Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-05-04 11:36:28 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 521/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 3.0.0  (landing page)
Erik Wright
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/DECIPHER
git_branch: RELEASE_3_19
git_last_commit: 1b13c4e
git_last_commit_date: 2024-04-30 10:25:51 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for DECIPHER on nebbiolo1


To the developers/maintainers of the DECIPHER package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DECIPHER.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: DECIPHER
Version: 3.0.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DECIPHER_3.0.0.tar.gz
StartedAt: 2024-05-03 22:25:05 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 22:53:38 -0400 (Fri, 03 May 2024)
EllapsedTime: 1713.3 seconds
RetCode: 0
Status:   OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DECIPHER_3.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DECIPHER.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘3.0.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is 11.9Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    data      7.6Mb
    extdata   1.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AlignSeqs: no visible binding for global variable ‘deltaGrulesRNA’
DesignSignatures: no visible binding for global variable ‘deltaHrules’
FindGenes: no visible binding for global variable ‘deltaHrulesRNA’
FindNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
LearnNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
PredictDBN: no visible binding for global variable ‘deltaGrulesRNA’
TreeLine: multiple local function definitions for ‘.minimize’ with
  different formal arguments
Undefined global functions or variables:
  deltaGrulesRNA deltaHrules deltaHrulesRNA
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
AlignSeqs          173.148  1.844 176.001
LearnNonCoding     119.939  6.367 130.247
MapCharacters       87.046  0.276  87.324
FindNonCoding       63.328  0.596  63.928
FindGenes           46.156  0.312  46.470
Genes-class         44.610  0.276  44.890
WriteGenes          44.634  0.220  44.854
ExtractGenes        43.543  0.264  43.811
BrowseSeqs          24.255  0.124  24.380
CorrectFrameshifts  16.773  0.072  16.845
DetectRepeats       15.119  0.048  15.167
AlignTranslation    11.790  0.072  11.864
StaggerAlignment    10.906  0.088  10.994
Taxa-class          10.168  0.020  10.188
IdTaxa               9.645  0.016   9.661
TreeLine             8.338  0.048   8.387
LearnTaxa            7.178  0.744   7.964
Clusterize           5.881  0.024   5.905
DesignArray          5.204  0.088   5.293
Array2Matrix         5.143  0.063   5.207
ScoreAlignment       5.142  0.048   5.190
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.


Installation output

DECIPHER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘DECIPHER’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function ‘alignProfiles._omp_fn.0’:
AlignProfiles.c:426:37: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  426 |                                 lGp *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:61:46: note: ‘lGp’ was declared here
   61 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
      |                                              ^~~
AlignProfiles.c:428:37: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  428 |                                 lGs *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:61:51: note: ‘lGs’ was declared here
   61 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, S, M, GP, GS, temp, avgM = 0;
      |                                                   ^~~
AlignProfiles.c: In function ‘alignProfilesAA._omp_fn.0’:
AlignProfiles.c:1270:37: warning: ‘lGp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1270 |                                 lGp *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:810:46: note: ‘lGp’ was declared here
  810 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
      |                                              ^~~
AlignProfiles.c:1272:37: warning: ‘lGs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1272 |                                 lGs *= tot;
      |                                 ~~~~^~~~~~
AlignProfiles.c:810:51: note: ‘lGs’ was declared here
  810 |         double *pprofile, *sprofile, gp, gs, lGp, lGs, M, GP, GS, R, temp, avgM = 0;
      |                                                   ^~~
AlignProfiles.c: In function ‘alignProfiles’:
AlignProfiles.c:379:25: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  379 |                 #pragma omp parallel for private(i,j,gp,gs,S,M,GP,GS,tot,lGp,lGs,temp) reduction(+:totM,avgM) num_threads(nthreads)
      |                         ^~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c AssignIndels.c -o AssignIndels.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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:463:49: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  463 |                         if ((!((s1 == 4) && (s2 == 4)) || j >= a[i]) && count > 3) {
      |                                             ~~~~^~~~~
CalculateDeltaG.c:463:36: 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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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:25:30: warning: missing braces around initializer [-Wmissing-braces]
   25 |         double dH_DR[4][4] = {
      |                              ^
   26 |                 -11.5, -7.8, -7, -8.3,
      |                 {                    }
   27 |                 -10.4, -12.8, -16.3, -9.1,
      |                 {                        }
   28 |                 -8.6, -8, -9.3, -5.9,
      |                 {                   }
