
 [3]   113 AAGUUGGUAUUCUAACGCCAUGG...--UCUCCGGUUCUCUUGGCUUU AE001273.1/773281...
 [4]   113 AAGUUGGUAUUCUAACGCCAUGG...--UCUCCAGUUCUCUUGGCUUU AE002160.2/53054-...
 [5]   113 AAGAUGAUAUUCUA-CGCCAUGG...GAUUGU-UGUUUUCUUGGCUUU AE015925.1/52097-...
 ...   ... ...
[23]   113 AAGUUGGUAUUCUAACGCCAUGG...--UCUCCGGUUCUCUUGGCUUU CP006674.1 Chlamy...
[24]   113 AAGAUGAUAUUCUG-CGCCAUGG...GAUUGU-UGUUUUCUUGGCUUU KE356008.1 Chlamy...
[25]   113 AAGUUGGUAUUCUAACGCCAUGG...--UCUCCGGUUCUCUUGGCUUU CVNC01000001.1 Ch...
[26]   113 AAGAUGAUAUUCUG-CGCCAUGG...GAUUGU-UGUUUUCUUGGCUUU AP006861.1 Chlamy...
[27]   113 AAGAUGAUAUUCUA-CGCCAUGG...GA-UGU-UGUUUUCUUGGCUUU CP015840.1 Chlamy...
> 
> y <- LearnNonCoding(RNA)
* 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: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’:
AlignProfiles.c:424:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  424 |     lGp *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:61:39: note: ‘lGp’ was declared here
   61 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
      |                                       ^~~
AlignProfiles.c:426:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  426 |     lGs *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:61:44: note: ‘lGs’ was declared here
   61 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
      |                                            ^~~
AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’:
AlignProfiles.c:1266:9: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1266 |     lGp *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:808:39: note: ‘lGp’ was declared here
  808 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
      |                                       ^~~
AlignProfiles.c:1268:9: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1268 |     lGs *= tot;
      |     ~~~~^~~~~~
AlignProfiles.c:808:44: note: ‘lGs’ was declared here
  808 |  double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
      |                                            ^~~
AlignProfiles.c: In function ‘alignProfiles’:
AlignProfiles.c:378:11: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  378 |   #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(nthreads)
      |           ^~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function ‘calculateHairpinDeltaG’:
CalculateDeltaG.c:463:28: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  463 |    if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
      |                        ~~~~^~~~~
CalculateDeltaG.c:463:15: warning: ‘s1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  463 |    if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
      |           ~~~~^~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function ‘calculateFISH’:
CalculateFISH.c:25:23: warning: missing braces around initializer [-Wmissing-braces]
   25 |  double dH_DR[4][4] = {
      |                       ^
   26 |   -11.5, -7.8, -7, -8.3,
      |   {                    }
   27 |   -10.4, -12.8, -16.3, -9.1,
      |   {                        }
   28 |   -8.6, -8, -9.3, -5.9,
      |   {                   }
   29 |   -7.8, -5.5, -9, -7.8
      |   {
   30 |  };
      |  }
CalculateFISH.c:31:23: warning: missing braces around initializer [-Wmissing-braces]
   31 |  double dS_DR[4][4] = {
      |                       ^
   32 |   -36.4, -21.6, -19.7, -23.9,
      |   {                         }
   33 |   -28.4, -31.9, -47.1, -23.5,
      |   {                         }
   34 |   -22.9, -17.1, -23.2, -12.3,
      |   {                         }
   35 |   -23.2, -13.5, -26.1, -21.9
      |   {
   36 |  };
      |  }
CalculateFISH.c:37:23: warning: missing braces around initializer [-Wmissing-braces]
   37 |  double dH_DD[4][4] = {
      |                       ^
   38 |   -7.9, -8.4, -7.8, -7.2,
      |   {                     }
   39 |   -8.5, -8, -10.6, -7.8,
      |   {                    }
   40 |   -8.2, -9.8, -8, -8.4,
      |   {                   }
   41 |   -7.2, -8.2, -8.5, -7.9
      |   {
   42 |  };
      |  }
CalculateFISH.c:43:23: warning: missing braces around initializer [-Wmissing-braces]
   43 |  double dS_DD[4][4] = {
      |                       ^
   44 |   -22.2, -22.4, -21, -20.4,
      |   {                       }
   45 |   -22.7, -19.9, -27.2, -21,
      |   {                       }
   46 |   -22.2, -24.4, -19.9, -22.4,
