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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 527/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 3.4.0  (landing page)
Erik Wright
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/DECIPHER
git_branch: RELEASE_3_21
git_last_commit: e154ba4
git_last_commit_date: 2025-04-15 10:10:51 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for DECIPHER on merida1

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: 3.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DECIPHER_3.4.0.tar.gz
StartedAt: 2025-10-14 02:30:25 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 03:05:19 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 2094.2 seconds
RetCode: 0
Status:   OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DECIPHER_3.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DECIPHER.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘3.4.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... INFO
  installed size is 12.9Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    data      7.5Mb
    extdata   2.8Mb
* 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 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 ‘.NNI’ with different
  formal arguments
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
AlignSeqs          458.438  6.977 522.087
LearnNonCoding     170.895  5.401 185.047
Treeline            93.226  1.706 100.704
FindNonCoding       86.117  5.192  96.193
ExtractGenes        61.191  1.357  67.716
Genes-class         58.250  1.601  61.732
FindGenes           58.688  1.143  64.180
BrowseSeqs          56.817  0.935  64.393
WriteGenes          55.304  1.796  59.793
InferRecombination  53.169  0.643  57.620
InferSelection      51.172  0.606  54.342
DistanceMatrix      42.284  1.403  53.400
CorrectFrameshifts  36.171  1.574  43.186
DetectRepeats       26.656  0.250  35.117
StaggerAlignment    25.527  1.027  31.639
AlignTranslation    24.668  0.320  26.945
InferDemography     22.506  0.150  24.190
TrimDNA             15.693  2.155  18.813
Taxa-class          16.090  0.921  18.672
IdTaxa              15.223  0.294  16.317
Clusterize          14.454  1.018  18.870
LearnTaxa            9.692  2.135  13.179
ScoreAlignment      11.369  0.365  13.215
Array2Matrix         9.443  0.085  10.427
DesignArray          9.272  0.070  10.219
TileSeqs             8.571  0.049   9.383
MapCharacters        7.697  0.359   9.117
AlignPairs           7.731  0.194   8.325
AlignSynteny         5.737  0.055   6.331
Cophenetic           5.024  0.042   6.091
TrainingSet_16S      4.977  0.080   5.369
Synteny-class        4.303  0.095   5.241
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.


Installation output

DECIPHER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘DECIPHER’ ...
** this is package ‘DECIPHER’ version ‘3.4.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c AlignProfiles.c -o AlignProfiles.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c AssignIndels.c -o AssignIndels.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c CalculateDeltaG.c -o CalculateDeltaG.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c:26:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -11.5, -7.8, -7, -8.3,
                ^~~~~~~~~~~~~~~~~~~~~
                {                    }
CalculateFISH.c:27:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -10.4, -12.8, -16.3, -9.1,
                ^~~~~~~~~~~~~~~~~~~~~~~~~
                {                        }
CalculateFISH.c:28:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -8.6, -8, -9.3, -5.9,
                ^~~~~~~~~~~~~~~~~~~~
                {                   }
CalculateFISH.c:29:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -7.8, -5.5, -9, -7.8
                ^~~~~~~~~~~~~~~~~~~~
                {                   }
CalculateFISH.c:32:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -36.4, -21.6, -19.7, -23.9,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
                {                         }
CalculateFISH.c:33:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -28.4, -31.9, -47.1, -23.5,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
                {                         }
CalculateFISH.c:34:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -22.9, -17.1, -23.2, -12.3,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
                {                         }
CalculateFISH.c:35:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -23.2, -13.5, -26.1, -21.9
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
                {                         }
CalculateFISH.c:38:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -7.9, -8.4, -7.8, -7.2,
                ^~~~~~~~~~~~~~~~~~~~~~
                {                     }
CalculateFISH.c:39:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -8.5, -8, -10.6, -7.8,
                ^~~~~~~~~~~~~~~~~~~~~
                {                    }
CalculateFISH.c:40:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -8.2, -9.8, -8, -8.4,
                ^~~~~~~~~~~~~~~~~~~~
                {                   }
CalculateFISH.c:41:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -7.2, -8.2, -8.5, -7.9
                ^~~~~~~~~~~~~~~~~~~~~~
                {                     }
CalculateFISH.c:44:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -22.2, -22.4, -21, -20.4,
                ^~~~~~~~~~~~~~~~~~~~~~~~
                {                       }
CalculateFISH.c:45:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -22.7, -19.9, -27.2, -21,
                ^~~~~~~~~~~~~~~~~~~~~~~~
                {                       }
CalculateFISH.c:46:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -22.2, -24.4, -19.9, -22.4,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
                {                         }
CalculateFISH.c:47:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -21.3, -22.2, -22.7, -22.2
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
                {                         }
CalculateFISH.c:50:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -6.6, -10.17, -7.65, -5.76,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
                {                         }
CalculateFISH.c:51:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -10.56, -12.21, -7.95, -7.65,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
                {                           }
CalculateFISH.c:52:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -13.37, -14.21, -12.21, -10.17,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                {                             }
CalculateFISH.c:53:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -8.11, -13.37, -10.56, -6.6
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~
                {                          }
CalculateFISH.c:56:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -18.38, -26.03, -19.18, -15.67,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                {                             }
CalculateFISH.c:57:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -28.25, -30.02, -19.18, -19.18,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                {                             }
CalculateFISH.c:58:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -35.68, -34.85, -30.02, -26.03,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                {                             }
CalculateFISH.c:59:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -22.59, -35.68, -28.25, -18.38
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                {                             }
24 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ChainSegments.c -o ChainSegments.o
ChainSegments.c:666:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Cluster.c -o Cluster.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ClusterME.c -o ClusterME.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ClusterML.c -o ClusterML.o
