Erik Wright
| Snapshot Date: 2025-06-12 13:25 -0400 (Thu, 12 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/DECIPHER |
| git_branch: devel |
| git_last_commit: f5796e8 |
| git_last_commit_date: 2025-04-15 10:10:51 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-13 12:08 -0400 (Fri, 13 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4797 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4538 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4571 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4515 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4483 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 521/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 3.5.0 (landing page) Erik Wright
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 3.5.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DECIPHER_3.5.0.tar.gz |
| StartedAt: 2025-06-12 20:11:49 -0400 (Thu, 12 Jun 2025) |
| EndedAt: 2025-06-12 20:29:17 -0400 (Thu, 12 Jun 2025) |
| EllapsedTime: 1048.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DECIPHER.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DECIPHER_3.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DECIPHER.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘3.5.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DECIPHER’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... INFO
installed size is 12.9Mb
sub-directories of 1Mb or more:
R 1.4Mb
data 7.5Mb
extdata 2.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AlignSeqs: no visible binding for global variable ‘deltaGrulesRNA’
DesignSignatures: no visible binding for global variable ‘deltaHrules’
FindGenes: no visible binding for global variable ‘deltaHrulesRNA’
FindNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
LearnNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
PredictDBN: no visible binding for global variable ‘deltaGrulesRNA’
Treeline: multiple local function definitions for ‘.NNI’ with different
formal arguments
Treeline: multiple local function definitions for ‘.minimize’ with
different formal arguments
Undefined global functions or variables:
deltaGrulesRNA deltaHrules deltaHrulesRNA
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AlignSeqs 193.858 4.607 200.747
LearnNonCoding 113.851 4.147 118.701
FindNonCoding 55.025 5.454 60.955
Treeline 53.424 2.405 58.873
ExtractGenes 39.185 1.206 40.739
FindGenes 36.902 1.442 44.864
Genes-class 34.606 1.430 36.188
WriteGenes 32.866 1.422 34.433
InferSelection 33.773 0.327 34.238
BrowseSeqs 31.683 0.576 33.081
DistanceMatrix 25.125 0.709 26.018
InferRecombination 20.561 0.381 21.051
CorrectFrameshifts 18.134 1.375 19.666
StaggerAlignment 12.318 1.009 13.413
DetectRepeats 13.087 0.122 13.285
AlignTranslation 12.395 0.220 12.764
TrimDNA 9.447 1.917 11.479
Taxa-class 9.308 0.433 9.813
IdTaxa 9.048 0.497 9.595
InferDemography 8.718 0.108 8.879
Clusterize 7.914 0.772 8.773
LearnTaxa 5.797 1.844 7.716
ScoreAlignment 5.810 0.345 6.191
Array2Matrix 5.588 0.069 5.675
DesignArray 5.543 0.028 5.591
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.
DECIPHER.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DECIPHER
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘DECIPHER’ ...
** this is package ‘DECIPHER’ version ‘3.5.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AlignProfiles.c -o AlignProfiles.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AssignIndels.c -o AssignIndels.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CalculateDeltaG.c -o CalculateDeltaG.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c:26:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-11.5, -7.8, -7, -8.3,
^~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:27:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-10.4, -12.8, -16.3, -9.1,
^~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:28:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-8.6, -8, -9.3, -5.9,
^~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:29:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-7.8, -5.5, -9, -7.8
^~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:32:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-36.4, -21.6, -19.7, -23.9,
^~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:33:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-28.4, -31.9, -47.1, -23.5,
^~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:34:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-22.9, -17.1, -23.2, -12.3,
^~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:35:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-23.2, -13.5, -26.1, -21.9
^~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:38:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-7.9, -8.4, -7.8, -7.2,
^~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:39:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-8.5, -8, -10.6, -7.8,
^~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:40:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-8.2, -9.8, -8, -8.4,
^~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:41:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-7.2, -8.2, -8.5, -7.9
^~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:44:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-22.2, -22.4, -21, -20.4,
^~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:45:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-22.7, -19.9, -27.2, -21,
^~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:46:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-22.2, -24.4, -19.9, -22.4,
^~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:47:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-21.3, -22.2, -22.7, -22.2
^~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:50:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-6.6, -10.17, -7.65, -5.76,
^~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:51:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-10.56, -12.21, -7.95, -7.65,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:52:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-13.37, -14.21, -12.21, -10.17,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:53:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-8.11, -13.37, -10.56, -6.6
^~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:56:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-18.38, -26.03, -19.18, -15.67,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:57:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-28.25, -30.02, -19.18, -19.18,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:58:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-35.68, -34.85, -30.02, -26.03,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
