Erik Wright
| Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/DECIPHER |
| git_branch: devel |
| git_last_commit: 9fb2779 |
| git_last_commit_date: 2025-10-29 10:09:13 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-21 11:38 -0500 (Fri, 21 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4602 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4566 |
| 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 526/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DECIPHER 3.7.0 (landing page) Erik Wright
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 3.7.0 |
| 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_3.7.0.tar.gz |
| StartedAt: 2025-11-20 20:34:41 -0500 (Thu, 20 Nov 2025) |
| EndedAt: 2025-11-20 20:52:30 -0500 (Thu, 20 Nov 2025) |
| EllapsedTime: 1068.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DECIPHER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DECIPHER_3.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/DECIPHER.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘3.7.0’
* 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 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... INFO
installed size is 13.5Mb
sub-directories of 1Mb or more:
R 2.0Mb
data 7.5Mb
extdata 2.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AlignSeqs: no visible binding for global variable ‘deltaGrulesRNA’
DesignSignatures: no visible binding for global variable ‘deltaHrules’
FindGenes: no visible binding for global variable ‘deltaHrulesRNA’
FindNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
LearnNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
PredictDBN: no visible binding for global variable ‘deltaGrulesRNA’
Treeline: multiple local function definitions for ‘.NNI’ with different
formal arguments
Treeline: multiple local function definitions for ‘.minimize’ with
different formal arguments
Undefined global functions or variables:
deltaGrulesRNA deltaHrules deltaHrulesRNA
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
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 191.251 4.556 197.818
LearnNonCoding 119.873 4.834 127.662
FindNonCoding 57.108 5.442 63.153
Treeline 50.033 2.338 52.812
ExtractGenes 37.539 1.333 44.485
FindGenes 36.116 1.301 41.457
Genes-class 34.554 1.470 36.289
InferSelection 35.263 0.354 35.797
WriteGenes 33.491 1.660 37.027
BrowseSeqs 32.092 0.513 32.809
DistanceMatrix 23.713 0.644 24.542
InferRecombination 21.340 0.468 21.978
CorrectFrameshifts 18.703 1.870 21.445
AlignTranslation 13.898 0.265 14.299
StaggerAlignment 12.648 0.866 13.602
DetectRepeats 13.143 0.155 13.416
TrimDNA 9.378 1.803 11.370
Taxa-class 9.816 0.445 10.323
IdTaxa 9.199 0.390 9.800
InferDemography 9.296 0.145 9.510
LearnTaxa 6.492 2.583 10.748
Clusterize 7.134 0.934 8.280
ScoreAlignment 6.057 0.333 6.429
DesignArray 5.682 0.054 5.773
Array2Matrix 5.601 0.040 5.675
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-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/4.6-x86_64/Resources/library’
* installing *source* package ‘DECIPHER’ ...
** this is package ‘DECIPHER’ version ‘3.7.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-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 | 0.063 | 0.021 | 0.097 | |
| Add2DB | 0.739 | 0.078 | 0.825 | |
| AdjustAlignment | 0.233 | 0.011 | 0.246 | |
| AlignDB | 1.668 | 0.042 | 1.728 | |
| AlignPairs | 4.413 | 0.110 | 4.561 | |
| AlignProfiles | 0.902 | 0.042 | 1.216 | |
| AlignSeqs | 191.251 | 4.556 | 197.818 | |