   29 |                 -7.8, -5.5, -9, -7.8
      |                 {
   30 |         };
      |         }
CalculateFISH.c:31:30: warning: missing braces around initializer [-Wmissing-braces]
   31 |         double dS_DR[4][4] = {
      |                              ^
   32 |                 -36.4, -21.6, -19.7, -23.9,
      |                 {                         }
   33 |                 -28.4, -31.9, -47.1, -23.5,
      |                 {                         }
   34 |                 -22.9, -17.1, -23.2, -12.3,
      |                 {                         }
   35 |                 -23.2, -13.5, -26.1, -21.9
      |                 {
   36 |         };
      |         }
CalculateFISH.c:37:30: warning: missing braces around initializer [-Wmissing-braces]
   37 |         double dH_DD[4][4] = {
      |                              ^
   38 |                 -7.9, -8.4, -7.8, -7.2,
      |                 {                     }
   39 |                 -8.5, -8, -10.6, -7.8,
      |                 {                    }
   40 |                 -8.2, -9.8, -8, -8.4,
      |                 {                   }
   41 |                 -7.2, -8.2, -8.5, -7.9
      |                 {
   42 |         };
      |         }
CalculateFISH.c:43:30: warning: missing braces around initializer [-Wmissing-braces]
   43 |         double dS_DD[4][4] = {
      |                              ^
   44 |                 -22.2, -22.4, -21, -20.4,
      |                 {                       }
   45 |                 -22.7, -19.9, -27.2, -21,
      |                 {                       }
   46 |                 -22.2, -24.4, -19.9, -22.4,
      |                 {                         }
   47 |                 -21.3, -22.2, -22.7, -22.2
      |                 {
   48 |         };
      |         }
CalculateFISH.c:49:30: warning: missing braces around initializer [-Wmissing-braces]
   49 |         double dH_RR[4][4] = {
      |                              ^
   50 |                 -6.6, -10.17, -7.65, -5.76,
      |                 {                         }
   51 |                 -10.56, -12.21, -7.95, -7.65,
      |                 {                           }
   52 |                 -13.37, -14.21, -12.21, -10.17,
      |                 {                             }
   53 |                 -8.11, -13.37, -10.56, -6.6
      |                 {
   54 |         };
      |         }
CalculateFISH.c:55:30: warning: missing braces around initializer [-Wmissing-braces]
   55 |         double dS_RR[4][4] = {
      |                              ^
   56 |                 -18.38, -26.03, -19.18, -15.67,
      |                 {                             }
   57 |                 -28.25, -30.02, -19.18, -19.18,
      |                 {                             }
   58 |                 -35.68, -34.85, -30.02, -26.03,
      |                 {                             }
   59 |                 -22.59, -35.68, -28.25, -18.38
      |                 {
   60 |         };
      |         }
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c ChainSegments.c -o ChainSegments.o
ChainSegments.c: In function ‘chainSegments’:
ChainSegments.c:524:49: warning: ‘upY’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  524 |                         if (minX == minY && upX == upY) {
      |                                             ~~~~^~~~~~
ChainSegments.c:524:49: warning: ‘upX’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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:418:50: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  418 |                                         minCs[i] = minC;
      |                                         ~~~~~~~~~^~~~~~
Cluster.c:246:57: note: ‘minC’ was declared here
  246 |         int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                         ^~~~
Cluster.c: In function ‘cluster._omp_fn.1’:
Cluster.c:442:72: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  442 |                                                 minCols[rowIndices[i]] = minC;
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
Cluster.c:246:57: note: ‘minC’ was declared here
  246 |         int k, dobj, clusterNum, minRow, minCol, index, minC, met;
      |                                                         ^~~~
Cluster.c: In function ‘cluster’:
Cluster.c:464:66: warning: ‘minC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  464 |                 rans[1*(length - 1) + k] = *(colNums + colIndices[minCol]); // column merged
      |                                                                  ^
Cluster.c:781:41: 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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include/Rdefines.h:38,
                 from ClusterML.c:16:
ClusterML.c: In function ‘clusterML’:
/home/biocbuild/bbs-3.19-bioc/R/include/R_ext/RS.h:55:25: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   55 | #define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
      |                         ^~~~~~~~~~
ClusterML.c:1206:14: note: ‘Up’ was declared here
 1206 |         int *Up;
      |              ^~
ClusterML.c:1293:17: warning: ‘node’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1293 |         #pragma omp parallel for private(j,k,o,p,y_i,row) num_threads(nthreads)
      |                 ^~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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:98:22: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   98 |         int i, j, k, m, w;
      |                      ^
ClusterMP.c:153:30: warning: ‘P’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  153 |                         int *P;
      |                              ^
ClusterMP.c: In function ‘clusterMP’:
ClusterMP.c:640:17: warning: ‘Up’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  640 |                 free(Up);
