Ulrich Bodenhofer
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/kebabs |
| git_branch: RELEASE_3_18 |
| git_last_commit: 79c8b1b |
| git_last_commit_date: 2023-10-24 10:39:53 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:51 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 1075/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| kebabs 1.36.0 (landing page) Ulrich Bodenhofer
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: kebabs |
| Version: 1.36.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings kebabs_1.36.0.tar.gz |
| StartedAt: 2023-11-02 11:38:11 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 11:42:27 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 256.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: kebabs.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings kebabs_1.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/kebabs.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘kebabs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘kebabs’ version ‘1.36.0’
* 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: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 11.7Mb
sub-directories of 1Mb or more:
R 1.5Mb
data 1.2Mb
libs 8.5Mb
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
performModelSelection 18.024 0.126 18.222
performGridSearch 8.101 0.859 9.249
getPredProfMixture-methods 3.314 0.640 5.055
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/kebabs.Rcheck/00check.log’
for details.
kebabs.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL kebabs
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ByteStringVector.c -o ByteStringVector.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ExplicitRepC.cpp -o ExplicitRepC.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c GappyPairC.cpp -o GappyPairC.o
GappyPairC.cpp: In function ‘SEXPREC* gappyPairKernelMatrixC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
GappyPairC.cpp:994:37: warning: ‘*((void*)& annX +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
994 | annptr = annX.ptr[iX];
| ~~~~~~~~~~~^
GappyPairC.cpp:3407:28: note: ‘*((void*)& annX +16)’ was declared here
3407 | ByteStringVector x, y, annX, annY, annCharset;
| ^~~~
GappyPairC.cpp:1160:41: warning: ‘*((void*)& annY +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1160 | annptr = annY.ptr[iY];
| ~~~~~~~~~~~^
GappyPairC.cpp:3407:34: note: ‘*((void*)& annY +16)’ was declared here
3407 | ByteStringVector x, y, annX, annY, annCharset;
| ^~~~
GappyPairC.cpp:3472:34: warning: ‘*((void*)& y +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
3472 | getKMPosDistGappy(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, offsetX, offsetY,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3473 | k, m, normalized, symmetric, reverseComplement, posSpec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3474 | distWeight, maxSeqLength, &alphaInf);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GappyPairC.cpp:3472:34: warning: ‘*((void*)& y +8)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c KernelUtils.cpp -o KernelUtils.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c MismatchC.cpp -o MismatchC.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c MotifC.cpp -o MotifC.o
MotifC.cpp: In function ‘void genPredProfileMotif(Rcpp::NumericMatrix, ByteStringVector, Rcpp::IntegerVector, int, ByteStringVector, ByteStringVector, int, bool, int, int, int, int, Rcpp::NumericMatrix, int, ByteStringVector, Rcpp::IntegerVector*, int, int, ByteStringVector, Rcpp::IntegerVector*, int, int, int, bool, bool, bool)’:
MotifC.cpp:3677:18: warning: ‘keyPool’ may be used uninitialized in this function [-Wmaybe-uninitialized]
3677 | pKeypool = keyPool;
| ~~~~~~~~~^~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c PredictionC.cpp -o PredictionC.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c PredictionProfileC.cpp -o PredictionProfileC.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_kebabs.cpp -o R_init_kebabs.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Rsvm.c -o Rsvm.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SpectrumC.cpp -o SpectrumC.o
SpectrumC.cpp: In function ‘SEXPREC* spectrumKernelMatrixC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
SpectrumC.cpp:679:37: warning: ‘*((void*)& annX +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
679 | annptr = annX.ptr[iX];
| ~~~~~~~~~~~^
SpectrumC.cpp:3156:28: note: ‘*((void*)& annX +16)’ was declared here
3156 | ByteStringVector x, y, annX, annY, annCharset;
| ^~~~
SpectrumC.cpp:835:41: warning: ‘*((void*)& annY +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
835 | annptr = annY.ptr[iY];
| ~~~~~~~~~~~^
SpectrumC.cpp:3156:34: note: ‘*((void*)& annY +16)’ was declared here
3156 | ByteStringVector x, y, annX, annY, annCharset;
| ^~~~
SpectrumC.cpp:3220:33: warning: ‘*((void*)& y +16)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
3220 | getKMPosDistSpec(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, offsetX, offsetY,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3221 | k, normalized, symmetric, reverseComplement, posSpec, distWeight,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3222 | maxSeqLength, &alphaInf);
| ~~~~~~~~~~~~~~~~~~~~~~~~
SpectrumC.cpp:3220:33: warning: ‘*((void*)& y +8)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SymmetricPairC.cpp -o SymmetricPairC.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Utils.cpp -o Utils.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c svm.cpp -o svm.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/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 -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-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 | 0.058 | 0.004 | 0.062 | |
| CrossValidationResultAccessors | 0.002 | 0.000 | 0.002 | |
| KBModelAccessors | 0.001 | 0.000 | 0.002 | |
| KernelMatrixAccessors | 0.000 | 0.001 | 0.001 | |
| LinearKernel | 4.663 | 0.074 | 4.754 | |
| ModelSelectionResultAccessors | 0.001 | 0.000 | 0.002 | |
| PredictionProfileAccessors | 0.002 | 0.000 | 0.002 | |
| ROCDataAccessors | 0.001 | 0.000 | 0.001 | |
| SVMAccess | 0.082 | 0.007 | 0.095 | |
| annotationSpecificKernel | 0.153 | 0.000 | 0.154 | |
| computeROCandAUC | 0.962 | 0.016 | 1.023 | |
| evaluatePrediction | 0.909 | 0.012 | 0.922 | |
| explicitRepresentation | 0.237 | 0.000 | 0.238 | |
| featureWeights | 0.809 | 0.028 | 0.839 | |
| gappyPairKernel | 0.009 | 0.000 | 0.009 | |
| genRandBioSeqs | 0.07 | 0.00 | 0.07 | |
| getPredProfMixture-methods | 3.314 | 0.640 | 5.055 | |
| getPredictionProfile-methods | 0.818 | 0.063 | 0.888 | |
| heatmap-methods | 0.542 | 0.052 | 0.596 | |
| kbsvm-methods | 0.175 | 0.020 | 0.197 | |
| kebabsCollectInfo | 0.007 | 0.021 | 0.038 | |
| kebabsOverview | 0.333 | 0.020 | 0.356 | |
| mismatchKernel | 0.005 | 0.004 | 0.009 | |
| motifKernel | 0.008 | 0.000 | 0.008 | |
| performCrossValidation-methods | 0.230 | 0.004 | 0.235 | |
| performGridSearch | 8.101 | 0.859 | 9.249 | |
| performModelSelection | 18.024 | 0.126 | 18.222 | |
| plot-methods | 0.597 | 0.004 | 0.615 | |
| positionDependentKernel | 0.015 | 0.001 | 0.015 | |
| predict-methods | 0.262 | 0.019 | 0.282 | |
| sequenceKernel | 0.059 | 0.000 | 0.060 | |
| show-methods | 0.034 | 0.000 | 0.035 | |
| spectrumKernel | 0.008 | 0.000 | 0.008 | |
| symmetricPairKernel | 0.115 | 0.008 | 0.123 | |