ClusterML.c:1887:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ClusterMP.c -o ClusterMP.o
ClusterMP.c:112:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Compositions.c -o Compositions.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Compression.c -o Compression.o
Compression.c:521:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
Compression.c:1408:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
Compression.c:1706:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ConsensusSequence.c -o ConsensusSequence.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DesignProbes.c -o DesignProbes.o
DesignProbes.c:72:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -0.816507461,-2.5401714,-1.647430026,-1.184658548
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                {                                                }
DesignProbes.c:73:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                                  }
DesignProbes.c:74:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                               }
DesignProbes.c:75:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                                 }
DesignProbes.c:79:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -0.141370102,-0.439805276,-0.285236035,-0.205111781
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                {                                                  }
DesignProbes.c:80:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                                 }
DesignProbes.c:81:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                                  }
DesignProbes.c:82:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                                  }
DesignProbes.c:86:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                0,0,0,0
                ^~~~~~~
                {      }
DesignProbes.c:87:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.545032445,1.254355018,1.491691514,1.329138183
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:88:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.150635633,0.582415494,1.075877275,1.187937642
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:89:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.203555051,1.001540513,0.864287715,0.717125848
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:90:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:86:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                0,0,0,0
                ^~~~~~~
                {
DesignProbes.c:91:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.630005348,0.18553379,0.730763505,0.709272397
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:92:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:93:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.856582783,-0.143236405,0.716721488,0.603652831
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                               }
DesignProbes.c:94:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.851622883,0.653168672,0.676545316,1.187937642
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:95:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:91:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.630005348,0.18553379,0.730763505,0.709272397
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:96:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.231861002,0.746214538,1.087821916,0.989140748
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:97:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.822113278,1.270687029,1.336192565,1.364584949
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:98:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:99:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.443665704,1.385046493,1.256013166,1.329138183
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:100:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:96:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.231861002,0.746214538,1.087821916,0.989140748
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:101:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.478009492,0.882097231,1.20450984,1.061002478
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:102:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.496720812,0.846496194,0.967868114,0.989140748
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:103:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.766581547,-0.024857805,0.50754303,0.709272397
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:104:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:105:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:101:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.478009492,0.882097231,1.20450984,1.061002478
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:106:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:107:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:108:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:109:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.76,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:110:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:106:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:86:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                0,0,0,0
                ^~~~~~~
                {
DesignProbes.c:111:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:112:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.295827995,0.84547091,0.91019099,1.256013166
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                            }
DesignProbes.c:113:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.755889609,0.241428373,0.396379912,0.676545316
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:114:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.99945386,0.740323132,0.435659206,0.864287715
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:115:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.55,0.48,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:111:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {
DesignProbes.c:116:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.843147406,0.101248351,0.49063599,0.50754303
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                            }
DesignProbes.c:117:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:118:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.0651638,0.249934344,0.699352949,0.716721488
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                            }
DesignProbes.c:119:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.871921533,0.59458138,0.396379912,1.075877275
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:120:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.56,0.49,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:116:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.843147406,0.101248351,0.49063599,0.50754303
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:121:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.07531714,0.318907854,0.653287717,0.967868114
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:122:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.099899195,0.730184613,0.661798984,1.336192565
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:123:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:124:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.45897431,1.318532145,0.91019099,1.491691514
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                            }
DesignProbes.c:125:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.56,0.49,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:121:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.07531714,0.318907854,0.653287717,0.967868114
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:126:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.242135174,0.894838095,1.108555445,1.20450984