      |                 ^~~~~~~~
ClusterMP.c:140:17: warning: ‘subM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  140 |         #pragma omp parallel for private(i,j,k,m,w) num_threads(nthreads)
      |                 ^~~
ClusterMP.c:140:17: warning: ‘nodes’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ClusterMP.c:140:17: warning: ‘lengths’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c Compositions.c -o Compositions.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c Compression.c -o Compression.o
Compression.c: In function ‘nbit._omp_fn.0’:
Compression.c:978:52: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  978 |                                         p[c] = ((k - 1) >> 8) & 0xFF; // length of run
      |                                                 ~~~^~~~
Compression.c:516:19: note: ‘k’ was declared here
  516 |         int i, j, k, pos;
      |                   ^
Compression.c:1012:54: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1012 |                                                 count++;
      |                                                 ~~~~~^~
Compression.c:544:43: note: ‘count’ was declared here
  544 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                                           ^~~~~
Compression.c:1011:62: warning: ‘word’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1011 |                                                 word = (word << 8) | (unsigned int)reorder(byte);
      |                                                        ~~~~~~^~~~~
Compression.c:544:37: note: ‘word’ was declared here
  544 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                                     ^~~~
Compression.c:1214:56: warning: ‘rev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1214 |                                                 p[c++] = rev == 0 ? 254 : 255;
      |                                                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
Compression.c:545:41: note: ‘rev’ was declared here
  545 |                 int lastTemp, currTemp, rev, len, len2, thresh = 1;
      |                                         ^~~
Compression.c:558:21: warning: ‘lower’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  558 |                 int lower = 0;
      |                     ^~~~~
Compression.c:1241:71: warning: ‘lastTriplet’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1241 |                                 if (threeBitEnd > threeBitBegin && (j - lastTriplet) > 20) {
      |                                                                    ~~~^~~~~~~~~~~~~~
Compression.c:631:26: note: ‘lastTriplet’ was declared here
  631 |                 int run, lastTriplet, lastCase;
      |                          ^~~~~~~~~~~
Compression.c:1031:79: warning: ‘dict’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1031 |                                                                 lastHit = dict[(word >> k) & 0xFF];
      |                                                                               ^
Compression.c:544:31: note: ‘dict’ was declared here
  544 |                 unsigned int *dict, word, count, lastHit, currHit, lastPos = 0;
      |                               ^~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c ConsensusSequence.c -o ConsensusSequence.o
ConsensusSequence.c: In function ‘consensusProfileAA’:
ConsensusSequence.c:455:53: warning: ‘lastPos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  455 |                                         *(runs + s) += weight;
      |                                                     ^~
ConsensusSequence.c:397:30: note: ‘lastPos’ was declared here
  397 |         int j, temp, length, lastPos, s = -1, value = -1, lastGap = start - 1;
      |                              ^~~~~~~
ConsensusSequence.c:1771:17: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1771 |         double *HEC, *s;
      |                 ^~~
ConsensusSequence.c: In function ‘colScores’:
ConsensusSequence.c:2046:48: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2046 |                         *(rans + k) += GO*(curr*total);
      |                                           ~~~~~^~~~~~~
ConsensusSequence.c:2046:48: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:1941:27: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1941 |         int do_DBN, n, l, d;
      |                           ^
ConsensusSequence.c:1940:17: warning: ‘DBN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1940 |         double *DBN, *s;
      |                 ^~~
ConsensusSequence.c: In function ‘colScoresAA’:
ConsensusSequence.c:2189:48: warning: ‘curr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2189 |                         *(rans + k) += GO*(curr*total);
      |                                           ~~~~~^~~~~~~
ConsensusSequence.c:2189:48: warning: ‘total’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ConsensusSequence.c:2084:27: warning: ‘d’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2084 |         int do_HEC, n, l, d;
      |                           ^
ConsensusSequence.c:2083:17: warning: ‘HEC’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2083 |         double *HEC, *s;
      |                 ^~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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:70:27: 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:77:27: 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:84:34: warning: missing braces around initializer [-Wmissing-braces]
   84 |         double sMM[4][5][5][4] = {
      |                                  ^
   85 |                 0,0,0,0
      |                 {{{
   86 |                 ,1.545032445,1.254355018,1.491691514,1.329138183