      |   {                         }
   47 |   -21.3, -22.2, -22.7, -22.2
      |   {
   48 |  };
      |  }
CalculateFISH.c:49:23: warning: missing braces around initializer [-Wmissing-braces]
   49 |  double dH_RR[4][4] = {
      |                       ^
   50 |   -6.6, -10.17, -7.65, -5.76,
      |   {                         }
   51 |   -10.56, -12.21, -7.95, -7.65,
      |   {                           }
   52 |   -13.37, -14.21, -12.21, -10.17,
      |   {                             }
   53 |   -8.11, -13.37, -10.56, -6.6
      |   {
   54 |  };
      |  }
CalculateFISH.c:55:23: warning: missing braces around initializer [-Wmissing-braces]
   55 |  double dS_RR[4][4] = {
      |                       ^
   56 |   -18.38, -26.03, -19.18, -15.67,
      |   {                             }
   57 |   -28.25, -30.02, -19.18, -19.18,
      |   {                             }
   58 |   -35.68, -34.85, -30.02, -26.03,
      |   {                             }
   59 |   -22.59, -35.68, -28.25, -18.38
      |   {
   60 |  };
      |  }
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function ‘chainSegments’:
ChainSegments.c:500:28: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  500 |    if (minX == minY && upX == upY) {
      |                        ~~~~^~~~~~
ChainSegments.c:500:28: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Cluster.c -o Cluster.o
Cluster.c: In function ‘cluster._omp_fn.0’:
Cluster.c:418:15: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  418 |      minCs[i] = minC;
      |      ~~~~~~~~~^~~~~~
Cluster.c:246:50: note: ‘minC’ was declared here
  246 |  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                  ^~~~
Cluster.c: In function ‘cluster._omp_fn.1’:
Cluster.c:442:30: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  442 |       minCols[rowIndices[i]] = minC;
      |       ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:50: note: ‘minC’ was declared here
  246 |  int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                  ^~~~
Cluster.c: In function ‘cluster’:
Cluster.c:464:52: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  464 |   rans[1*(length - 1) + k] = *(colNums + colIndices[minCol]); // column merged
      |                                                    ^
Cluster.c:781:13: warning: ‘nDiv’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  781 |     nDiv[j] -= dMatrix2[length*colIndices[j] - colIndices[j]*(colIndices[j] + 1)/2 + rowIndices[i] - colIndices[j]]; // col sums
      |             ^~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ClusterML.c -o ClusterML.o
In file included from /home/biocbuild/R/R-4.3.1/include/Rdefines.h:38,
                 from ClusterML.c:11:
ClusterML.c: In function ‘clusterML’:
/home/biocbuild/R/R-4.3.1/include/R_ext/RS.h:55:25: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   55 | #define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
      |                         ^~~~~~~~~~
ClusterML.c:1126:7: note: ‘Up’ was declared here
 1126 |  int *Up;
      |       ^~
ClusterML.c:1210:10: warning: ‘node’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1210 |  #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
      |          ^~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ClusterMP.c -o ClusterMP.o
ClusterMP.c: In function ‘clusterMP._omp_fn.0’:
ClusterMP.c:98:15: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   98 |  int i, j, k, m, w;
      |               ^
ClusterMP.c:151:9: warning: ‘P’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  151 |    int *P;
      |         ^
ClusterMP.c: In function ‘clusterMP’:
ClusterMP.c:566:3: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  566 |   free(Up);
      |   ^~~~~~~~
ClusterMP.c:139:10: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  139 |  #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
      |          ^~~
ClusterMP.c:139:10: warning: ‘nodes’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ClusterMP.c:139:10: warning: ‘lengths’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Compositions.c -o Compositions.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Compression.c -o Compression.o
Compression.c: In function ‘nbit._omp_fn.0’:
Compression.c: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:1029:23: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1029 |         lastHit = dict[(word >> k) & 0xFF];