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:127:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.911428974,0.524430101,0.653287717,1.087821916
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:128:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.503209827,0.274849491,0.49063599,0.730763505
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:129:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:130:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.55,0.48,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:126:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.242135174,0.894838095,1.108555445,1.20450984
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:131:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.55,0.48,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:132:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.56,0.49,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:133:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.56,0.49,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:134:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.55,0.48,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:135:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:131:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.55,0.48,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:111:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {
DesignProbes.c:136:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:137:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.100661785,0.969784756,1.318532145,1.385046493
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:138:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.565895968,-0.060347902,0.59458138,0.653168672
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:139:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.782168488,0.788161238,0.740323132,1.001540513
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:140:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.46,0.55,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:136:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {
DesignProbes.c:141:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.468913405,-0.469855984,0.274849491,-0.024857805
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                                }
DesignProbes.c:142:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:143:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.258195131,-0.70438632,0.249934344,-0.143236405
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                               }
DesignProbes.c:144:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.502914193,-0.060347902,0.241428373,0.582415494
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                               }
DesignProbes.c:145:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.47,0.56,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:141:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.468913405,-0.469855984,0.274849491,-0.024857805
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:146:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.584083861,0.258975454,0.524430101,0.846496194
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:147:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.968040559,0.797499702,0.730184613,1.270687029
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:148:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:149:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.081040749,0.969784756,0.84547091,1.254355018
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:150:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.47,0.56,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:146:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.584083861,0.258975454,0.524430101,0.846496194
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:151:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.048553951,0.728354541,0.894838095,0.882097231
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:152:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.88611252,0.258975454,0.318907854,0.746214538
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:153:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.239520858,-0.469855984,0.101248351,0.18553379
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:154:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:155:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.46,0.55,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:151:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.048553951,0.728354541,0.894838095,0.882097231
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:156:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.46,0.55,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:157:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.47,0.56,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:158:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.47,0.56,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:159:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.46,0.55,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:160:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:156:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.46,0.55,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:136:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {
DesignProbes.c:161:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:162:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.566899704,1.081040749,1.45897431,1.443665704
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:163:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.976725675,0.502914193,0.871921533,0.851622883
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:164:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.482046826,0.782168488,0.99945386,1.203555051
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:165:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.76
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:161:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {
DesignProbes.c:166:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.798628781,0.239520858,0.503209827,0.766581547
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:167:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:168:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.141098246,0.258195131,1.0651638,0.856582783
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                            }
DesignProbes.c:169:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.976725675,0.565895968,0.755889609,1.150635633
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:170:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:166:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.798628781,0.239520858,0.503209827,0.766581547
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:171:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.125403302,0.88611252,0.911428974,1.496720812
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:172:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.68169282,0.968040559,1.099899195,1.822113278
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:173:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:174:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.566899704,1.100661785,1.295827995,1.545032445
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:175:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:171:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.125403302,0.88611252,0.911428974,1.496720812
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:176:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.35948517,1.048553951,1.242135174,1.478009492
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:177:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.125403302,0.584083861,1.07531714,1.231861002