CalculateFISH.c:59:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-22.59, -35.68, -28.25, -18.38
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
24 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ChainSegments.c -o ChainSegments.o
ChainSegments.c:666:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Cluster.c -o Cluster.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ClusterME.c -o ClusterME.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ClusterML.c -o ClusterML.o
ClusterML.c:1887:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ClusterMP.c -o ClusterMP.o
ClusterMP.c:112:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Compositions.c -o Compositions.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Compression.c -o Compression.o
Compression.c:521:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
Compression.c:1408:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
Compression.c:1706:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ConsensusSequence.c -o ConsensusSequence.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DesignProbes.c -o DesignProbes.o
DesignProbes.c:72:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-0.816507461,-2.5401714,-1.647430026,-1.184658548
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:73:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,-1.854740485,-2.479102613,-2.826248182,-1.647430026
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:74:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,-2.48761723,-4.694133177,-2.479102613,-2.5401714
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:75:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,-0.495794417,-2.48761723,-1.854740485,-0.816507461
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:79:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-0.141370102,-0.439805276,-0.285236035,-0.205111781
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:80:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,-0.321129768,-0.429231826,-0.48933661,-0.285236035
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:81:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,-0.430706047,-0.812742218,-0.429231826,-0.439805276
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:82:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,-0.085841845,-0.430706047,-0.321129768,-0.141370102
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:86:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
0,0,0,0
^~~~~~~
{ }
DesignProbes.c:87:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.545032445,1.254355018,1.491691514,1.329138183
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:88:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.150635633,0.582415494,1.075877275,1.187937642
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:89:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.203555051,1.001540513,0.864287715,0.717125848
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:90:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.75,0.65,0.69,0.78
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:86:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
0,0,0,0
^~~~~~~
{
DesignProbes.c:91:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.630005348,0.18553379,0.730763505,0.709272397
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:92:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:93:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.856582783,-0.143236405,0.716721488,0.603652831
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:94:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.851622883,0.653168672,0.676545316,1.187937642
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:95:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.75,0.65,0.69,0.78
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:91:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.630005348,0.18553379,0.730763505,0.709272397
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:96:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.231861002,0.746214538,1.087821916,0.989140748
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:97:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.822113278,1.270687029,1.336192565,1.364584949
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:98:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:99:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.443665704,1.385046493,1.256013166,1.329138183
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:100:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.75,0.65,0.69,0.78
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:96:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.231861002,0.746214538,1.087821916,0.989140748
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:101:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.478009492,0.882097231,1.20450984,1.061002478
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:102:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.496720812,0.846496194,0.967868114,0.989140748
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:103:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.766581547,-0.024857805,0.50754303,0.709272397
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:104:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:105:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.75,0.65,0.69,0.78
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:101:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.478009492,0.882097231,1.20450984,1.061002478
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:106:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.75,0.65,0.69,0.78
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:107:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.75,0.65,0.69,0.78
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:108:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.75,0.65,0.69,0.78
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:109:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.76,0.65,0.69,0.78
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:110:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:106:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.75,0.65,0.69,0.78
^~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:86:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
0,0,0,0
^~~~~~~
{
DesignProbes.c:111:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:112:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.295827995,0.84547091,0.91019099,1.256013166
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:113:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.755889609,0.241428373,0.396379912,0.676545316
