Erik Wright
| Snapshot Date: 2023-10-15 14:00:13 -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) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:58 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 505/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 2.28.0 (landing page) Erik Wright
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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. |
| 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: 2023-10-16 00:39:33 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 01:07:04 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 1650.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DECIPHER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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/meat/DECIPHER.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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 148.354 1.503 199.218
FindNonCoding 77.093 5.688 122.554
LearnNonCoding 74.689 5.433 108.583
WriteGenes 57.932 2.196 82.473
ExtractGenes 56.973 1.269 76.019
Genes-class 54.798 1.536 75.922
BrowseSeqs 55.221 0.595 70.988
FindGenes 52.661 1.256 73.883
AlignSeqs 38.384 0.439 49.504
DetectRepeats 36.799 0.259 47.030
CorrectFrameshifts 34.592 1.278 46.588
StaggerAlignment 27.452 1.027 37.008
AlignTranslation 24.412 0.295 31.513
TreeLine 17.541 0.542 27.581
Taxa-class 17.057 0.584 25.804
IdTaxa 15.085 0.483 20.993
Clusterize 12.739 0.208 16.612
LearnTaxa 9.940 2.552 16.288
ScoreAlignment 10.844 0.329 14.765
TileSeqs 9.517 0.067 13.907
Array2Matrix 9.309 0.061 11.852
DesignArray 9.064 0.050 11.684
AlignSynteny 5.804 0.054 7.520
TrainingSet_16S 5.367 0.133 8.238
Synteny-class 4.640 0.118 8.493
* 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/meat/DECIPHER.Rcheck/00check.log’
for details.
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-x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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
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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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: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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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: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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CommonGaps.c -o CommonGaps.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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: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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ConsolidateGaps.c -o ConsolidateGaps.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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: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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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: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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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: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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:49:6: 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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:183:6: 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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:159:6: 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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RawVectors.c -o RawVectors.o
RawVectors.c:41:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
RawVectors.c:36:9: warning: unused variable 'j' [-Wunused-variable]
int i, j, k;
^