      |                       ^
Compression.c:542:17: note: ‘dict’ was declared here
  542 |   unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                 ^~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function ‘consensusProfile’:
ConsensusSequence.c:1578:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1578 |  double *DBN, *s;
      |          ^~~
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:455:18: warning: ‘lastPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  455 |      *(runs + s) += weight;
      |                  ^~
ConsensusSequence.c:397:23: note: ‘lastPos’ was declared here
  397 |  int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
      |                       ^~~~~~~
ConsensusSequence.c:1771:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1771 |  double *HEC, *s;
      |          ^~~
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:2046:27: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2046 |    *(rans + k) += GO*(curr*total);
      |                      ~~~~~^~~~~~~
ConsensusSequence.c:2046:27: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:1941:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1941 |  int do_DBN, n, l, d;
      |                    ^
ConsensusSequence.c:1940:10: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1940 |  double *DBN, *s;
      |          ^~~
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2189:27: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2189 |    *(rans + k) += GO*(curr*total);
      |                      ~~~~~^~~~~~~
ConsensusSequence.c:2189:27: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:2084:20: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2084 |  int do_HEC, n, l, d;
      |                    ^
ConsensusSequence.c:2083:10: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2083 |  double *HEC, *s;
      |          ^~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:70:20: warning: missing braces around initializer [-Wmissing-braces]
   70 |  double NN[4][4] = {
      |                    ^
   71 |   -0.816507461,-2.5401714,-1.647430026,-1.184658548
      |   {
   72 |   ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
      |   }{
   73 |   ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
      |   }{
   74 |   ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
      |   }{
   75 |  };
      |  }
DesignProbes.c:77:20: warning: missing braces around initializer [-Wmissing-braces]
   77 |  double PM[4][4] = {
      |                    ^
   78 |   -0.141370102,-0.439805276,-0.285236035,-0.205111781
      |   {
   79 |   ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
      |   }{
   80 |   ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
      |   }{
   81 |   ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
      |   }{
   82 |  };
      |  }
DesignProbes.c:84:27: warning: missing braces around initializer [-Wmissing-braces]
   84 |  double sMM[4][5][5][4] = {
      |                           ^
   85 |   0,0,0,0
      |   {{{
   86 |   ,1.545032445,1.254355018,1.491691514,1.329138183
      |   }{
   87 |   ,1.150635633,0.582415494,1.075877275,1.187937642
      |   }{
   88 |   ,1.203555051,1.001540513,0.864287715,0.717125848
      |   }{
   89 |   ,0.75,0.65,0.69,0.78
      |   }{
   90 |   ,0.630005348,0.18553379,0.730763505,0.709272397
      |   -
      |   }},{{
   91 |   ,0,0,0,0
      |   }{
   92 |   ,0.856582783,-0.143236405,0.716721488,0.603652831
      |   }{
   93 |   ,0.851622883,0.653168672,0.676545316,1.187937642
      |   }{
   94 |   ,0.75,0.65,0.69,0.78
      |   }{
   95 |   ,1.231861002,0.746214538,1.087821916,0.989140748
      |   -
      |   }},{{
   96 |   ,1.822113278,1.270687029,1.336192565,1.364584949
      |   }{
   97 |   ,0,0,0,0
      |   }{
   98 |   ,1.443665704,1.385046493,1.256013166,1.329138183
      |   }{
   99 |   ,0.75,0.65,0.69,0.78
      |   }{
  100 |   ,1.478009492,0.882097231,1.20450984,1.061002478
      |   -
      |   }},{{
  101 |   ,1.496720812,0.846496194,0.967868114,0.989140748
      |   }{
  102 |   ,0.766581547,-0.024857805,0.50754303,0.709272397
      |   }{
  103 |   ,0,0,0,0
      |   }{
  104 |   ,0.75,0.65,0.69,0.78
      |   }{
  105 |   ,0.75,0.65,0.69,0.78
      |   -
      |   }},{{
  106 |   ,0.75,0.65,0.69,0.78
      |   }{