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:114:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.99945386,0.740323132,0.435659206,0.864287715
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:115:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.65,0.55,0.48,0.69
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:111:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{
DesignProbes.c:116:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.843147406,0.101248351,0.49063599,0.50754303
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:117:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:118:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.0651638,0.249934344,0.699352949,0.716721488
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:119:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.871921533,0.59458138,0.396379912,1.075877275
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:120:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.65,0.56,0.49,0.69
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:116:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.843147406,0.101248351,0.49063599,0.50754303
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:121:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.07531714,0.318907854,0.653287717,0.967868114
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:122:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.099899195,0.730184613,0.661798984,1.336192565
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:123:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:124:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.45897431,1.318532145,0.91019099,1.491691514
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:125:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.65,0.56,0.49,0.69
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:121:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.07531714,0.318907854,0.653287717,0.967868114
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:126:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.242135174,0.894838095,1.108555445,1.20450984
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:127:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.911428974,0.524430101,0.653287717,1.087821916
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:128:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.503209827,0.274849491,0.49063599,0.730763505
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:129:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:130:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.65,0.55,0.48,0.69
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:126:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.242135174,0.894838095,1.108555445,1.20450984
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:131:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.65,0.55,0.48,0.69
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:132:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.65,0.56,0.49,0.69
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:133:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.65,0.56,0.49,0.69
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:134:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.65,0.55,0.48,0.69
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:135:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:131:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.65,0.55,0.48,0.69
^~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:111:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{
DesignProbes.c:136:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:137:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.100661785,0.969784756,1.318532145,1.385046493
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:138:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.565895968,-0.060347902,0.59458138,0.653168672
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:139:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.782168488,0.788161238,0.740323132,1.001540513
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:140:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.68,0.46,0.55,0.65
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:136:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{
DesignProbes.c:141:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.468913405,-0.469855984,0.274849491,-0.024857805
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:142:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:143:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.258195131,-0.70438632,0.249934344,-0.143236405
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:144:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.502914193,-0.060347902,0.241428373,0.582415494
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:145:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.68,0.47,0.56,0.65
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:141:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.468913405,-0.469855984,0.274849491,-0.024857805
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:146:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.584083861,0.258975454,0.524430101,0.846496194
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:147:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.968040559,0.797499702,0.730184613,1.270687029
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:148:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:149:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.081040749,0.969784756,0.84547091,1.254355018
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:150:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.68,0.47,0.56,0.65
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:146:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.584083861,0.258975454,0.524430101,0.846496194
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:151:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.048553951,0.728354541,0.894838095,0.882097231
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:152:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.88611252,0.258975454,0.318907854,0.746214538
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:153:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.239520858,-0.469855984,0.101248351,0.18553379
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:154:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:155:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.68,0.46,0.55,0.65