RawVectors.c:116:6: 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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ReplaceChars.c -o ReplaceChars.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:40:6: 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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:82:6: 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/4.3-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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 -single_module -multiply_defined suppress -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 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-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)
DECIPHER.Rcheck/DECIPHER-Ex.timings
| name | user | system | elapsed | |
| AA_REDUCED | 0.127 | 0.024 | 0.192 | |
| Add2DB | 0.520 | 0.026 | 0.776 | |
| AdjustAlignment | 0.435 | 0.021 | 0.568 | |
| AlignDB | 1.903 | 0.048 | 2.478 | |
| AlignProfiles | 1.441 | 0.065 | 1.922 | |
| AlignSeqs | 38.384 | 0.439 | 49.504 | |
| AlignSynteny | 5.804 | 0.054 | 7.520 | |
| AlignTranslation | 24.412 | 0.295 | 31.513 | |
| AmplifyDNA | 0.003 | 0.004 | 0.008 | |
| Array2Matrix | 9.309 | 0.061 | 11.852 | |
| BrowseDB | 0.048 | 0.004 | 0.065 | |
| BrowseSeqs | 55.221 | 0.595 | 70.988 | |
| CalculateEfficiencyArray | 0.034 | 0.005 | 0.051 | |
| CalculateEfficiencyFISH | 0.009 | 0.001 | 0.011 | |
| CalculateEfficiencyPCR | 0.010 | 0.000 | 0.012 | |
| Clusterize | 12.739 | 0.208 | 16.612 | |
| Codec | 1.453 | 0.024 | 1.878 | |
| ConsensusSequence | 0.375 | 0.017 | 0.499 | |
| Cophenetic | 0.347 | 0.007 | 0.450 | |
| CorrectFrameshifts | 34.592 | 1.278 | 46.588 | |
| CreateChimeras | 1.627 | 0.015 | 2.094 | |
| DB2Seqs | 0.030 | 0.025 | 0.075 | |
| DesignArray | 9.064 | 0.050 | 11.684 | |
| DesignPrimers | 0.002 | 0.001 | 0.003 | |
| DesignProbes | 0.001 | 0.002 | 0.005 | |
| DesignSignatures | 0.002 | 0.002 | 0.004 | |
| DetectRepeats | 36.799 | 0.259 | 47.030 | |
| DigestDNA | 0.309 | 0.017 | 0.393 | |
| Disambiguate | 0.112 | 0.006 | 0.145 | |
| DistanceMatrix | 0.095 | 0.018 | 0.141 | |
| ExtractGenes | 56.973 | 1.269 | 76.019 | |
| FindChimeras | 0.138 | 0.009 | 0.188 | |
| FindGenes | 52.661 | 1.256 | 73.883 | |
| FindNonCoding | 77.093 | 5.688 | 122.554 | |
| FindSynteny | 2.912 | 0.073 | 4.042 | |
| FormGroups | 0.108 | 0.008 | 0.161 | |
| Genes-class | 54.798 | 1.536 | 75.922 | |
| HEC_MI | 0.388 | 0.021 | 0.545 | |
| IdConsensus | 1.456 | 0.124 | 2.110 | |
| IdLengths | 0.034 | 0.007 | 0.057 | |
| IdTaxa | 15.085 | 0.483 | 20.993 | |
| IdentifyByRank | 0.079 | 0.007 | 0.111 | |
| LearnNonCoding | 74.689 | 5.433 | 108.583 | |
| LearnTaxa | 9.940 | 2.552 | 16.288 | |
| MIQS | 0.065 | 0.015 | 0.106 | |
| MODELS | 0.003 | 0.001 | 0.004 | |
| MapCharacters | 148.354 | 1.503 | 199.218 | |
| MaskAlignment | 0.999 | 0.066 | 1.352 | |
| MeltDNA | 0.069 | 0.004 | 0.088 | |
| NNLS | 0.005 | 0.002 | 0.011 | |
| NonCoding-class | 0.103 | 0.026 | 0.172 | |
| NonCodingRNA | 0.179 | 0.036 | 0.266 | |
| OrientNucleotides | 1.685 | 0.023 | 2.166 | |
| PFASUM | 0.044 | 0.014 | 0.069 | |
| PredictDBN | 0.020 | 0.008 | 0.033 | |
| PredictHEC | 0.429 | 0.019 | 0.564 | |
| RESTRICTION_ENZYMES | 0.005 | 0.014 | 0.025 | |
| ReadDendrogram | 0.025 | 0.003 | 0.035 | |
| RemoveGaps | 0.024 | 0.003 | 0.035 | |
| ScoreAlignment | 10.844 | 0.329 | 14.765 | |
| SearchDB | 0.061 | 0.010 | 0.100 | |
| Seqs2DB | 0.157 | 0.005 | 0.215 | |
| StaggerAlignment | 27.452 | 1.027 | 37.008 | |
| Synteny-class | 4.640 | 0.118 | 8.493 | |
| Taxa-class | 17.057 | 0.584 | 25.804 | |
| TerminalChar | 0.022 | 0.003 | 0.035 | |
| TileSeqs | 9.517 | 0.067 | 13.907 | |
| TrainingSet_16S | 5.367 | 0.133 | 8.238 | |
| TreeLine | 17.541 | 0.542 | 27.581 | |
| TrimDNA | 0.338 | 0.023 | 0.575 | |
| WriteDendrogram | 0.008 | 0.002 | 0.010 | |
| WriteGenes | 57.932 | 2.196 | 82.473 | |
| deltaGrules | 0.015 | 0.005 | 0.031 | |
| deltaGrulesRNA | 0.033 | 0.006 | 0.046 | |
| deltaHrules | 0.029 | 0.004 | 0.043 | |
| deltaHrulesRNA | 0.028 | 0.004 | 0.042 | |
| deltaSrules | 0.096 | 0.018 | 0.146 | |
| deltaSrulesRNA | 0.026 | 0.004 | 0.038 | |