  107 |   ,0.75,0.65,0.69,0.78
      |   }{
  108 |   ,0.76,0.65,0.69,0.78
      |   }{
  109 |   ,0,0,0,0
      |   }{
  110 |   ,0,0,0,0
      |   -
      |   }}},{{{
  111 |   ,1.295827995,0.84547091,0.91019099,1.256013166
      |   }{
  112 |   ,0.755889609,0.241428373,0.396379912,0.676545316
      |   }{
  113 |   ,0.99945386,0.740323132,0.435659206,0.864287715
      |   }{
  114 |   ,0.65,0.55,0.48,0.69
      |   }{
  115 |   ,0.843147406,0.101248351,0.49063599,0.50754303
      |   -
      |   }},{{
  116 |   ,0,0,0,0
      |   }{
  117 |   ,1.0651638,0.249934344,0.699352949,0.716721488
      |   }{
  118 |   ,0.871921533,0.59458138,0.396379912,1.075877275
      |   }{
  119 |   ,0.65,0.56,0.49,0.69
      |   }{
  120 |   ,1.07531714,0.318907854,0.653287717,0.967868114
      |   -
      |   }},{{
  121 |   ,1.099899195,0.730184613,0.661798984,1.336192565
      |   }{
  122 |   ,0,0,0,0
      |   }{
  123 |   ,1.45897431,1.318532145,0.91019099,1.491691514
      |   }{
  124 |   ,0.65,0.56,0.49,0.69
      |   }{
  125 |   ,1.242135174,0.894838095,1.108555445,1.20450984
      |   -
      |   }},{{
  126 |   ,0.911428974,0.524430101,0.653287717,1.087821916
      |   }{
  127 |   ,0.503209827,0.274849491,0.49063599,0.730763505
      |   }{
  128 |   ,0,0,0,0
      |   }{
  129 |   ,0.65,0.55,0.48,0.69
      |   }{
  130 |   ,0.65,0.55,0.48,0.69
      |   -
      |   }},{{
  131 |   ,0.65,0.56,0.49,0.69
      |   }{
  132 |   ,0.65,0.56,0.49,0.69
      |   }{
  133 |   ,0.65,0.55,0.48,0.69
      |   }{
  134 |   ,0,0,0,0
      |   }{
  135 |   ,0,0,0,0
      |   -
      |   }}},{{{
  136 |   ,1.100661785,0.969784756,1.318532145,1.385046493
      |   }{
  137 |   ,0.565895968,-0.060347902,0.59458138,0.653168672
      |   }{
  138 |   ,0.782168488,0.788161238,0.740323132,1.001540513
      |   }{
  139 |   ,0.68,0.46,0.55,0.65
      |   }{
  140 |   ,0.468913405,-0.469855984,0.274849491,-0.024857805
      |   -
      |   }},{{
  141 |   ,0,0,0,0
      |   }{
  142 |   ,0.258195131,-0.70438632,0.249934344,-0.143236405
      |   }{
  143 |   ,0.502914193,-0.060347902,0.241428373,0.582415494
      |   }{
  144 |   ,0.68,0.47,0.56,0.65
      |   }{
  145 |   ,0.584083861,0.258975454,0.524430101,0.846496194
      |   -
      |   }},{{
  146 |   ,0.968040559,0.797499702,0.730184613,1.270687029
      |   }{
  147 |   ,0,0,0,0
      |   }{
  148 |   ,1.081040749,0.969784756,0.84547091,1.254355018
      |   }{
  149 |   ,0.68,0.47,0.56,0.65
      |   }{
  150 |   ,1.048553951,0.728354541,0.894838095,0.882097231
      |   -
      |   }},{{
  151 |   ,0.88611252,0.258975454,0.318907854,0.746214538
      |   }{
  152 |   ,0.239520858,-0.469855984,0.101248351,0.18553379
      |   }{
  153 |   ,0,0,0,0
      |   }{
  154 |   ,0.68,0.46,0.55,0.65
      |   }{
  155 |   ,0.68,0.46,0.55,0.65
      |   -
      |   }},{{
  156 |   ,0.68,0.47,0.56,0.65
      |   }{
  157 |   ,0.68,0.47,0.56,0.65
      |   }{
  158 |   ,0.68,0.46,0.55,0.65
      |   }{
  159 |   ,0,0,0,0
      |   }{
  160 |   ,0,0,0,0
      |   -
      |   }}},{{{
  161 |   ,1.566899704,1.081040749,1.45897431,1.443665704
      |   }{
  162 |   ,0.976725675,0.502914193,0.871921533,0.851622883
      |   }{
  163 |   ,1.482046826,0.782168488,0.99945386,1.203555051
      |   }{
  164 |   ,0.85,0.68,0.65,0.76
      |   }{
  165 |   ,0.798628781,0.239520858,0.503209827,0.766581547
      |   -
      |   }},{{
  166 |   ,0,0,0,0
      |   }{
  167 |   ,1.141098246,0.258195131,1.0651638,0.856582783
      |   }{
  168 |   ,0.976725675,0.565895968,0.755889609,1.150635633
      |   }{
  169 |   ,0.85,0.68,0.65,0.75
      |   }{
  170 |   ,1.125403302,0.88611252,0.911428974,1.496720812
      |   -
      |   }},{{
  171 |   ,1.68169282,0.968040559,1.099899195,1.822113278
      |   }{
  172 |   ,0,0,0,0
      |   }{
  173 |   ,1.566899704,1.100661785,1.295827995,1.545032445
      |   }{
  174 |   ,0.85,0.68,0.65,0.75
      |   }{
  175 |   ,1.35948517,1.048553951,1.242135174,1.478009492
      |   -
      |   }},{{
  176 |   ,1.125403302,0.584083861,1.07531714,1.231861002
      |   }{
  177 |   ,0.798628781,0.468913405,0.843147406,0.630005348
      |   }{
  178 |   ,0,0,0,0
      |   }{
  179 |   ,0.85,0.68,0.65,0.75
      |   }{
  180 |   ,0.85,0.68,0.65,0.75
      |   -
      |   }},{{
  181 |   ,0.85,0.68,0.65,0.75
      |   }{
  182 |   ,0.85,0.68,0.65,0.75
      |   }{