      |                 }{
   87 |                 ,1.150635633,0.582415494,1.075877275,1.187937642
      |                 }{
   88 |                 ,1.203555051,1.001540513,0.864287715,0.717125848
      |                 }{
   89 |                 ,0.75,0.65,0.69,0.78
      |                 }{
   90 |                 ,0.630005348,0.18553379,0.730763505,0.709272397
      |                 -
      |                 }},{{
   91 |                 ,0,0,0,0
      |                 }{
   92 |                 ,0.856582783,-0.143236405,0.716721488,0.603652831
      |                 }{
   93 |                 ,0.851622883,0.653168672,0.676545316,1.187937642
      |                 }{
   94 |                 ,0.75,0.65,0.69,0.78
      |                 }{
   95 |                 ,1.231861002,0.746214538,1.087821916,0.989140748
      |                 -
      |                 }},{{
   96 |                 ,1.822113278,1.270687029,1.336192565,1.364584949
      |                 }{
   97 |                 ,0,0,0,0
      |                 }{
   98 |                 ,1.443665704,1.385046493,1.256013166,1.329138183
      |                 }{
   99 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  100 |                 ,1.478009492,0.882097231,1.20450984,1.061002478
      |                 -
      |                 }},{{
  101 |                 ,1.496720812,0.846496194,0.967868114,0.989140748
      |                 }{
  102 |                 ,0.766581547,-0.024857805,0.50754303,0.709272397
      |                 }{
  103 |                 ,0,0,0,0
      |                 }{
  104 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  105 |                 ,0.75,0.65,0.69,0.78
      |                 -
      |                 }},{{
  106 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  107 |                 ,0.75,0.65,0.69,0.78
      |                 }{
  108 |                 ,0.76,0.65,0.69,0.78
      |                 }{
  109 |                 ,0,0,0,0
      |                 }{
  110 |                 ,0,0,0,0
      |                 -
      |                 }}},{{{
  111 |                 ,1.295827995,0.84547091,0.91019099,1.256013166
      |                 }{
  112 |                 ,0.755889609,0.241428373,0.396379912,0.676545316
      |                 }{
  113 |                 ,0.99945386,0.740323132,0.435659206,0.864287715
      |                 }{
  114 |                 ,0.65,0.55,0.48,0.69
      |                 }{
  115 |                 ,0.843147406,0.101248351,0.49063599,0.50754303
      |                 -
      |                 }},{{
  116 |                 ,0,0,0,0
      |                 }{
  117 |                 ,1.0651638,0.249934344,0.699352949,0.716721488
      |                 }{
  118 |                 ,0.871921533,0.59458138,0.396379912,1.075877275
      |                 }{
  119 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  120 |                 ,1.07531714,0.318907854,0.653287717,0.967868114
      |                 -
      |                 }},{{
  121 |                 ,1.099899195,0.730184613,0.661798984,1.336192565
      |                 }{
  122 |                 ,0,0,0,0
      |                 }{
  123 |                 ,1.45897431,1.318532145,0.91019099,1.491691514
      |                 }{
  124 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  125 |                 ,1.242135174,0.894838095,1.108555445,1.20450984
      |                 -
      |                 }},{{
  126 |                 ,0.911428974,0.524430101,0.653287717,1.087821916
      |                 }{
  127 |                 ,0.503209827,0.274849491,0.49063599,0.730763505
      |                 }{
  128 |                 ,0,0,0,0
      |                 }{
  129 |                 ,0.65,0.55,0.48,0.69
      |                 }{
  130 |                 ,0.65,0.55,0.48,0.69
      |                 -
      |                 }},{{
  131 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  132 |                 ,0.65,0.56,0.49,0.69
      |                 }{
  133 |                 ,0.65,0.55,0.48,0.69
      |                 }{
  134 |                 ,0,0,0,0
      |                 }{
  135 |                 ,0,0,0,0
      |                 -
      |                 }}},{{{
  136 |                 ,1.100661785,0.969784756,1.318532145,1.385046493
      |                 }{
  137 |                 ,0.565895968,-0.060347902,0.59458138,0.653168672
      |                 }{
  138 |                 ,0.782168488,0.788161238,0.740323132,1.001540513
      |                 }{
  139 |                 ,0.68,0.46,0.55,0.65
      |                 }{
  140 |                 ,0.468913405,-0.469855984,0.274849491,-0.024857805
      |                 -
      |                 }},{{
  141 |                 ,0,0,0,0
      |                 }{
  142 |                 ,0.258195131,-0.70438632,0.249934344,-0.143236405
      |                 }{
  143 |                 ,0.502914193,-0.060347902,0.241428373,0.582415494
      |                 }{
  144 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  145 |                 ,0.584083861,0.258975454,0.524430101,0.846496194
      |                 -
      |                 }},{{
  146 |                 ,0.968040559,0.797499702,0.730184613,1.270687029
      |                 }{
  147 |                 ,0,0,0,0
      |                 }{
  148 |                 ,1.081040749,0.969784756,0.84547091,1.254355018
      |                 }{
  149 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  150 |                 ,1.048553951,0.728354541,0.894838095,0.882097231
      |                 -
      |                 }},{{
  151 |                 ,0.88611252,0.258975454,0.318907854,0.746214538
      |                 }{
  152 |                 ,0.239520858,-0.469855984,0.101248351,0.18553379
