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This page was generated on 2025-09-29 12:04 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4833
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4621
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4566
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 527/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 3.5.0  (landing page)
Erik Wright
Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 Sep 2025)
git_url: https://git.bioconductor.org/packages/DECIPHER
git_branch: devel
git_last_commit: f5796e8
git_last_commit_date: 2025-04-15 10:10:51 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for DECIPHER on lconway

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: 3.5.0
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_3.5.0.tar.gz
StartedAt: 2025-09-28 20:40:14 -0400 (Sun, 28 Sep 2025)
EndedAt: 2025-09-28 20:58:27 -0400 (Sun, 28 Sep 2025)
EllapsedTime: 1092.9 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_3.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DECIPHER.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘3.5.0’
* 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: ‘MacOSX11.3.1.sdk’
* checking installed package size ... INFO
  installed size is 13.5Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    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          200.506  4.785 207.710
LearnNonCoding     117.603  5.026 126.697
FindNonCoding       56.459  4.996  61.881
Treeline            52.237  2.094  54.661
ExtractGenes        39.947  1.416  45.492
FindGenes           36.662  1.268  38.172
Genes-class         35.521  1.622  37.409
InferSelection      34.984  0.318  35.454
WriteGenes          33.511  1.753  35.455
BrowseSeqs          34.224  0.686  35.506
DistanceMatrix      25.937  0.858  31.623
InferRecombination  21.308  0.437  21.859
CorrectFrameshifts  19.440  1.870  22.216
StaggerAlignment    13.148  1.006  14.296
DetectRepeats       13.997  0.139  14.207
AlignTranslation    12.225  0.296  13.046
TrimDNA              9.903  2.456  12.577
Taxa-class           9.839  0.518  10.446
Clusterize           8.717  0.967   9.965
IdTaxa               9.066  0.434   9.551
InferDemography      9.278  0.126   9.457
LearnTaxa            6.178  2.212   8.713
ScoreAlignment       6.393  0.474   6.927
DesignArray          6.181  0.035   6.251
AlignPairs           5.020  0.109   5.161
Array2Matrix         4.884  0.051   5.194
* 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-3.22-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 ‘3.5.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.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_REDUCED0.0490.0070.056
Add2DB0.7350.0730.814
AdjustAlignment0.2370.0160.257
AlignDB1.3180.0321.357
AlignPairs5.0200.1095.161
AlignProfiles1.1610.0491.218
AlignSeqs200.506 4.785207.710
AlignSynteny2.9750.0393.030
AlignTranslation12.225 0.29613.046
AmplifyDNA0.0030.0030.007
Array2Matrix4.8840.0515.194
BLOSUM0.0150.0070.069
BrowseDB0.0370.0050.051
BrowseSeqs34.224 0.68635.506
CalculateEfficiencyArray0.0160.0120.031
CalculateEfficiencyFISH0.0060.0000.005
CalculateEfficiencyPCR0.0060.0000.007
Clusterize8.7170.9679.965
Codec1.1670.0151.188
ConsensusSequence0.2130.0100.225
Cophenetic2.4640.0282.510
CorrectFrameshifts19.440 1.87022.216
CreateChimeras0.9560.0140.975
DB2Seqs0.0450.0210.099
DesignArray6.1810.0356.251
DesignPrimers0.0130.0020.015
DesignProbes0.0160.0010.018
DesignSignatures0.0150.0020.019
DetectRepeats13.997 0.13914.207
DigestDNA0.1710.0080.181
Disambiguate0.0510.0020.054
DistanceMatrix25.937 0.85831.623
ExtractGenes39.947 1.41645.492
FindChimeras0.0750.0050.084
FindGenes36.662 1.26838.172
FindNonCoding56.459 4.99661.881
FindSynteny1.9740.1032.099
FormGroups0.0660.0060.073
Genes-class35.521 1.62237.409
HEC_MI0.1810.0130.197
IdConsensus0.4760.1050.591
IdLengths0.0360.0090.046
IdTaxa9.0660.4349.551
IdentifyByRank0.0360.0030.038
IndexSeqs0.9660.0090.979
InferDemography9.2780.1269.457
InferRecombination21.308 0.43721.859
InferSelection34.984 0.31835.454
InvertedIndex-class0.5900.0050.598
LearnNonCoding117.603 5.026126.697
LearnTaxa6.1782.2128.713
MIQS0.0400.0110.052
MMLSUM0.0060.0150.021
MODELS0.0020.0010.001
MapCharacters3.8670.1994.098
MaskAlignment0.5670.0180.587
MeltDNA0.0760.0040.080
NNLS0.0040.0010.004
NonCoding-class0.0460.0180.066
NonCodingRNA0.0820.0430.129
OrientNucleotides0.5090.0090.520
PAM0.0060.0040.011
PFASUM0.0090.0040.014
PredictDBN0.0080.0020.009
PredictHEC0.2730.0220.299
RESTRICTION_ENZYMES0.0020.0050.007
ReadDendrogram0.0260.0070.033
RemoveGaps0.0120.0010.013
ScoreAlignment6.3930.4746.927
SearchDB0.0580.0060.066
SearchIndex1.4180.2131.662
Seqs2DB0.1070.0040.112
StaggerAlignment13.148 1.00614.296
Synteny-class2.4190.0672.500
Taxa-class 9.839 0.51810.446
TerminalChar0.0090.0020.011
TileSeqs4.3580.0774.451
TrainingSet_16S2.1130.0542.192
Treeline52.237 2.09454.661
TrimDNA 9.903 2.45612.577
WriteDendrogram0.0050.0010.005
WriteGenes33.511 1.75335.455
deltaGrules0.0080.0140.022
deltaGrulesRNA0.0150.0150.030
deltaHrules0.0120.0130.026
deltaHrulesRNA0.0140.0130.027
deltaSrules0.0700.0090.080
deltaSrulesRNA0.0140.0120.027