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:151:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.048553951,0.728354541,0.894838095,0.882097231
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:156:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.68,0.46,0.55,0.65
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:157:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.68,0.47,0.56,0.65
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:158:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.68,0.47,0.56,0.65
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:159:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.68,0.46,0.55,0.65
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:160:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:156:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.68,0.46,0.55,0.65
^~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:136:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{
DesignProbes.c:161:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:162:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.566899704,1.081040749,1.45897431,1.443665704
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:163:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.976725675,0.502914193,0.871921533,0.851622883
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:164:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.482046826,0.782168488,0.99945386,1.203555051
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:165:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.85,0.68,0.65,0.76
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:161:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{
DesignProbes.c:166:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.798628781,0.239520858,0.503209827,0.766581547
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:167:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:168:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.141098246,0.258195131,1.0651638,0.856582783
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:169:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.976725675,0.565895968,0.755889609,1.150635633
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:170:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.85,0.68,0.65,0.75
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:166:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.798628781,0.239520858,0.503209827,0.766581547
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:171:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.125403302,0.88611252,0.911428974,1.496720812
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:172:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.68169282,0.968040559,1.099899195,1.822113278
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:173:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:174:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.566899704,1.100661785,1.295827995,1.545032445
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:175:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.85,0.68,0.65,0.75
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:171:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.125403302,0.88611252,0.911428974,1.496720812
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:176:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.35948517,1.048553951,1.242135174,1.478009492
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:177:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.125403302,0.584083861,1.07531714,1.231861002
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:178:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.798628781,0.468913405,0.843147406,0.630005348
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:179:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:180:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.85,0.68,0.65,0.75
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:176:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,1.35948517,1.048553951,1.242135174,1.478009492
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:181:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.85,0.68,0.65,0.75
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:182:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.85,0.68,0.65,0.75
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:183:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.85,0.68,0.65,0.75
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:184:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.85,0.68,0.65,0.75
^~~~~~~~~~~~~~~~~~~
{ }
DesignProbes.c:185:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{ }
DesignProbes.c:181:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0.85,0.68,0.65,0.75
^~~~~~~~~~~~~~~~~~~
{
DesignProbes.c:161:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,0,0,0,0
^~~~~~~
{
DesignProbes.c:59:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
133 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Diff.c -o Diff.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c:522:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
DistanceMatrix.c:1118:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c EnumerateSequence.c -o EnumerateSequence.o
EnumerateSequence.c:298:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
EnumerateSequence.c:871:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ExpandAmbiguities.c -o ExpandAmbiguities.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FindFrameshifts.c -o FindFrameshifts.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GeneFinding.c -o GeneFinding.o
GeneFinding.c:3261:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
GeneFinding.c:3338:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
GeneFinding.c:3395:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GetPools.c -o GetPools.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Import.c -o Import.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c InformationContent.c -o InformationContent.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IntDist.c -o IntDist.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ManipulateXStringSet.c -o ManipulateXStringSet.o
ManipulateXStringSet.c:55:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
ManipulateXStringSet.c:692:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
ManipulateXStringSet.c:822:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
ManipulateXStringSet.c:925:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
ManipulateXStringSet.c:1019:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
5 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c:80:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-7.9,-8.4,-7.8,-7.2