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:178:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.798628781,0.468913405,0.843147406,0.630005348
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:179:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:180:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:176:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.35948517,1.048553951,1.242135174,1.478009492
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:181:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:182:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:183:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:184:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:185:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0        
                 ^~~~~~~
                 {      }
DesignProbes.c:181:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:161:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {
DesignProbes.c:59:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
133 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Diff.c -o Diff.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c:522:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
DistanceMatrix.c:1118:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c:298:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
EnumerateSequence.c:871:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ExpandAmbiguities.c -o ExpandAmbiguities.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FindFrameshifts.c -o FindFrameshifts.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c GeneFinding.c -o GeneFinding.o
GeneFinding.c:3261:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
GeneFinding.c:3338:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
GeneFinding.c:3395:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c GetPools.c -o GetPools.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Import.c -o Import.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c InformationContent.c -o InformationContent.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IntDist.c -o IntDist.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ManipulateXStringSet.c -o ManipulateXStringSet.o
ManipulateXStringSet.c:55:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
ManipulateXStringSet.c:692:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
ManipulateXStringSet.c:822:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
ManipulateXStringSet.c:925:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
ManipulateXStringSet.c:1019:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
5 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c:80:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -7.9,-8.4,-7.8,-7.2
                ^~~~~~~~~~~~~~~~~~~
                {                  }
MeltPolymer.c:81:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-8.5,-8.0,-10.6,-7.8
                 ^~~~~~~~~~~~~~~~~~~~
                 {                   }
MeltPolymer.c:82:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-8.2,-9.8,-8.0,-8.4
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
MeltPolymer.c:83:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-7.2,-8.2,-8.5,-7.9
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
MeltPolymer.c:89:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -22.2,-22.4,-21.0,-20.4
                ^~~~~~~~~~~~~~~~~~~~~~~
                {                      }
MeltPolymer.c:90:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-22.7,-19.9,-27.2,-21.0
                 ^~~~~~~~~~~~~~~~~~~~~~~
                 {                      }
MeltPolymer.c:91:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-22.2,-24.4,-19.9,-22.4
                 ^~~~~~~~~~~~~~~~~~~~~~~
                 {                      }
MeltPolymer.c:92:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-21.3,-22.2,-22.7,-22.2
                 ^~~~~~~~~~~~~~~~~~~~~~~
                 {                      }
8 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c MovingAverage.c -o MovingAverage.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c NNLS.c -o NNLS.o
NNLS.c:50:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Order.c -o Order.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c:188:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
PairwiseAlignment.c:1034:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PopulationGenetics.c -o PopulationGenetics.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PredictDBN.c -o PredictDBN.o
PredictDBN.c:160:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PredictHEC.c -o PredictHEC.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_decipher.c -o R_init_decipher.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Search.c -o Search.o
Search.c:106:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c:41:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Translate.c -o Translate.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Utils.c -o Utils.o
Utils.c:230:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
Utils.c:343:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c VectorSums.c -o VectorSums.o
VectorSums.c:83:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterME.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 PopulationGenetics.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 -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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_REDUCED0.1000.0170.120
Add2DB1.4550.1561.685
AdjustAlignment0.4360.0280.487
AlignDB2.4780.0682.645
AlignPairs7.7310.1948.325
AlignProfiles1.6790.0651.845
AlignSeqs458.438 6.977522.087
AlignSynteny5.7370.0556.331
AlignTranslation24.668 0.32026.945
AmplifyDNA0.0040.0050.009
Array2Matrix 9.443 0.08510.427
BLOSUM0.0250.0100.040
BrowseDB0.0940.0070.123
BrowseSeqs56.817 0.93564.393
CalculateEfficiencyArray0.0260.0100.055
CalculateEfficiencyFISH0.0100.0010.010
CalculateEfficiencyPCR0.0090.0000.010
Clusterize14.454 1.01818.870
Codec1.2640.0231.699
ConsensusSequence0.4000.0230.524
Cophenetic5.0240.0426.091
CorrectFrameshifts36.171 1.57443.186
CreateChimeras1.6960.0272.087
DB2Seqs0.0630.0361.806
DesignArray 9.272 0.07010.219
DesignPrimers0.0170.0030.020
DesignProbes0.0170.0020.020
DesignSignatures0.0200.0050.025
DetectRepeats26.656 0.25035.117
DigestDNA0.3130.0170.358
Disambiguate0.1170.0080.135
DistanceMatrix42.284 1.40353.400
ExtractGenes61.191 1.35767.716
FindChimeras0.1490.0090.174
FindGenes58.688 1.14364.180
FindNonCoding86.117 5.19296.193
FindSynteny3.4240.0923.693
FormGroups0.1250.0070.138
Genes-class58.250 1.60161.732
HEC_MI0.2960.0240.322
IdConsensus0.8780.0471.012
IdLengths0.0580.0070.072
IdTaxa15.223 0.29416.317
IdentifyByRank0.0750.0040.083
IndexSeqs1.5470.0141.636
InferDemography22.506 0.15024.190
InferRecombination53.169 0.64357.620
InferSelection51.172 0.60654.342
InvertedIndex-class0.8750.0070.929
LearnNonCoding170.895 5.401185.047
LearnTaxa 9.692 2.13513.179
MIQS0.0630.0160.088
MMLSUM0.0120.0180.030
MODELS0.0030.0010.004
MapCharacters7.6970.3599.117
MaskAlignment1.2060.1111.583
MeltDNA0.1390.0170.207
NNLS0.0060.0030.012
NonCoding-class0.0980.0360.162
NonCodingRNA0.1480.0460.228
OrientNucleotides0.8970.0571.095
PAM0.0120.0090.037
PFASUM0.0150.0100.036
PredictDBN0.0160.0050.022
PredictHEC0.6000.0480.826
RESTRICTION_ENZYMES0.0060.0160.028
ReadDendrogram0.0420.0060.054
RemoveGaps0.0260.0020.034
ScoreAlignment11.369 0.36513.215
SearchDB0.0930.0070.125
SearchIndex2.2140.1482.695
Seqs2DB0.2000.0080.249
StaggerAlignment25.527 1.02731.639
Synteny-class4.3030.0955.241
Taxa-class16.090 0.92118.672
TerminalChar0.0130.0030.016
TileSeqs8.5710.0499.383
TrainingSet_16S4.9770.0805.369
Treeline 93.226 1.706100.704
TrimDNA15.693 2.15518.813
WriteDendrogram0.0070.0020.010
WriteGenes55.304 1.79659.793
deltaGrules0.0140.0120.026
deltaGrulesRNA0.0240.0120.037
deltaHrules0.0240.0130.038
deltaHrulesRNA0.0240.0120.038
deltaSrules0.0940.0060.103
deltaSrulesRNA0.0220.0120.036