| AlignSynteny | 2.476 | 0.024 | 2.508 | |
| AlignTranslation | 13.898 | 0.265 | 14.299 | |
| AmplifyDNA | 0.002 | 0.004 | 0.008 | |
| Array2Matrix | 5.601 | 0.040 | 5.675 | |
| BLOSUM | 0.015 | 0.007 | 0.024 | |
| BrowseDB | 0.049 | 0.005 | 0.055 | |
| BrowseSeqs | 32.092 | 0.513 | 32.809 | |
| CalculateEfficiencyArray | 0.012 | 0.004 | 0.017 | |
| CalculateEfficiencyFISH | 0.004 | 0.000 | 0.004 | |
| CalculateEfficiencyPCR | 0.004 | 0.000 | 0.004 | |
| Clusterize | 7.134 | 0.934 | 8.280 | |
| Codec | 1.134 | 0.018 | 1.161 | |
| ConsensusSequence | 0.154 | 0.007 | 0.162 | |
| Cophenetic | 1.757 | 0.021 | 1.840 | |
| CorrectFrameshifts | 18.703 | 1.870 | 21.445 | |
| CreateChimeras | 0.854 | 0.012 | 0.873 | |
| DB2Seqs | 0.039 | 0.023 | 0.095 | |
| DesignArray | 5.682 | 0.054 | 5.773 | |
| DesignPrimers | 0.015 | 0.002 | 0.017 | |
| DesignProbes | 0.016 | 0.002 | 0.017 | |
| DesignSignatures | 0.016 | 0.002 | 0.018 | |
| DetectRepeats | 13.143 | 0.155 | 13.416 | |
| DigestDNA | 0.167 | 0.012 | 0.182 | |
| Disambiguate | 0.055 | 0.004 | 0.059 | |
| DistanceMatrix | 23.713 | 0.644 | 24.542 | |
| ExtractGenes | 37.539 | 1.333 | 44.485 | |
| FindChimeras | 0.066 | 0.012 | 0.233 | |
| FindGenes | 36.116 | 1.301 | 41.457 | |
| FindNonCoding | 57.108 | 5.442 | 63.153 | |
| FindSynteny | 1.841 | 0.073 | 1.929 | |
| FormGroups | 0.061 | 0.004 | 0.065 | |
| Genes-class | 34.554 | 1.470 | 36.289 | |
| HEC_MI | 0.188 | 0.018 | 0.209 | |
| IdConsensus | 0.497 | 0.132 | 0.645 | |
| IdLengths | 0.037 | 0.004 | 0.041 | |
| IdTaxa | 9.199 | 0.390 | 9.800 | |
| IdentifyByRank | 0.046 | 0.004 | 0.050 | |
| IndexSeqs | 1.176 | 0.014 | 1.206 | |
| InferDemography | 9.296 | 0.145 | 9.510 | |
| InferRecombination | 21.340 | 0.468 | 21.978 | |
| InferSelection | 35.263 | 0.354 | 35.797 | |
| InvertedIndex-class | 0.656 | 0.009 | 0.670 | |
| LearnNonCoding | 119.873 | 4.834 | 127.662 | |
| LearnTaxa | 6.492 | 2.583 | 10.748 | |
| MIQS | 0.092 | 0.213 | 0.409 | |
| MMLSUM | 0.008 | 0.016 | 0.024 | |
| MODELS | 0.002 | 0.000 | 0.002 | |
| MapCharacters | 3.696 | 0.087 | 3.815 | |
| MaskAlignment | 0.539 | 0.021 | 0.569 | |
| MeltDNA | 0.070 | 0.004 | 0.075 | |
| NNLS | 0.003 | 0.000 | 0.003 | |
| NonCoding-class | 0.047 | 0.016 | 0.065 | |
| NonCodingRNA | 0.081 | 0.048 | 0.136 | |
| OrientNucleotides | 0.484 | 0.007 | 0.494 | |
| PAM | 0.008 | 0.006 | 0.016 | |
| PFASUM | 0.009 | 0.007 | 0.016 | |
| PredictDBN | 0.008 | 0.002 | 0.010 | |
| PredictHEC | 0.248 | 0.015 | 0.266 | |
| RESTRICTION_ENZYMES | 0.003 | 0.006 | 0.009 | |
| ReadDendrogram | 0.022 | 0.003 | 0.025 | |
| RemoveGaps | 0.010 | 0.001 | 0.011 | |
| ScoreAlignment | 6.057 | 0.333 | 6.429 | |
| SearchDB | 0.057 | 0.003 | 0.060 | |
| SearchIndex | 1.448 | 0.104 | 1.562 | |
| Seqs2DB | 0.118 | 0.010 | 0.130 | |
| StaggerAlignment | 12.648 | 0.866 | 13.602 | |
| Synteny-class | 2.348 | 0.044 | 2.402 | |
| Taxa-class | 9.816 | 0.445 | 10.323 | |
| TerminalChar | 0.008 | 0.002 | 0.011 | |
| TileSeqs | 4.042 | 0.021 | 4.076 | |
| TrainingSet_16S | 1.984 | 0.043 | 2.037 | |
| Treeline | 50.033 | 2.338 | 52.812 | |
| TrimDNA | 9.378 | 1.803 | 11.370 | |
| WriteDendrogram | 0.004 | 0.000 | 0.004 | |
| WriteGenes | 33.491 | 1.660 | 37.027 | |
| deltaGrules | 0.008 | 0.012 | 0.022 | |
| deltaGrulesRNA | 0.013 | 0.013 | 0.026 | |
| deltaHrules | 0.012 | 0.012 | 0.024 | |
| deltaHrulesRNA | 0.011 | 0.011 | 0.022 | |
| deltaSrules | 0.048 | 0.004 | 0.052 | |
| deltaSrulesRNA | 0.010 | 0.010 | 0.023 | |