      |                 }{
  153 |                 ,0,0,0,0
      |                 }{
  154 |                 ,0.68,0.46,0.55,0.65
      |                 }{
  155 |                 ,0.68,0.46,0.55,0.65
      |                 -
      |                 }},{{
  156 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  157 |                 ,0.68,0.47,0.56,0.65
      |                 }{
  158 |                 ,0.68,0.46,0.55,0.65
      |                 }{
  159 |                 ,0,0,0,0
      |                 }{
  160 |                 ,0,0,0,0
      |                 -
      |                 }}},{{{
  161 |                 ,1.566899704,1.081040749,1.45897431,1.443665704
      |                 }{
  162 |                 ,0.976725675,0.502914193,0.871921533,0.851622883
      |                 }{
  163 |                 ,1.482046826,0.782168488,0.99945386,1.203555051
      |                 }{
  164 |                 ,0.85,0.68,0.65,0.76
      |                 }{
  165 |                 ,0.798628781,0.239520858,0.503209827,0.766581547
      |                 -
      |                 }},{{
  166 |                 ,0,0,0,0
      |                 }{
  167 |                 ,1.141098246,0.258195131,1.0651638,0.856582783
      |                 }{
  168 |                 ,0.976725675,0.565895968,0.755889609,1.150635633
      |                 }{
  169 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  170 |                 ,1.125403302,0.88611252,0.911428974,1.496720812
      |                 -
      |                 }},{{
  171 |                 ,1.68169282,0.968040559,1.099899195,1.822113278
      |                 }{
  172 |                 ,0,0,0,0
      |                 }{
  173 |                 ,1.566899704,1.100661785,1.295827995,1.545032445
      |                 }{
  174 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  175 |                 ,1.35948517,1.048553951,1.242135174,1.478009492
      |                 -
      |                 }},{{
  176 |                 ,1.125403302,0.584083861,1.07531714,1.231861002
      |                 }{
  177 |                 ,0.798628781,0.468913405,0.843147406,0.630005348
      |                 }{
  178 |                 ,0,0,0,0
      |                 }{
  179 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  180 |                 ,0.85,0.68,0.65,0.75
      |                 -
      |                 }},{{
  181 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  182 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  183 |                 ,0.85,0.68,0.65,0.75
      |                 }{
  184 |                 ,0,0,0,0
      |                 }{
  185 |         };
      |         }}}
DesignProbes.c: In function ‘designProbes._omp_fn.0’:
DesignProbes.c:838:85: warning: ‘lastCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  838 |                                                                 cycles += lastCycle - thisCycle;
      |                                                                           ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:269:58: note: ‘lastCycle’ was declared here
  269 |                         int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                                          ^~~~~~~~~
DesignProbes.c:838:85: warning: ‘thisCycle’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  838 |                                                                 cycles += lastCycle - thisCycle;
      |                                                                           ~~~~~~~~~~^~~~~~~~~~~
DesignProbes.c:269:69: note: ‘thisCycle’ was declared here
  269 |                         int MM, num, thisStart, thisEnd, lastCycle, thisCycle, cycles;
      |                                                                     ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c Diff.c -o Diff.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘firstSeqsPosEqual’:
DistanceMatrix.c:796:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  796 |                 if (!ci)
      |                 ^~
DistanceMatrix.c:799:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  799 |                         while (i < ex) {
      |                         ^~~~~
DistanceMatrix.c:818:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  818 |                 if (!cj)
      |                 ^~
DistanceMatrix.c:821:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  821 |                         while (j < ey) {
      |                         ^~~~~
DistanceMatrix.c: In function ‘computeOverlap._omp_fn.0’:
DistanceMatrix.c:1053:53: warning: ‘one’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1053 |                                                 two != one) {
      |                                                 ~~~~^~~~~~
DistanceMatrix.c:1028:29: note: ‘one’ was declared here
 1028 |                         int one, two;
      |                             ^~~
DistanceMatrix.c:1340:61: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1340 |                                                 if (w1 - p1 + p2 > w2 - t2) {
      |                                                     ~~~~~~~~^~~~
DistanceMatrix.c:883:76: note: ‘p2’ was declared here
  883 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                            ^~
DistanceMatrix.c:1340:56: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1340 |                                                 if (w1 - p1 + p2 > w2 - t2) {
      |                                                     ~~~^~~~
DistanceMatrix.c:883:72: note: ‘p1’ was declared here
  883 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                        ^~
DistanceMatrix.c:1374:66: warning: ‘off’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1374 |                                         (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