  183 |   ,0.85,0.68,0.65,0.75
      |   }{
  184 |   ,0,0,0,0
      |   }{
  185 |  };
      |  }}}
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c: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/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Diff.c -o Diff.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘firstSeqsPosEqual’:
DistanceMatrix.c:794:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  794 |   if (!ci)
      |   ^~
DistanceMatrix.c:797:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  797 |    while (i < ex) {
      |    ^~~~~
DistanceMatrix.c:816:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  816 |   if (!cj)
      |   ^~
DistanceMatrix.c:819:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  819 |    while (j < ey) {
      |    ^~~~~
DistanceMatrix.c: In function ‘similarities._omp_fn.0’:
DistanceMatrix.c:1040:33: warning: ‘off’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1040 |     (w1 <= w2[i] && (double)(OV + off)/(double)w2[i] < coverage)))) {
      |                             ~~~~^~~~~~
DistanceMatrix.c:881:42: note: ‘off’ was declared here
  881 |  int i, j, n, s, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, *r, useMax;
      |                                          ^~~
DistanceMatrix.c:1040:33: warning: ‘OV’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1040 |     (w1 <= w2[i] && (double)(OV + off)/(double)w2[i] < coverage)))) {
      |                             ~~~~^~~~~~
DistanceMatrix.c:881:38: note: ‘OV’ was declared here
  881 |  int i, j, n, s, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, *r, useMax;
      |                                      ^~
DistanceMatrix.c:1059:40: warning: ‘ov’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1059 |       rans[i] = (double)s/((double)(ov + count + g2));
      |                                     ~~~^~~~~~~
DistanceMatrix.c:881:34: note: ‘ov’ was declared here
  881 |  int i, j, n, s, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, *r, useMax;
      |                                  ^~
DistanceMatrix.c:1044:9: warning: ‘o’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1044 |      if (o == 1) {
      |         ^
DistanceMatrix.c:881:58: note: ‘o’ was declared here
  881 |  int i, j, n, s, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, *r, useMax;
      |                                                          ^
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function ‘pop’:
EnumerateSequence.c:321:8: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  321 |  x = x + (x >> 4) & 0xF0F0F0F;
      |      ~~^~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c FindFrameshifts.c -o FindFrameshifts.o
FindFrameshifts.c: In function ‘findFrameshifts’:
FindFrameshifts.c:381:14: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  381 |    } else if (k == 2) {
      |              ^
FindFrameshifts.c:318:19: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  318 |     if (C[k*rc + j*r + i] >= 0) {
      |                  ~^~
FindFrameshifts.c:370:8: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  370 |      i += B[k*rc + j*r + i];
      |      ~~^~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/include/Rdefines.h:41,
                 from FindFrameshifts.c:11:
/home/biocbuild/R/R-4.3.1/include/Rinternals.h:894:16: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  894 | #define eval   Rf_eval
      |                ^~~~~~~
FindFrameshifts.c:162:24: note: ‘utilsPackage’ was declared here
  162 |  SEXP percentComplete, utilsPackage;
      |                        ^~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/include/Rdefines.h:41,
                 from FindFrameshifts.c:11:
/home/biocbuild/R/R-4.3.1/include/Rinternals.h:894:16: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  894 | #define eval   Rf_eval
      |                ^~~~~~~
FindFrameshifts.c:162:7: note: ‘percentComplete’ was declared here
  162 |  SEXP percentComplete, utilsPackage;
      |       ^~~~~~~~~~~~~~~
FindFrameshifts.c:468:12: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  468 |     before = *rPercentComplete;
      |     ~~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c GeneFinding.c -o GeneFinding.o
GeneFinding.c: In function ‘scoreCodonModel’:
GeneFinding.c:422:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  422 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c:432:29: warning: ‘lastVal’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  432 |      score += codons[lastVal*64 + val];
      |                      ~~~~~~~^~~
GeneFinding.c: In function ‘startCodonModel’:
GeneFinding.c:791:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  791 |    val = getBaseRC(x_i.ptr[j++]);
      |                           ^
GeneFinding.c: In function ‘scoreStartCodonModel’:
GeneFinding.c:892:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  892 |    val = getBaseRC(x_i.ptr[j++]);
      |                           ^
GeneFinding.c: In function ‘initialCodonModel’:
GeneFinding.c:973:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  973 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘scoreInitialCodonModel’:
GeneFinding.c:1059:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1059 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘terminationCodonModel’:
GeneFinding.c:1131:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1131 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘scoreTerminationCodonModel’:
GeneFinding.c:1216:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1216 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘getRegion’:
GeneFinding.c:1286:23: warning: ‘x_i.length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1286 |     (s == 0 && j >= 0 && j + w <= x_i.length)) {
      |     ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
GeneFinding.c:1289:39: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1289 |       seq[k] = getBaseLetterRC(x_i.ptr[j--]);
      |                                       ^
GeneFinding.c: In function ‘autocorrelationModel’:
GeneFinding.c:1379:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1379 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘scoreAutocorrelationModel’:
GeneFinding.c:1496:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1496 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘couplingModel’:
GeneFinding.c:1598:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1598 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘scoreCouplingModel’:
GeneFinding.c:1712:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1712 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1826:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1826 |     val = getBaseRC(x_i.ptr[j++]);
      |                            ^
GeneFinding.c: In function ‘scoreNucleotideBiasModel’:
GeneFinding.c:1913:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1913 |     val = getBaseRC(x_i.ptr[j++]);
      |                            ^
GeneFinding.c: In function ‘upstreamMotifModel’:
GeneFinding.c:1990:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1990 |      val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
      |                                          ^
GeneFinding.c: In function ‘scoreUpstreamMotifModel’:
GeneFinding.c:2090:42: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2090 |      val += mult[k - 1]*getBaseRC(x_i.ptr[j + k - 1]);
      |                                          ^
GeneFinding.c: In function ‘scoreRunLengthModel’:
GeneFinding.c:2307:28: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2307 |     val = getBaseRC(x_i.ptr[j++]);
      |                            ^
GeneFinding.c: In function ‘stopCodonModel’:
GeneFinding.c:2419:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2419 |    val = getBaseRC(x_i.ptr[j++]);
      |                           ^
GeneFinding.c: In function ‘scoreStopCodonModel’:
GeneFinding.c:2520:27: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2520 |    val = getBaseRC(x_i.ptr[j++]);
      |                           ^
GeneFinding.c: In function ‘codonFrequencies’:
GeneFinding.c:2578:31: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2578 |     val += 4*getBaseRC(x_i.ptr[j++]);
      |                               ^
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c GetPools.c -o GetPools.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Import.c -o Import.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c InformationContent.c -o InformationContent.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c IntDist.c -o IntDist.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ManipulateXStringSet.c -o ManipulateXStringSet.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function ‘meltPolymer’:
MeltPolymer.c:79:20: warning: missing braces around initializer [-Wmissing-braces]
   79 |  double dH[4][4] = {
      |                    ^
   80 |   -7.9,-8.4,-7.8,-7.2
      |   {
   81 |   ,-8.5,-8.0,-10.6,-7.8
      |   }{
   82 |   ,-8.2,-9.8,-8.0,-8.4
      |   }{
   83 |   ,-7.2,-8.2,-8.5,-7.9
      |   }{
   84 |  };
      |  }
MeltPolymer.c:88:20: warning: missing braces around initializer [-Wmissing-braces]
   88 |  double dS[4][4] = {
      |                    ^
   89 |   -22.2,-22.4,-21.0,-20.4
      |   {
   90 |   ,-22.7,-19.9,-27.2,-21.0
      |   }{
   91 |   ,-22.2,-24.4,-19.9,-22.4
      |   }{
   92 |   ,-21.3,-22.2,-22.7,-22.2
      |   }{
   93 |  };
      |  }
MeltPolymer.c:358:24: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  358 |      *(rans + k + l*s) += 1;
      |                        ^~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c NNLS.c -o NNLS.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Order.c -o Order.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’:
PairwiseAlignment.c:469:11: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  469 |     P2[i] = p2;
      |     ~~~~~~^~~~
PairwiseAlignment.c:172:12: note: ‘p2’ was declared here
  172 |  int *p1, *p2, *p3, *p4;
      |            ^~
PairwiseAlignment.c:468:11: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  468 |     P1[i] = p1;
      |     ~~~~~~^~~~
PairwiseAlignment.c:172:7: note: ‘p1’ was declared here
  172 |  int *p1, *p2, *p3, *p4;
      |       ^~
PairwiseAlignment.c:473:11: warning: ‘p4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  473 |     P4[i] = p4;
      |     ~~~~~~^~~~
PairwiseAlignment.c:172:22: note: ‘p4’ was declared here
  172 |  int *p1, *p2, *p3, *p4;
      |                      ^~
PairwiseAlignment.c:472:11: warning: ‘p3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  472 |     P3[i] = p3;
      |     ~~~~~~^~~~
PairwiseAlignment.c:172:17: note: ‘p3’ was declared here
  172 |  int *p1, *p2, *p3, *p4;
      |                 ^~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function ‘predictDBN’:
PredictDBN.c:869:29: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  869 |         range2[0] = nucs[pos[prev]];// + 1;
      |                             ^
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c PredictHEC.c -o PredictHEC.o
PredictHEC.c: In function ‘predictHEC’:
PredictHEC.c:255:4: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  255 |    SET_VECTOR_ELT(ret, i, ans);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:233:16: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  233 |      states[j] = 'C';
      |      ~~~~~~~~~~^~~~~
PredictHEC.c:237:18: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  237 |     *(rans + 3*j + 1) = E;
      |      ~~~~~~~~~~~~^~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c R_init_decipher.c -o R_init_decipher.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Translate.c -o Translate.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Utils.c -o Utils.o
Utils.c: In function ‘intMatchSelfOnce’:
Utils.c:654:21: warning: variable ‘start’ set but not used [-Wunused-but-set-variable]
  654 |  int i, j, k, temp, start = 0;
      |                     ^~~~~
Utils.c: In function ‘matchOverlap._omp_fn.0’:
Utils.c:823:11: warning: ‘one’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  823 |       two != one) {
      |       ~~~~^~~~~~
Utils.c:798:8: note: ‘one’ was declared here
  798 |    int one, two;
      |        ^~~
Utils.c: In function ‘splitPartitions’:
Utils.c:1315:21: warning: ‘change’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1315 |   } else if (change - j >= m && // large enough partition
      |              ~~~~~~~^~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c VectorSums.c -o VectorSums.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.o ClusterMP.o Compositions.o Compression.o ConsensusSequence.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o IntDist.o ManipulateXStringSet.o MeltPolymer.o MovingAverage.o NNLS.o Order.o PairwiseAlignment.o PredictDBN.o PredictHEC.o R_init_decipher.o S4Vectors_stubs.o TerminalMismatch.o Translate.o Utils.o VectorSums.o XVector_stubs.o -fopenmp -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-DECIPHER/00new/DECIPHER/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DECIPHER)