Erik Wright
| Snapshot Date: 2025-01-23 13:00 -0500 (Thu, 23 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/DECIPHER |
| git_branch: RELEASE_3_20 |
| git_last_commit: 7d5caa2 |
| git_last_commit_date: 2024-10-29 09:38:53 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-27 12:08 -0500 (Mon, 27 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 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 516/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 3.2.0 (landing page) Erik Wright
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 3.2.0 |
| 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_3.2.0.tar.gz |
| StartedAt: 2025-01-24 02:24:03 -0500 (Fri, 24 Jan 2025) |
| EndedAt: 2025-01-24 03:01:20 -0500 (Fri, 24 Jan 2025) |
| EllapsedTime: 2237.1 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_3.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DECIPHER.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘3.2.0’
* 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 12.5Mb
sub-directories of 1Mb or more:
R 1.5Mb
data 7.5Mb
extdata 2.5Mb
* 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 451.688 12.769 567.787
TreeLine 203.457 5.181 233.426
LearnNonCoding 155.471 6.700 171.810
FindNonCoding 84.485 6.861 100.192
ExtractGenes 74.178 1.841 88.700
Genes-class 73.389 2.310 81.597
FindGenes 72.036 1.831 81.569
WriteGenes 70.686 2.269 79.567
BrowseSeqs 53.631 1.006 59.094
CorrectFrameshifts 34.639 1.960 44.653
DetectRepeats 28.806 0.244 35.659
StaggerAlignment 26.053 1.306 29.787
AlignTranslation 23.283 0.501 27.263
Taxa-class 15.908 1.203 18.171
MapCharacters 15.571 0.958 18.448
IdTaxa 15.186 0.697 16.779
LearnTaxa 10.219 3.286 15.290
Cophenetic 13.098 0.111 19.034
ScoreAlignment 11.150 0.342 12.247
Clusterize 10.223 0.898 18.140
DesignArray 9.203 0.074 10.948
Array2Matrix 8.800 0.102 9.411
TileSeqs 8.749 0.064 9.610
AlignSynteny 6.212 0.079 8.014
AlignPairs 5.918 0.245 8.259
TrainingSet_16S 5.079 0.070 5.824
Synteny-class 4.769 0.229 6.132
PredictHEC 0.607 0.027 6.869
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.20-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/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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:715:6: 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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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:1584:6: 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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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:320:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
DistanceMatrix.c:914:6: 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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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:689:6: warning: unused variable 'nthreads' [-Wunused-variable]
int nthreads = asInteger(nThreads);
^
ManipulateXStringSet.c:818:6: 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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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 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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-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 | 0.102 | 0.018 | 0.130 | |
| Add2DB | 1.517 | 0.163 | 2.058 | |
| AdjustAlignment | 0.407 | 0.034 | 0.689 | |
| AlignDB | 2.470 | 0.071 | 2.844 | |
| AlignPairs | 5.918 | 0.245 | 8.259 | |