      |                                                              ~~~~^~~~~~
DistanceMatrix.c:883:96: note: ‘off’ was declared here
  883 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                                                ^~~
DistanceMatrix.c:1374:66: warning: ‘OV’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1374 |                                         (w1 <= w2 && (double)(OV + off)/(double)w2 < coverage)))) {
      |                                                              ~~~~^~~~~~
DistanceMatrix.c:883:92: note: ‘OV’ was declared here
  883 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                                            ^~
DistanceMatrix.c:1379:91: warning: ‘ov’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1379 |                                                         sim[i] = (double)pos/((double)(ov - g2));
      |                                                                                       ~~~~^~~~~
DistanceMatrix.c:883:88: note: ‘ov’ was declared here
  883 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                                        ^~
DistanceMatrix.c:1378:52: warning: ‘o’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1378 |                                                 if (o == 1) {
      |                                                    ^
DistanceMatrix.c:883:112: note: ‘o’ was declared here
  883 |         int i, j, k, l, n, p, d, lx, new, *t, *keep, *I, *X, *OX, pos, p1, p2, t1, t2, ov, OV, off, g1, g2, g, o, count, useMax;
      |                                                                                                                ^
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c: In function ‘pop’:
EnumerateSequence.c:545:15: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  545 |         x = x + (x >> 4) & 0xF0F0F0F;
      |             ~~^~~~~~~~~~
EnumerateSequence.c: In function ‘enumerateSequence’:
EnumerateSequence.c:358:17: warning: ‘tot’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  358 |         #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
      |                 ^~~
EnumerateSequence.c:358:17: warning: ‘mN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
EnumerateSequence.c: In function ‘enumerateSequenceReducedAA’:
EnumerateSequence.c:955:17: warning: ‘tot’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  955 |         #pragma omp parallel for private(i,j,k,x_i,rans,sum,ambiguous) num_threads(nthreads)
      |                 ^~~
EnumerateSequence.c:955:17: warning: ‘mN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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:381:35: warning: ‘K’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  381 |                         } else if (k == 2) {
      |                                   ^
FindFrameshifts.c:318:47: warning: ‘J’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  318 |                                 if (C[k*rc + j*r + i] >= 0) {
      |                                              ~^~
FindFrameshifts.c:320:48: warning: ‘I’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  320 |                                         pos = i*3 + k + 1;
      |                                               ~^~
In file included from /home/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:41,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.19-bioc/R/include/Rinternals.h:901:33: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  901 | #define eval                    Rf_eval
      |                                 ^~~~~~~
FindFrameshifts.c:162:31: note: ‘utilsPackage’ was declared here
  162 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:41,
                 from FindFrameshifts.c:11:
/home/biocbuild/bbs-3.19-bioc/R/include/Rinternals.h:901:33: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  901 | #define eval                    Rf_eval
      |                                 ^~~~~~~
FindFrameshifts.c:162:14: note: ‘percentComplete’ was declared here
  162 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
FindFrameshifts.c:468:40: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  468 |                                 before = *rPercentComplete;
      |                                 ~~~~~~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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:421:56: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  421 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c:432:64: warning: ‘lastVal’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  432 |                                         score += codons[lastVal*64 + val];
      |                                                         ~~~~~~~^~~
GeneFinding.c: In function ‘startCodonModel’:
GeneFinding.c:791:48: 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:892:48: 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:973:59: 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:1059:59: 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:1131:59: 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:1216:59: 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:1286:51: 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:1289:81: 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:1379:59: 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:1496:59: 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:1598:59: 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:1711:56: warning: ‘x_i.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1711 |                                 val = getBaseRC(x_i.ptr[j++]);
      |                                                        ^
GeneFinding.c: In function ‘nucleotideBiasModel’:
GeneFinding.c:1826:56: 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:1913:56: 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:1990:77: 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:2090:77: 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:2307:56: 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:2419:48: 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:2520:48: 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:2578:59: 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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c GetPools.c -o GetPools.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c Import.c -o Import.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c InformationContent.c -o InformationContent.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c IntDist.c -o IntDist.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c ManipulateXStringSet.c -o ManipulateXStringSet.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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:79:27: warning: missing braces around initializer [-Wmissing-braces]
   79 |         double dH[4][4] = {
      |                           ^
   80 |                 -7.9,-8.4,-7.8,-7.2
      |                 {
   81 |                 ,-8.5,-8.0,-10.6,-7.8
      |                 }{
   82 |                 ,-8.2,-9.8,-8.0,-8.4
      |                 }{
   83 |                 ,-7.2,-8.2,-8.5,-7.9
      |                 }{
   84 |         };
      |         }
MeltPolymer.c:88:27: warning: missing braces around initializer [-Wmissing-braces]
   88 |         double dS[4][4] = {
      |                           ^
   89 |                 -22.2,-22.4,-21.0,-20.4
      |                 {
   90 |                 ,-22.7,-19.9,-27.2,-21.0
      |                 }{
   91 |                 ,-22.2,-24.4,-19.9,-22.4
      |                 }{
   92 |                 ,-21.3,-22.2,-22.7,-22.2
      |                 }{
   93 |         };
      |         }
MeltPolymer.c:358:59: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  358 |                                         *(rans + k + l*s) += 1;
      |                                                           ^~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c MovingAverage.c -o MovingAverage.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c NNLS.c -o NNLS.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c Order.c -o Order.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c: In function ‘alignPair._omp_fn.0’:
PairwiseAlignment.c:472:39: warning: ‘p2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  472 |                                 P2[i] = p2;
      |                                 ~~~~~~^~~~
PairwiseAlignment.c:175:19: note: ‘p2’ was declared here
  175 |         int *p1, *p2, *p3, *p4;
      |                   ^~
PairwiseAlignment.c:471:39: warning: ‘p1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  471 |                                 P1[i] = p1;
      |                                 ~~~~~~^~~~
PairwiseAlignment.c:175:14: note: ‘p1’ was declared here
  175 |         int *p1, *p2, *p3, *p4;
      |              ^~
PairwiseAlignment.c:476:39: warning: ‘p4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  476 |                                 P4[i] = p4;
      |                                 ~~~~~~^~~~
PairwiseAlignment.c:175:29: note: ‘p4’ was declared here
  175 |         int *p1, *p2, *p3, *p4;
      |                             ^~
PairwiseAlignment.c:475:39: warning: ‘p3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  475 |                                 P3[i] = p3;
      |                                 ~~~~~~^~~~
PairwiseAlignment.c:175:24: note: ‘p3’ was declared here
  175 |         int *p1, *p2, *p3, *p4;
      |                        ^~
PairwiseAlignment.c: In function ‘alignPairs’:
PairwiseAlignment.c:1107:17: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1107 |         #pragma omp parallel for private(i) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
PairwiseAlignment.c:1107:17: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
PairwiseAlignment.c:1107:17: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c PredictDBN.c -o PredictDBN.o
PredictDBN.c: In function ‘predictDBN’:
PredictDBN.c:873:85: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  873 |                                                                 range2[0] = nucs[pos[prev]];// + 1;
      |                                                                                     ^
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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:255:25: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  255 |                         SET_VECTOR_ELT(ret, i, ans);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
PredictHEC.c:42:15: warning: ‘states’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   42 |         char *states;
      |               ^~~~~~
PredictHEC.c:237:46: warning: ‘rans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  237 |                                 *(rans + 3*j + 1) = E;
      |                                  ~~~~~~~~~~~~^~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c Search.c -o Search.o
Search.c: In function ‘searchIndex._omp_fn.0’:
Search.c:515:47: warning: ‘s_j.length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  515 |                                         bound = s_j.length - 1; // right bound
      |                                         ~~~~~~^~~~~~~~~~~~~~~~
Search.c:443:51: note: ‘s_j.length’ was declared here
  443 |                                 Chars_holder p_i, s_j;
      |                                                   ^~~
