Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 505/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 2.28.0  (landing page)
Erik Wright
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/DECIPHER
git_branch: RELEASE_3_17
git_last_commit: 9be570c
git_last_commit_date: 2023-04-25 10:21:15 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for DECIPHER on kjohnson2


To the developers/maintainers of the DECIPHER package:
- 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: 2.28.0
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_2.28.0.tar.gz
StartedAt: 2023-10-17 14:14:22 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 14:34:44 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 1222.0 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_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DECIPHER.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘2.28.0’
* 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 ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    data      7.5Mb
    extdata   2.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DesignSignatures: no visible binding for global variable ‘deltaHrules’
FindGenes: no visible binding for global variable ‘deltaHrulesRNA’
FindNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
LearnNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
PredictDBN: no visible binding for global variable ‘deltaGrulesRNA’
TreeLine: multiple local function definitions for ‘.minimize’ with
  different formal arguments
Undefined global functions or variables:
  deltaGrulesRNA deltaHrules deltaHrulesRNA
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking 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
MapCharacters      101.613  0.914 157.312
FindNonCoding       68.397  3.170 105.551
LearnNonCoding      57.366  3.255  93.216
WriteGenes          39.422  0.791  61.534
ExtractGenes        39.130  0.638  59.026
FindGenes           37.259  0.692  57.955
Genes-class         37.007  0.768  57.812
BrowseSeqs          34.326  0.454  53.037
AlignSeqs           27.208  0.337  41.449
CorrectFrameshifts  19.832  1.007  30.263
DetectRepeats       20.276  0.237  31.022
StaggerAlignment    16.792  0.371  26.280
AlignTranslation    15.112  0.258  22.474
Taxa-class          12.293  0.327  19.372
TreeLine            11.108  0.218  17.245
IdTaxa              10.733  0.140  16.727
LearnTaxa            6.825  0.877  11.734
Clusterize           7.206  0.159  11.193
ScoreAlignment       7.212  0.143  11.335
TileSeqs             6.207  0.072   9.685
Array2Matrix         6.014  0.059   9.218
DesignArray          5.961  0.055   9.249
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/Resources/library’
* installing *source* package ‘DECIPHER’ ...
** 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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c:90:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
AlignProfiles.c:826:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c AssignIndels.c -o AssignIndels.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c CalculateDeltaG.c -o CalculateDeltaG.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ChainSegments.c -o ChainSegments.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Cluster.c -o Cluster.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ClusterML.c -o ClusterML.o
ClusterML.c:6750:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
ClusterML.c:5064:13: warning: unused function 'L_unknown_SIMD' [-Wunused-function]
static void L_unknown_SIMD(double *__restrict Ls, const int i3, const int i1, const int i2, const double *P1, const double *P2, const double epsilon, const double inv_epsilon, const int root)
            ^
ClusterML.c:5666:13: warning: unused function 'L_unknown_5_SIMD' [-Wunused-function]
static void L_unknown_5_SIMD(double *__restrict Ls, const int i3, const int i1, const int i2, const double *P1, const double *P2, const double epsilon, const double inv_epsilon, const int root)
            ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ClusterMP.c -o ClusterMP.o
ClusterMP.c:83:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c CommonGaps.c -o CommonGaps.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Compositions.c -o Compositions.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Compression.c -o Compression.o
Compression.c:520:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
Compression.c:1405:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
Compression.c:1701:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ConsensusSequence.c -o ConsensusSequence.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ConsolidateGaps.c -o ConsolidateGaps.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DesignProbes.c -o DesignProbes.o
DesignProbes.c:71:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -0.816507461,-2.5401714,-1.647430026,-1.184658548
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                {                                                }
DesignProbes.c:72:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-1.854740485,-2.479102613,-2.826248182,-1.647430026
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                                  }
DesignProbes.c:73:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-2.48761723,-4.694133177,-2.479102613,-2.5401714
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                               }
DesignProbes.c:74:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-0.495794417,-2.48761723,-1.854740485,-0.816507461
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                                 }
DesignProbes.c:78:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                -0.141370102,-0.439805276,-0.285236035,-0.205111781
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                {                                                  }
DesignProbes.c:79:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-0.321129768,-0.429231826,-0.48933661,-0.285236035
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                                 }
DesignProbes.c:80:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-0.430706047,-0.812742218,-0.429231826,-0.439805276
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                                  }
DesignProbes.c:81:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,-0.085841845,-0.430706047,-0.321129768,-0.141370102
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                                  }
DesignProbes.c:85:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                0,0,0,0
                ^~~~~~~
                {      }
DesignProbes.c:86:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.545032445,1.254355018,1.491691514,1.329138183
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:87:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.150635633,0.582415494,1.075877275,1.187937642