| AlignProfiles | 1.698 | 0.070 | 2.327 | |
| AlignSeqs | 451.688 | 12.769 | 567.787 | |
| AlignSynteny | 6.212 | 0.079 | 8.014 | |
| AlignTranslation | 23.283 | 0.501 | 27.263 | |
| AmplifyDNA | 0.004 | 0.006 | 0.014 | |
| Array2Matrix | 8.800 | 0.102 | 9.411 | |
| BLOSUM | 0.026 | 0.011 | 0.044 | |
| BrowseDB | 0.085 | 0.006 | 0.153 | |
| BrowseSeqs | 53.631 | 1.006 | 59.094 | |
| CalculateEfficiencyArray | 0.027 | 0.009 | 0.042 | |
| CalculateEfficiencyFISH | 0.010 | 0.001 | 0.011 | |
| CalculateEfficiencyPCR | 0.010 | 0.000 | 0.012 | |
| Clusterize | 10.223 | 0.898 | 18.140 | |
| Codec | 1.349 | 0.017 | 1.567 | |
| ConsensusSequence | 0.395 | 0.022 | 0.473 | |
| Cophenetic | 13.098 | 0.111 | 19.034 | |
| CorrectFrameshifts | 34.639 | 1.960 | 44.653 | |
| CreateChimeras | 1.786 | 0.023 | 2.109 | |
| DB2Seqs | 0.066 | 0.026 | 0.236 | |
| DesignArray | 9.203 | 0.074 | 10.948 | |
| DesignPrimers | 0.020 | 0.002 | 0.025 | |
| DesignProbes | 0.019 | 0.002 | 0.021 | |
| DesignSignatures | 0.020 | 0.004 | 0.028 | |
| DetectRepeats | 28.806 | 0.244 | 35.659 | |
| DigestDNA | 0.325 | 0.018 | 0.390 | |
| Disambiguate | 0.123 | 0.008 | 0.152 | |
| DistanceMatrix | 0.110 | 0.021 | 0.153 | |
| ExtractGenes | 74.178 | 1.841 | 88.700 | |
| FindChimeras | 0.151 | 0.006 | 0.196 | |
| FindGenes | 72.036 | 1.831 | 81.569 | |
| FindNonCoding | 84.485 | 6.861 | 100.192 | |
| FindSynteny | 3.470 | 0.092 | 3.969 | |
| FormGroups | 0.135 | 0.012 | 0.151 | |
| Genes-class | 73.389 | 2.310 | 81.597 | |
| HEC_MI | 0.385 | 0.029 | 0.871 | |
| IdConsensus | 0.891 | 0.084 | 1.459 | |
| IdLengths | 0.059 | 0.005 | 0.067 | |
| IdTaxa | 15.186 | 0.697 | 16.779 | |
| IdentifyByRank | 0.080 | 0.005 | 0.086 | |
| IndexSeqs | 1.547 | 0.014 | 1.657 | |
| InvertedIndex-class | 0.874 | 0.021 | 0.943 | |
| LearnNonCoding | 155.471 | 6.700 | 171.810 | |
| LearnTaxa | 10.219 | 3.286 | 15.290 | |
| MIQS | 0.064 | 0.016 | 0.110 | |
| MMLSUM | 0.011 | 0.014 | 0.036 | |
| MODELS | 0.003 | 0.001 | 0.005 | |
| MapCharacters | 15.571 | 0.958 | 18.448 | |
| MaskAlignment | 1.037 | 0.060 | 1.360 | |
| MeltDNA | 0.120 | 0.007 | 0.159 | |
| NNLS | 0.006 | 0.003 | 0.009 | |
| NonCoding-class | 0.104 | 0.033 | 0.518 | |
| NonCodingRNA | 0.180 | 0.046 | 0.669 | |
| OrientNucleotides | 0.819 | 0.013 | 0.865 | |
| PAM | 0.012 | 0.007 | 0.024 | |
| PFASUM | 0.015 | 0.008 | 0.029 | |
| PredictDBN | 0.016 | 0.004 | 0.023 | |
| PredictHEC | 0.607 | 0.027 | 6.869 | |
| RESTRICTION_ENZYMES | 0.005 | 0.010 | 0.016 | |
| ReadDendrogram | 0.042 | 0.007 | 0.260 | |
| RemoveGaps | 0.027 | 0.002 | 0.030 | |
| ScoreAlignment | 11.150 | 0.342 | 12.247 | |
| SearchDB | 0.097 | 0.013 | 0.158 | |
| SearchIndex | 2.191 | 0.143 | 2.500 | |
| Seqs2DB | 0.209 | 0.007 | 0.259 | |
| StaggerAlignment | 26.053 | 1.306 | 29.787 | |
| Synteny-class | 4.769 | 0.229 | 6.132 | |
| Taxa-class | 15.908 | 1.203 | 18.171 | |
| TerminalChar | 0.013 | 0.002 | 0.019 | |
| TileSeqs | 8.749 | 0.064 | 9.610 | |
| TrainingSet_16S | 5.079 | 0.070 | 5.824 | |
| TreeLine | 203.457 | 5.181 | 233.426 | |
| TrimDNA | 0.328 | 0.016 | 0.600 | |
| WriteDendrogram | 0.008 | 0.001 | 0.010 | |
| WriteGenes | 70.686 | 2.269 | 79.567 | |
| deltaGrules | 0.015 | 0.012 | 0.063 | |
| deltaGrulesRNA | 0.031 | 0.013 | 0.070 | |
| deltaHrules | 0.028 | 0.012 | 0.070 | |
| deltaHrulesRNA | 0.026 | 0.013 | 0.067 | |
| deltaSrules | 0.097 | 0.011 | 0.144 | |
| deltaSrulesRNA | 0.025 | 0.014 | 0.038 | |