Search.c:443:51: warning: ‘s_j.ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:449:37: warning: ‘maxLen’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  449 |                                 int maxLen; // maximum observed length
      |                                     ^~~~~~
Search.c: In function ‘searchIndex’:
Search.c:969:33: warning: ‘ans3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  969 |                                 SET_VECTOR_ELT(ans3, k, ans);
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
Search.c:208:17: warning: ‘matrices’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  208 |         #pragma omp parallel for private(i,j,k,p,c) schedule(dynamic) num_threads(nthreads)
      |                 ^~~
Search.c:208:17: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:17: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:17: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:17: warning: ‘lkup_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:17: warning: ‘lkup_row’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:17: warning: ‘dS’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Search.c:208:17: warning: ‘sM’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c Translate.c -o Translate.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c Utils.c -o Utils.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:41,
                 from Utils.c:16:
Utils.c: In function ‘matchOrder’:
/home/biocbuild/bbs-3.19-bioc/R/include/Rinternals.h:901:33: warning: ‘utilsPackage’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  901 | #define eval                    Rf_eval
      |                                 ^~~~~~~
Utils.c:333:31: note: ‘utilsPackage’ was declared here
  333 |         SEXP percentComplete, utilsPackage;
      |                               ^~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/include/Rdefines.h:41,
                 from Utils.c:16:
/home/biocbuild/bbs-3.19-bioc/R/include/Rinternals.h:901:33: warning: ‘percentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  901 | #define eval                    Rf_eval
      |                                 ^~~~~~~
Utils.c:333:14: note: ‘percentComplete’ was declared here
  333 |         SEXP percentComplete, utilsPackage;
      |              ^~~~~~~~~~~~~~~
Utils.c:431:40: warning: ‘rPercentComplete’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  431 |                                 before = *rPercentComplete;
      |                                 ~~~~~~~^~~~~~~~~~~~~~~~~~~
Utils.c: In function ‘splitPartitions’:
Utils.c:982:35: warning: ‘change’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  982 |                 } else if (change - j >= m && // large enough partition
      |                            ~~~~~~~^~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c VectorSums.c -o VectorSums.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-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 ClusterMP.o Compositions.o Compression.o ConsensusSequence.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o IntDist.o ManipulateXStringSet.o MeltPolymer.o MovingAverage.o NNLS.o Order.o PairwiseAlignment.o PredictDBN.o PredictHEC.o R_init_decipher.o S4Vectors_stubs.o Search.o TerminalMismatch.o Translate.o Utils.o VectorSums.o XVector_stubs.o -fopenmp -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-DECIPHER/00new/DECIPHER/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DECIPHER)

Tests output


Example timings

DECIPHER.Rcheck/DECIPHER-Ex.timings

nameusersystemelapsed
AA_REDUCED0.0420.0050.046
Add2DB0.6140.0680.685
AdjustAlignment0.1920.0160.208
AlignDB1.2160.0961.312
AlignPairs3.7630.1283.893
AlignProfiles1.1480.0881.238
AlignSeqs173.148 1.844176.001
AlignSynteny2.5600.0162.576
AlignTranslation11.790 0.07211.864
AmplifyDNA0.0000.0040.003
Array2Matrix5.1430.0635.207
BLOSUM0.0170.0040.029
BrowseDB0.0520.0000.053
BrowseSeqs24.255 0.12424.380
CalculateEfficiencyArray0.0230.0040.027
CalculateEfficiencyFISH0.0040.0000.004
CalculateEfficiencyPCR0.0030.0000.004
Clusterize5.8810.0245.905
Codec1.1590.0041.162
ConsensusSequence0.1450.0160.161
Cophenetic0.2050.0000.205
CorrectFrameshifts16.773 0.07216.845
CreateChimeras0.6610.0000.661
DB2Seqs0.0290.0050.037
DesignArray5.2040.0885.293
DesignPrimers0.0090.0000.008
DesignProbes0.0040.0040.007
DesignSignatures0.0080.0000.009
DetectRepeats15.119 0.04815.167
DigestDNA0.1280.0000.128
Disambiguate0.0440.0000.045
DistanceMatrix0.0390.0080.047
ExtractGenes43.543 0.26443.811
FindChimeras0.0600.0040.065
FindGenes46.156 0.31246.470
FindNonCoding63.328 0.59663.928
FindSynteny1.3960.0281.427
FormGroups0.0640.0040.069
Genes-class44.610 0.27644.890
HEC_MI0.3460.0040.350
IdConsensus0.4100.0120.421
IdLengths0.0310.0000.031
IdTaxa9.6450.0169.661
IdentifyByRank0.0280.0000.028
IndexSeqs0.8950.0000.895
InvertedIndex-class0.5150.0000.515
LearnNonCoding119.939 6.367130.247
LearnTaxa7.1780.7447.964
MIQS0.0420.0040.046
MMLSUM0.010.000.01
MODELS0.0020.0000.002
MapCharacters87.046 0.27687.324
MaskAlignment0.4600.0110.470
MeltDNA0.0690.0000.069
NNLS0.0040.0000.004
NonCoding-class0.0510.0100.062
NonCodingRNA0.1150.0010.116
OrientNucleotides0.4220.0040.426
PAM0.010.000.01
PFASUM0.0110.0000.012
PredictDBN0.0050.0040.008
PredictHEC0.2450.0080.253
RESTRICTION_ENZYMES0.0010.0030.005
ReadDendrogram0.0230.0000.023
RemoveGaps0.0120.0000.011
ScoreAlignment5.1420.0485.190
SearchDB0.0490.0000.050
SearchIndex0.9690.0280.997
Seqs2DB0.1220.0080.130
StaggerAlignment10.906 0.08810.994
Synteny-class1.8400.0041.843
Taxa-class10.168 0.02010.188
TerminalChar0.0030.0040.007
TileSeqs3.2000.0483.248
TrainingSet_16S1.7150.0271.741
TreeLine8.3380.0488.387
TrimDNA0.1340.0080.142
WriteDendrogram0.0000.0040.003
WriteGenes44.634 0.22044.854
deltaGrules0.0030.0080.011
deltaGrulesRNA0.0240.0000.024
deltaHrules0.0170.0040.021
deltaHrulesRNA0.020.000.02
deltaSrules0.0510.0000.051
deltaSrulesRNA0.0170.0000.018