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:88:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.203555051,1.001540513,0.864287715,0.717125848
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:89:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:85:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                0,0,0,0
                ^~~~~~~
                {
DesignProbes.c:90:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.630005348,0.18553379,0.730763505,0.709272397
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:91:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:92:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.856582783,-0.143236405,0.716721488,0.603652831
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                               }
DesignProbes.c:93:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.851622883,0.653168672,0.676545316,1.187937642
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:94:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:90:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.630005348,0.18553379,0.730763505,0.709272397
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:95:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.231861002,0.746214538,1.087821916,0.989140748
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:96:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.822113278,1.270687029,1.336192565,1.364584949
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:97:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:98:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.443665704,1.385046493,1.256013166,1.329138183
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:99:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:95:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.231861002,0.746214538,1.087821916,0.989140748
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:100:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.478009492,0.882097231,1.20450984,1.061002478
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:101:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.496720812,0.846496194,0.967868114,0.989140748
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:102:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.766581547,-0.024857805,0.50754303,0.709272397
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:103:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:104:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:100:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.478009492,0.882097231,1.20450984,1.061002478
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:105:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.75,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
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]
                ,0.76,0.65,0.69,0.78
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:109:4: 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:85:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                0,0,0,0
                ^~~~~~~
                {
DesignProbes.c:110:4: 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]
                ,1.295827995,0.84547091,0.91019099,1.256013166
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                            }
DesignProbes.c:112:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.755889609,0.241428373,0.396379912,0.676545316
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:113:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.99945386,0.740323132,0.435659206,0.864287715
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:114:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.55,0.48,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:110:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {
DesignProbes.c:115:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.843147406,0.101248351,0.49063599,0.50754303
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                            }
DesignProbes.c:116:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:117:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.0651638,0.249934344,0.699352949,0.716721488
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                            }
DesignProbes.c:118:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.871921533,0.59458138,0.396379912,1.075877275
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:119:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.56,0.49,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:115:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.843147406,0.101248351,0.49063599,0.50754303
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:120:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.07531714,0.318907854,0.653287717,0.967868114
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:121:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.099899195,0.730184613,0.661798984,1.336192565
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:122:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:123:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.45897431,1.318532145,0.91019099,1.491691514
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                            }
DesignProbes.c:124:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.56,0.49,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:120:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.07531714,0.318907854,0.653287717,0.967868114
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:125:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.242135174,0.894838095,1.108555445,1.20450984
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:126:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.911428974,0.524430101,0.653287717,1.087821916
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:127:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.503209827,0.274849491,0.49063599,0.730763505
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:128:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:129:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.55,0.48,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:125:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.242135174,0.894838095,1.108555445,1.20450984
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:130:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.55,0.48,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:131:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.65,0.56,0.49,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
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]
                ,0.65,0.55,0.48,0.69
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:134:4: 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:110:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {
DesignProbes.c:135:4: 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]
                ,1.100661785,0.969784756,1.318532145,1.385046493
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:137:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.565895968,-0.060347902,0.59458138,0.653168672
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:138:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.782168488,0.788161238,0.740323132,1.001540513
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:139:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.46,0.55,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:135:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {
DesignProbes.c:140:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.468913405,-0.469855984,0.274849491,-0.024857805
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                                }
DesignProbes.c:141:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:142:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.258195131,-0.70438632,0.249934344,-0.143236405
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                               }
DesignProbes.c:143:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.502914193,-0.060347902,0.241428373,0.582415494
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                               }
DesignProbes.c:144:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.47,0.56,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:140:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.468913405,-0.469855984,0.274849491,-0.024857805
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:145:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.584083861,0.258975454,0.524430101,0.846496194
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:146:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.968040559,0.797499702,0.730184613,1.270687029
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:147:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:148:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.081040749,0.969784756,0.84547091,1.254355018
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:149:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.47,0.56,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:145:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.584083861,0.258975454,0.524430101,0.846496194
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:150:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.048553951,0.728354541,0.894838095,0.882097231
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:151:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.88611252,0.258975454,0.318907854,0.746214538
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:152:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.239520858,-0.469855984,0.101248351,0.18553379
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:153:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:154:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.46,0.55,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:150:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.048553951,0.728354541,0.894838095,0.882097231
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:155:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.46,0.55,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:156:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.68,0.47,0.56,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
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]
                ,0.68,0.46,0.55,0.65
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:159:4: 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:135:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {
DesignProbes.c:160:4: 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]
                ,1.566899704,1.081040749,1.45897431,1.443665704
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:162:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.976725675,0.502914193,0.871921533,0.851622883
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:163:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.482046826,0.782168488,0.99945386,1.203555051
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:164:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.76
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:160:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {
DesignProbes.c:165:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.798628781,0.239520858,0.503209827,0.766581547
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:166:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:167:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.141098246,0.258195131,1.0651638,0.856582783
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                            }
DesignProbes.c:168:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.976725675,0.565895968,0.755889609,1.150635633
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:169:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:165:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.798628781,0.239520858,0.503209827,0.766581547
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:170:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.125403302,0.88611252,0.911428974,1.496720812
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:171:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.68169282,0.968040559,1.099899195,1.822113278
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:172:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:173:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.566899704,1.100661785,1.295827995,1.545032445
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:174:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:170:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.125403302,0.88611252,0.911428974,1.496720812
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:175:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.35948517,1.048553951,1.242135174,1.478009492
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:176:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.125403302,0.584083861,1.07531714,1.231861002
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                             }
DesignProbes.c:177:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.798628781,0.468913405,0.843147406,0.630005348
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {                                              }
DesignProbes.c:178:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {      }
DesignProbes.c:179:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
DesignProbes.c:175:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,1.35948517,1.048553951,1.242135174,1.478009492
