Ulrich Bodenhofer
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/kebabs |
| git_branch: devel |
| git_last_commit: 56e9334 |
| git_last_commit_date: 2024-10-29 09:56:18 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1073/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| kebabs 1.41.0 (landing page) Ulrich Bodenhofer
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.41.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings kebabs_1.41.0.tar.gz |
| StartedAt: 2024-12-23 23:15:25 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 23:20:59 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 333.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: kebabs.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings kebabs_1.41.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/kebabs.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘kebabs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘kebabs’ version ‘1.41.0’
* 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 (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 7.5Mb
sub-directories of 1Mb or more:
R 1.4Mb
data 1.2Mb
libs 4.6Mb
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
performModelSelection 8.499 0.336 8.837
LinearKernel 6.379 0.027 6.408
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/kebabs.Rcheck/00check.log’
for details.
kebabs.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL kebabs
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c ByteStringVector.c -o ByteStringVector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c ExplicitRepC.cpp -o ExplicitRepC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c KernelUtils.cpp -o KernelUtils.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c PredictionC.cpp -o PredictionC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c PredictionProfileC.cpp -o PredictionProfileC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c R_init_kebabs.cpp -o R_init_kebabs.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c Rsvm.c -o Rsvm.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c SymmetricPairC.cpp -o SymmetricPairC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c Utils.cpp -o Utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c svm.cpp -o svm.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/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/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/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 | 0.051 | 0.001 | 0.053 | |
| CrossValidationResultAccessors | 0.001 | 0.000 | 0.002 | |
| KBModelAccessors | 0.001 | 0.000 | 0.001 | |
| KernelMatrixAccessors | 0.001 | 0.000 | 0.001 | |
| LinearKernel | 6.379 | 0.027 | 6.408 | |
| ModelSelectionResultAccessors | 0.001 | 0.001 | 0.001 | |
| PredictionProfileAccessors | 0.002 | 0.000 | 0.001 | |
| ROCDataAccessors | 0.000 | 0.001 | 0.001 | |
| SVMAccess | 0.083 | 0.005 | 0.088 | |
| annotationSpecificKernel | 0.099 | 0.002 | 0.102 | |
| computeROCandAUC | 0.460 | 0.008 | 0.468 | |
| evaluatePrediction | 0.365 | 0.016 | 0.383 | |
| explicitRepresentation | 0.142 | 0.030 | 0.172 | |
| featureWeights | 0.144 | 0.007 | 0.152 | |
| gappyPairKernel | 0.007 | 0.002 | 0.008 | |
| genRandBioSeqs | 0.049 | 0.000 | 0.051 | |
| getPredProfMixture-methods | 3.037 | 0.216 | 3.254 | |
| getPredictionProfile-methods | 0.539 | 0.055 | 0.594 | |
| heatmap-methods | 0.359 | 0.057 | 0.417 | |
| kbsvm-methods | 0.150 | 0.009 | 0.159 | |
| kebabsCollectInfo | 0.015 | 0.007 | 0.025 | |
| kebabsOverview | 0.213 | 0.015 | 0.228 | |
| mismatchKernel | 0.006 | 0.001 | 0.008 | |
| motifKernel | 0.005 | 0.002 | 0.006 | |
| performCrossValidation-methods | 0.168 | 0.011 | 0.178 | |
| performGridSearch | 4.812 | 0.028 | 4.840 | |
| performModelSelection | 8.499 | 0.336 | 8.837 | |
| plot-methods | 0.224 | 0.006 | 0.231 | |
| positionDependentKernel | 0.011 | 0.001 | 0.012 | |
| predict-methods | 0.169 | 0.007 | 0.176 | |
| sequenceKernel | 0.037 | 0.003 | 0.040 | |
| show-methods | 0.023 | 0.003 | 0.026 | |
| spectrumKernel | 0.006 | 0.001 | 0.007 | |
| symmetricPairKernel | 0.113 | 0.010 | 0.124 | |