Ulrich Bodenhofer
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/kebabs |
| git_branch: RELEASE_3_20 |
| git_last_commit: 43a1703 |
| git_last_commit_date: 2024-10-29 09:56:18 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 1080/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| kebabs 1.40.0 (landing page) Ulrich Bodenhofer
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| 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: 1.40.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings kebabs_1.40.0.tar.gz |
| StartedAt: 2024-11-20 09:14:18 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 09:18:08 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 230.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: kebabs.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings kebabs_1.40.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/kebabs.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
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 ‘1.40.0’
* 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 (conda-forge gcc 14.2.0-1) 14.2.0’
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... NOTE
installed size is 11.4Mb
sub-directories of 1Mb or more:
R 1.5Mb
data 1.2Mb
libs 8.2Mb
* 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 loading without being on the library search path ... 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 ... 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 8.837 0.191 9.160
LinearKernel 7.235 0.035 7.288
performGridSearch 4.904 0.267 5.191
* 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
‘/home/biocbuild/bbs-3.20-bioc/meat/kebabs.Rcheck/00check.log’
for details.
kebabs.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL kebabs
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c GappyPairC.cpp -o GappyPairC.o
In function 'void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]',
inlined from '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)' at GappyPairC.cpp:3480:33:
GappyPairC.cpp:1157:38: warning: 'y.ByteStringVector::nchar' may be used uninitialized [-Wmaybe-uninitialized]
1157 | seqnchar = y.nchar[iY];
| ~~~~~~~~~~^
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:3409:25: note: 'y.ByteStringVector::nchar' was declared here
3409 | ByteStringVector x, y, annX, annY, annCharset;
| ^
In function 'void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]',
inlined from '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)' at GappyPairC.cpp:3480:33:
GappyPairC.cpp:1156:34: warning: 'y.ByteStringVector::ptr' may be used uninitialized [-Wmaybe-uninitialized]
1156 | seqptr = y.ptr[iY];
| ~~~~~~~~^
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:3409:25: note: 'y.ByteStringVector::ptr' was declared here
3409 | ByteStringVector x, y, annX, annY, annCharset;
| ^
GappyPairC.cpp:3535:33: warning: 'annY.ByteStringVector::ptr' may be used uninitialized [-Wmaybe-uninitialized]
3535 | getKMStdAnnGappy(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3536 | k, m, normalized, symmetric, presence, reverseComplement,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3537 | maxSeqLength, dimFeatureSpace, &alphaInf);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GappyPairC.cpp:3409:34: note: 'annY.ByteStringVector::ptr' was declared here
3409 | ByteStringVector x, y, annX, annY, annCharset;
| ^~~~
GappyPairC.cpp:3535:33: warning: 'annX.ByteStringVector::ptr' may be used uninitialized [-Wmaybe-uninitialized]
3535 | getKMStdAnnGappy(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3536 | k, m, normalized, symmetric, presence, reverseComplement,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3537 | maxSeqLength, dimFeatureSpace, &alphaInf);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GappyPairC.cpp:3409:28: note: 'annX.ByteStringVector::ptr' was declared here
3409 | ByteStringVector x, y, annX, annY, annCharset;
| ^~~~
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c MismatchC.cpp -o MismatchC.o
MismatchC.cpp: In function 'SEXPREC* getMismatchKernelMatrix(Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, int, int, bool, bool, int, alphaInfo*)':
MismatchC.cpp:432:41: warning: 'currValSqrt' may be used uninitialized [-Wmaybe-uninitialized]
432 | km(i,j) = kernelVal / currValSqrt;
| ~~~~~~~~~~^~~~~~~~~~~~~
MismatchC.cpp:368:32: note: 'currValSqrt' was declared here
368 | double kernelVal, currVal, currValSqrt;
| ^~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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 [-Wmaybe-uninitialized]
3677 | pKeypool = keyPool;
| ~~~~~~~~~^~~~~~~~~
MotifC.cpp:3514:11: note: 'keyPool' was declared here
3514 | char *keyPool;
| ^~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SpectrumC.cpp -o SpectrumC.o
In function 'void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]',
