Ulrich Bodenhofer
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/kebabs |
| git_branch: RELEASE_3_21 |
| git_last_commit: b65d0fb |
| git_last_commit_date: 2025-04-15 10:35:57 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1101/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| kebabs 1.42.0 (landing page) Ulrich Bodenhofer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the kebabs package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/kebabs.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: kebabs |
| Version: 1.42.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:kebabs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings kebabs_1.42.0.tar.gz |
| StartedAt: 2025-10-14 05:39:14 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 05:45:33 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 378.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: kebabs.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:kebabs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings kebabs_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/kebabs.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘kebabs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘kebabs’ version ‘1.42.0’
* 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 ‘kebabs’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
BioVector-class.Rd: XStringSet-class
BioVector.Rd: XStringSet, metadata, mcols, elementMetadata,
DNAStringSet, RNAStringSet, AAStringSet
ExplicitRepresentation-class.Rd: dgRMatrix-class
LinearKernel.Rd: dgCMatrix-class
annotationSpecificKernel.Rd: DNAStringSet-class, RNAStringSet-class,
AAStringSet-class, mcols, metadata
explicitRepresentation.Rd: DNAStringSet-class, RNAStringSet-class,
AAStringSet-class
gappyPairKernel.Rd: DNAStringSet-class, RNAStringSet-class,
AAStringSet-class
getPredProfMixture-methods.Rd: DNAString-class, RNAString-class,
AAString-class, DNAStringSet-class, RNAStringSet-class,
AAStringSet-class
getPredictionProfile-methods.Rd: DNAString-class, RNAString-class,
AAString-class, DNAStringSet-class, RNAStringSet-class,
AAStringSet-class
kbsvm-methods.Rd: DNAStringSet-class, RNAStringSet-class,
AAStringSet-class, DNAStringSet, RNAStringSet, AAStringSet,
XStringSet-class
mismatchKernel.Rd: DNAStringSet-class, RNAStringSet-class,
AAStringSet-class
motifKernel.Rd: DNAStringSet-class, RNAStringSet-class,
AAStringSet-class
plot-methods.Rd: mcols
positionDependentKernel.Rd: DNAStringSet-class, RNAStringSet-class,
AAStringSet-class, metadata, mcols
predict-methods.Rd: DNAStringSet-class, RNAStringSet-class,
AAStringSet-class
sequenceKernel.Rd: DNAStringSet-class, RNAStringSet-class,
AAStringSet-class
spectrumKernel.Rd: DNAStringSet-class, RNAStringSet-class,
AAStringSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
performModelSelection 9.440 0.070 9.979
LinearKernel 8.412 0.069 8.812
performGridSearch 5.487 0.104 6.309
computeROCandAUC 3.584 1.209 5.144
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/kebabs.Rcheck/00check.log’
for details.
kebabs.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL kebabs
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘kebabs’ ...
** this is package ‘kebabs’ version ‘1.42.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
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 -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/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 -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ByteStringVector.c -o ByteStringVector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ExplicitRepC.cpp -o ExplicitRepC.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GappyPairC.cpp -o GappyPairC.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c KernelUtils.cpp -o KernelUtils.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MismatchC.cpp -o MismatchC.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MotifC.cpp -o MotifC.o
MotifC.cpp:2927:14: warning: variable 'dimFeatureSpace' set but not used [-Wunused-but-set-variable]
uint64_t dimFeatureSpace;
^
MotifC.cpp:3511:41: warning: variable 'dimFeatureSpace' set but not used [-Wunused-but-set-variable]
uint64_t keyPoolSize, poolNextFree, dimFeatureSpace;
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PredictionC.cpp -o PredictionC.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PredictionProfileC.cpp -o PredictionProfileC.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_kebabs.cpp -o R_init_kebabs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rsvm.c -o Rsvm.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseMatrixHash.cpp -o SparseMatrixHash.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SpectrumC.cpp -o SpectrumC.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SymmetricPairC.cpp -o SymmetricPairC.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Utils.cpp -o Utils.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/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 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/S4Vectors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c svm.cpp -o svm.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o kebabs.so Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o Rsvm.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o svm.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-kebabs/00new/kebabs/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 (kebabs)
kebabs.Rcheck/kebabs-Ex.timings
| name | user | system | elapsed | |
| BioVector | 0.117 | 0.006 | 0.127 | |
| CrossValidationResultAccessors | 0.003 | 0.001 | 0.004 | |
| KBModelAccessors | 0.002 | 0.001 | 0.003 | |
| KernelMatrixAccessors | 0.002 | 0.001 | 0.002 | |
| LinearKernel | 8.412 | 0.069 | 8.812 | |
| ModelSelectionResultAccessors | 0.002 | 0.001 | 0.003 | |
| PredictionProfileAccessors | 0.003 | 0.001 | 0.004 | |
| ROCDataAccessors | 0.002 | 0.001 | 0.003 | |
| SVMAccess | 0.125 | 0.016 | 0.163 | |
| annotationSpecificKernel | 0.210 | 0.009 | 0.234 | |
| computeROCandAUC | 3.584 | 1.209 | 5.144 | |
| evaluatePrediction | 0.986 | 0.026 | 1.059 | |
| explicitRepresentation | 0.809 | 0.020 | 0.885 | |
| featureWeights | 0.353 | 0.023 | 0.408 | |
| gappyPairKernel | 0.016 | 0.003 | 0.019 | |
| genRandBioSeqs | 0.106 | 0.004 | 0.121 | |
| getPredProfMixture-methods | 3.758 | 0.283 | 4.344 | |
| getPredictionProfile-methods | 1.699 | 0.056 | 1.931 | |
| heatmap-methods | 0.712 | 0.060 | 0.851 | |
| kbsvm-methods | 0.402 | 0.036 | 0.466 | |
| kebabsCollectInfo | 0.090 | 0.011 | 0.109 | |
| kebabsOverview | 0.477 | 0.038 | 0.559 | |
| mismatchKernel | 0.016 | 0.004 | 0.042 | |
| motifKernel | 0.014 | 0.004 | 0.020 | |
| performCrossValidation-methods | 0.423 | 0.037 | 0.554 | |
| performGridSearch | 5.487 | 0.104 | 6.309 | |
| performModelSelection | 9.440 | 0.070 | 9.979 | |
| plot-methods | 0.543 | 0.027 | 0.582 | |
| positionDependentKernel | 0.021 | 0.008 | 0.030 | |
| predict-methods | 0.430 | 0.025 | 0.493 | |
| sequenceKernel | 0.066 | 0.008 | 0.076 | |
| show-methods | 0.050 | 0.016 | 0.069 | |
| spectrumKernel | 0.013 | 0.004 | 0.016 | |
| symmetricPairKernel | 0.187 | 0.019 | 0.207 | |