^~~~~~~~~~~~~~~~~~~
{ }
MeltPolymer.c:81:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,-8.5,-8.0,-10.6,-7.8
^~~~~~~~~~~~~~~~~~~~
{ }
MeltPolymer.c:82:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,-8.2,-9.8,-8.0,-8.4
^~~~~~~~~~~~~~~~~~~
{ }
MeltPolymer.c:83:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,-7.2,-8.2,-8.5,-7.9
^~~~~~~~~~~~~~~~~~~
{ }
MeltPolymer.c:89:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
-22.2,-22.4,-21.0,-20.4
^~~~~~~~~~~~~~~~~~~~~~~
{ }
MeltPolymer.c:90:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,-22.7,-19.9,-27.2,-21.0
^~~~~~~~~~~~~~~~~~~~~~~
{ }
MeltPolymer.c:91:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,-22.2,-24.4,-19.9,-22.4
^~~~~~~~~~~~~~~~~~~~~~~
{ }
MeltPolymer.c:92:4: warning: suggest braces around initialization of subobject [-Wmissing-braces]
,-21.3,-22.2,-22.7,-22.2
^~~~~~~~~~~~~~~~~~~~~~~
{ }
8 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MovingAverage.c -o MovingAverage.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c NNLS.c -o NNLS.o
NNLS.c:50:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Order.c -o Order.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PairwiseAlignment.c -o PairwiseAlignment.o
PairwiseAlignment.c:188:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
PairwiseAlignment.c:1034:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PopulationGenetics.c -o PopulationGenetics.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PredictDBN.c -o PredictDBN.o
PredictDBN.c:160:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PredictHEC.c -o PredictHEC.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_decipher.c -o R_init_decipher.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Search.c -o Search.o
Search.c:106:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c:41:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Translate.c -o Translate.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Utils.c -o Utils.o
Utils.c:230:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
Utils.c:343:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c VectorSums.c -o VectorSums.o
VectorSums.c:83:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o DECIPHER.so AlignProfiles.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o Cluster.o ClusterME.o ClusterML.o ClusterMP.o Compositions.o Compression.o ConsensusSequence.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o GeneFinding.o GetPools.o Import.o InformationContent.o IntDist.o ManipulateXStringSet.o MeltPolymer.o MovingAverage.o NNLS.o Order.o PairwiseAlignment.o PopulationGenetics.o PredictDBN.o PredictHEC.o R_init_decipher.o S4Vectors_stubs.o Search.o TerminalMismatch.o Translate.o Utils.o VectorSums.o XVector_stubs.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-DECIPHER/00new/DECIPHER/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DECIPHER)
DECIPHER.Rcheck/DECIPHER-Ex.timings
| name | user | system | elapsed | |
| AA_REDUCED | 0.048 | 0.007 | 0.054 | |
| Add2DB | 0.674 | 0.073 | 0.752 | |
| AdjustAlignment | 0.223 | 0.012 | 0.238 | |
| AlignDB | 1.326 | 0.032 | 1.368 | |
| AlignPairs | 4.815 | 0.109 | 4.952 | |
| AlignProfiles | 1.077 | 0.053 | 1.137 | |
| AlignSeqs | 193.858 | 4.607 | 200.747 | |
| AlignSynteny | 2.773 | 0.027 | 2.806 | |
| AlignTranslation | 12.395 | 0.220 | 12.764 | |
| AmplifyDNA | 0.002 | 0.003 | 0.005 | |
| Array2Matrix | 5.588 | 0.069 | 5.675 | |
| BLOSUM | 0.015 | 0.006 | 0.023 | |
| BrowseDB | 0.043 | 0.004 | 0.048 | |
| BrowseSeqs | 31.683 | 0.576 | 33.081 | |
| CalculateEfficiencyArray | 0.015 | 0.004 | 0.020 | |
| CalculateEfficiencyFISH | 0.005 | 0.000 | 0.005 | |
| CalculateEfficiencyPCR | 0.006 | 0.000 | 0.006 | |
| Clusterize | 7.914 | 0.772 | 8.773 | |
| Codec | 1.207 | 0.017 | 1.311 | |
| ConsensusSequence | 0.220 | 0.011 | 0.232 | |
| Cophenetic | 2.488 | 0.029 | 2.532 | |
| CorrectFrameshifts | 18.134 | 1.375 | 19.666 | |
| CreateChimeras | 0.826 | 0.014 | 0.843 | |
| DB2Seqs | 0.041 | 0.018 | 0.082 | |
| DesignArray | 5.543 | 0.028 | 5.591 | |
| DesignPrimers | 0.014 | 0.001 | 0.017 | |
| DesignProbes | 0.013 | 0.001 | 0.015 | |
| DesignSignatures | 0.015 | 0.002 | 0.016 | |
| DetectRepeats | 13.087 | 0.122 | 13.285 | |
| DigestDNA | 0.166 | 0.007 | 0.174 | |
| Disambiguate | 0.060 | 0.003 | 0.064 | |
| DistanceMatrix | 25.125 | 0.709 | 26.018 | |
| ExtractGenes | 39.185 | 1.206 | 40.739 | |
| FindChimeras | 0.099 | 0.005 | 0.196 | |
| FindGenes | 36.902 | 1.442 | 44.864 | |
| FindNonCoding | 55.025 | 5.454 | 60.955 | |
| FindSynteny | 1.803 | 0.074 | 1.897 | |
| FormGroups | 0.060 | 0.006 | 0.066 | |
| Genes-class | 34.606 | 1.430 | 36.188 | |
| HEC_MI | 0.186 | 0.010 | 0.198 | |
| IdConsensus | 0.454 | 0.044 | 0.503 | |
| IdLengths | 0.034 | 0.005 | 0.039 | |
| IdTaxa | 9.048 | 0.497 | 9.595 | |
| IdentifyByRank | 0.032 | 0.004 | 0.036 | |
| IndexSeqs | 0.960 | 0.009 | 0.975 | |
| InferDemography | 8.718 | 0.108 | 8.879 | |
| InferRecombination | 20.561 | 0.381 | 21.051 | |
| InferSelection | 33.773 | 0.327 | 34.238 | |
| InvertedIndex-class | 0.569 | 0.003 | 0.575 | |
| LearnNonCoding | 113.851 | 4.147 | 118.701 | |
| LearnTaxa | 5.797 | 1.844 | 7.716 | |
| MIQS | 0.034 | 0.009 | 0.043 | |
| MMLSUM | 0.007 | 0.013 | 0.020 | |
| MODELS | 0.002 | 0.001 | 0.002 | |
| MapCharacters | 3.680 | 0.184 | 3.898 | |
| MaskAlignment | 0.548 | 0.018 | 0.571 | |
| MeltDNA | 0.069 | 0.004 | 0.075 | |
| NNLS | 0.003 | 0.000 | 0.004 | |
| NonCoding-class | 0.047 | 0.013 | 0.060 | |
| NonCodingRNA | 0.081 | 0.034 | 0.115 | |
| OrientNucleotides | 0.454 | 0.007 | 0.465 | |
| PAM | 0.006 | 0.004 | 0.011 | |
| PFASUM | 0.009 | 0.004 | 0.013 | |
| PredictDBN | 0.009 | 0.001 | 0.010 | |
| PredictHEC | 0.249 | 0.014 | 0.265 | |
| RESTRICTION_ENZYMES | 0.002 | 0.003 | 0.005 | |
| ReadDendrogram | 0.071 | 0.009 | 0.081 | |
| RemoveGaps | 0.015 | 0.001 | 0.016 | |
| ScoreAlignment | 5.810 | 0.345 | 6.191 | |
| SearchDB | 0.081 | 0.017 | 0.098 | |
| SearchIndex | 1.391 | 0.177 | 1.582 | |
| Seqs2DB | 0.110 | 0.004 | 0.116 | |
| StaggerAlignment | 12.318 | 1.009 | 13.413 | |
| Synteny-class | 2.224 | 0.051 | 2.312 | |
| Taxa-class | 9.308 | 0.433 | 9.813 | |
| TerminalChar | 0.007 | 0.002 | 0.010 | |
| TileSeqs | 4.101 | 0.030 | 4.154 | |
| TrainingSet_16S | 2.058 | 0.049 | 2.139 | |
| Treeline | 53.424 | 2.405 | 58.873 | |
| TrimDNA | 9.447 | 1.917 | 11.479 | |
| WriteDendrogram | 0.004 | 0.001 | 0.005 | |
| WriteGenes | 32.866 | 1.422 | 34.433 | |
| deltaGrules | 0.008 | 0.022 | 0.042 | |
| deltaGrulesRNA | 0.013 | 0.012 | 0.026 | |
| deltaHrules | 0.013 | 0.011 | 0.025 | |
| deltaHrulesRNA | 0.012 | 0.009 | 0.021 | |
| deltaSrules | 0.076 | 0.013 | 0.090 | |
| deltaSrulesRNA | 0.014 | 0.011 | 0.025 | |