inlined from '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)' at SpectrumC.cpp:3228:32:
SpectrumC.cpp:832:38: warning: 'y.ByteStringVector::nchar' may be used uninitialized [-Wmaybe-uninitialized]
832 | seqnchar = y.nchar[iY];
| ~~~~~~~~~~^
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:3158:25: note: 'y.ByteStringVector::nchar' was declared here
3158 | ByteStringVector x, y, annX, annY, annCharset;
| ^
In function 'void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]',
inlined from '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)' at SpectrumC.cpp:3228:32:
SpectrumC.cpp:831:34: warning: 'y.ByteStringVector::ptr' may be used uninitialized [-Wmaybe-uninitialized]
831 | seqptr = y.ptr[iY];
| ~~~~~~~~^
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:3158:25: note: 'y.ByteStringVector::ptr' was declared here
3158 | ByteStringVector x, y, annX, annY, annCharset;
| ^
SpectrumC.cpp:3283:32: warning: 'annY.ByteStringVector::ptr' may be used uninitialized [-Wmaybe-uninitialized]
3283 | getKMStdAnnSpec(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3284 | k, normalized, symmetric, presence, reverseComplement, maxSeqLength,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3285 | dimFeatureSpace, &alphaInf);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
SpectrumC.cpp:3158:34: note: 'annY.ByteStringVector::ptr' was declared here
3158 | ByteStringVector x, y, annX, annY, annCharset;
| ^~~~
SpectrumC.cpp:3283:32: warning: 'annX.ByteStringVector::ptr' may be used uninitialized [-Wmaybe-uninitialized]
3283 | getKMStdAnnSpec(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3284 | k, normalized, symmetric, presence, reverseComplement, maxSeqLength,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3285 | dimFeatureSpace, &alphaInf);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
SpectrumC.cpp:3158:28: note: 'annX.ByteStringVector::ptr' was declared here
3158 | ByteStringVector x, y, annX, annY, annCharset;
| ^~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Utils.cpp -o Utils.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.4.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.4.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c svm.cpp -o svm.o
svm.cpp: In function 'svm_model* svm_train(const svm_problem*, const svm_parameter*)':
svm.cpp:42:38: warning: argument 1 range [18446744056529682432, 18446744073709551608] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
42 | #define Malloc(type,n) (type *)malloc((n)*sizeof(type))
| ~~~~~~^~~~~~~~~~~~~~~~~~
svm.cpp:2382:34: note: in expansion of macro 'Malloc'
2382 | model->sv_coef = Malloc(double *,nr_class-1);
| ^~~~~~
In file included from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/cstdlib:79,
from /home/biocbuild/R/R-4.4.1/include/R.h:39,
from svm.cpp:1:
/home/biocbuild/miniforge3/aarch64-conda-linux-gnu/sysroot/usr/include/stdlib.h:465:14: note: in a call to allocation function 'void* malloc(size_t)' declared here
465 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur;
| ^~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/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-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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 | 0.563 | 0.008 | 0.573 | |
| CrossValidationResultAccessors | 0.002 | 0.000 | 0.002 | |
| KBModelAccessors | 0.001 | 0.000 | 0.001 | |
| KernelMatrixAccessors | 0.001 | 0.000 | 0.001 | |
| LinearKernel | 7.235 | 0.035 | 7.288 | |
| ModelSelectionResultAccessors | 0.002 | 0.000 | 0.001 | |
| PredictionProfileAccessors | 0.002 | 0.000 | 0.002 | |
| ROCDataAccessors | 0.001 | 0.000 | 0.001 | |
| SVMAccess | 0.099 | 0.008 | 0.108 | |
| annotationSpecificKernel | 0.148 | 0.004 | 0.153 | |
| computeROCandAUC | 0.534 | 0.048 | 0.583 | |
| evaluatePrediction | 0.509 | 0.016 | 0.526 | |
| explicitRepresentation | 0.219 | 0.012 | 0.232 | |
| featureWeights | 0.16 | 0.00 | 0.16 | |
| gappyPairKernel | 0.01 | 0.00 | 0.01 | |
| genRandBioSeqs | 0.065 | 0.000 | 0.066 | |
| getPredProfMixture-methods | 3.943 | 0.092 | 3.861 | |
| getPredictionProfile-methods | 0.749 | 0.044 | 0.707 | |
| heatmap-methods | 0.455 | 0.036 | 0.434 | |
| kbsvm-methods | 0.204 | 0.000 | 0.181 | |
| kebabsCollectInfo | 0.024 | 0.030 | 0.057 | |
| kebabsOverview | 0.243 | 0.063 | 0.309 | |
| mismatchKernel | 0.009 | 0.000 | 0.010 | |
| motifKernel | 0.005 | 0.003 | 0.009 | |
| performCrossValidation-methods | 0.178 | 0.004 | 0.186 | |
| performGridSearch | 4.904 | 0.267 | 5.191 | |
| performModelSelection | 8.837 | 0.191 | 9.160 | |
| plot-methods | 0.260 | 0.008 | 0.270 | |
| positionDependentKernel | 0.013 | 0.000 | 0.014 | |
| predict-methods | 0.185 | 0.012 | 0.199 | |
| sequenceKernel | 0.043 | 0.000 | 0.044 | |
| show-methods | 0.026 | 0.005 | 0.033 | |
| spectrumKernel | 0.007 | 0.001 | 0.008 | |
| symmetricPairKernel | 0.112 | 0.000 | 0.113 | |