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:180:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {                  }
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]
                ,0,0,0,0        
                 ^~~~~~~
                 {      }
DesignProbes.c:180:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0.85,0.68,0.65,0.75
                 ^~~~~~~~~~~~~~~~~~~
                 {
DesignProbes.c:160:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                ,0,0,0,0
                 ^~~~~~~
                 {
DesignProbes.c:58:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
133 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Diff.c -o Diff.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c:319:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
DistanceMatrix.c:850:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c EnumerateSequence.c -o EnumerateSequence.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ExpandAmbiguities.c -o ExpandAmbiguities.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FindFrameshifts.c -o FindFrameshifts.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c GeneFinding.c -o GeneFinding.o
GeneFinding.c:3302:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
GeneFinding.c:3377:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
GeneFinding.c:3432:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c GetPools.c -o GetPools.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Import.c -o Import.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c InformationContent.c -o InformationContent.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c InsertGaps.c -o InsertGaps.o
InsertGaps.c:48:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IntDist.c -o IntDist.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c MovingAverage.c -o MovingAverage.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c MultiMatch.c -o MultiMatch.o
MultiMatch.c:220:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
MultiMatch.c:249:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
MultiMatch.c:357:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
MultiMatch.c:459:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
MultiMatch.c:571:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
MultiMatch.c:871:21: warning: variable 'start' set but not used [-Wunused-but-set-variable]
        int i, j, k, temp, start = 0;
                           ^
MultiMatch.c:957:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
MultiMatch.c:1200:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
MultiMatch.c:1253:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
9 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c NNLS.c -o NNLS.o
NNLS.c:49:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Order.c -o Order.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c:183:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PredictDBN.c -o PredictDBN.o
PredictDBN.c:159:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c PredictHEC.c -o PredictHEC.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_decipher.c -o R_init_decipher.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RawVectors.c -o RawVectors.o
RawVectors.c:36:9: warning: unused variable 'j' [-Wunused-variable]
        int i, j, k;
               ^
RawVectors.c:41:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
RawVectors.c:116:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RemoveGaps.c -o RemoveGaps.o
RemoveGaps.c:46:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
RemoveGaps.c:169:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ReplaceChars.c -o ReplaceChars.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c SphericalKmeans.c -o SphericalKmeans.o
SphericalKmeans.c:51:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c:40:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Translate.c -o Translate.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c VectorSums.c -o VectorSums.o
VectorSums.c:82:6: warning: unused variable 'nthreads' [-Wunused-variable]
        int nthreads = asInteger(nThreads);
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterML.o ClusterMP.o CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o InsertGaps.o IntDist.o MeltPolymer.o MovingAverage.o MultiMatch.o NNLS.o Order.o PairwiseAlignment.o PredictDBN.o PredictHEC.o R_init_decipher.o RawVectors.o RemoveGaps.o ReplaceChars.o S4Vectors_stubs.o SphericalKmeans.o TerminalMismatch.o Translate.o VectorSums.o XVector_stubs.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/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_REDUCED0.0760.0130.132
Add2DB0.2980.0150.476
AdjustAlignment0.2350.0150.381
AlignDB1.1430.0361.778
AlignProfiles0.9180.0291.427
AlignSeqs27.208 0.33741.449
AlignSynteny3.2630.0524.412
AlignTranslation15.112 0.25822.474
AmplifyDNA0.0030.0010.005
Array2Matrix6.0140.0599.218
BrowseDB0.0300.0030.050
BrowseSeqs34.326 0.45453.037
CalculateEfficiencyArray0.0240.0040.036
CalculateEfficiencyFISH0.0050.0000.006
CalculateEfficiencyPCR0.0050.0000.008
Clusterize 7.206 0.15911.193
Codec1.0750.0141.674
ConsensusSequence0.2190.0110.351
Cophenetic0.1820.0070.281
CorrectFrameshifts19.832 1.00730.263
CreateChimeras0.9280.0121.442
DB2Seqs0.0200.0190.096
DesignArray5.9610.0559.249
DesignPrimers0.0010.0010.002
DesignProbes0.0000.0010.004
DesignSignatures0.0010.0010.002
DetectRepeats20.276 0.23731.022
DigestDNA0.1810.0090.292
Disambiguate0.0600.0040.102
DistanceMatrix0.0670.0100.121
ExtractGenes39.130 0.63859.026
FindChimeras0.0850.0060.157
FindGenes37.259 0.69257.955
FindNonCoding 68.397 3.170105.551
FindSynteny1.7130.0432.723
FormGroups0.0530.0050.090
Genes-class37.007 0.76857.812
HEC_MI0.2850.0150.448
IdConsensus0.8960.0461.439
IdLengths0.0240.0030.042
IdTaxa10.733 0.14016.727
IdentifyByRank0.0270.0030.047
LearnNonCoding57.366 3.25593.216
LearnTaxa 6.825 0.87711.734
MIQS0.0510.0080.089
MODELS0.0020.0000.005
MapCharacters101.613 0.914157.312
MaskAlignment0.6360.0241.016
MeltDNA0.0510.0050.086
NNLS0.0040.0020.008
NonCoding-class0.0640.0180.118
NonCodingRNA0.1170.0330.212
OrientNucleotides1.3600.0222.119
PFASUM0.0340.0060.065
PredictDBN0.0160.0030.030
PredictHEC0.2840.0200.464
RESTRICTION_ENZYMES0.0030.0070.026
ReadDendrogram0.0170.0040.033
RemoveGaps0.0160.0020.030
ScoreAlignment 7.212 0.14311.335
SearchDB0.0430.0060.074
Seqs2DB0.1080.0060.172
StaggerAlignment16.792 0.37126.280
Synteny-class3.0610.0614.761
Taxa-class12.293 0.32719.372
TerminalChar0.0160.0020.028
TileSeqs6.2070.0729.685
TrainingSet_16S2.6540.0564.169
TreeLine11.108 0.21817.245
TrimDNA0.2460.0110.393
WriteDendrogram0.0040.0000.009
WriteGenes39.422 0.79161.534
deltaGrules0.0110.0110.032
deltaGrulesRNA0.0240.0100.044
deltaHrules0.0210.0100.046
deltaHrulesRNA0.0200.0090.046
deltaSrules0.0870.0060.145
deltaSrulesRNA0.0190.0100.037