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 12:02 -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. |
| Package: kebabs |
| Version: 1.40.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings kebabs_1.40.0.tar.gz |
| StartedAt: 2024-11-20 04:56:31 -0500 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 05:01:07 -0500 (Wed, 20 Nov 2024) |
| EllapsedTime: 275.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: kebabs.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings kebabs_1.40.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/kebabs.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘1.40.0’
* 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 (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... NOTE
installed size is 11.5Mb
sub-directories of 1Mb or more:
R 1.5Mb
data 1.2Mb
libs 8.3Mb
* 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 6.993 0.017 7.081
LinearKernel 4.459 0.550 5.029
* 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
‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/kebabs.Rcheck/00check.log’
for details.
kebabs.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL kebabs
###
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Utils.cpp -o Utils.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-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-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-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 | 0.449 | 0.001 | 0.450 | |
| CrossValidationResultAccessors | 0.001 | 0.000 | 0.001 | |
| KBModelAccessors | 0.001 | 0.000 | 0.001 | |
| KernelMatrixAccessors | 0.001 | 0.000 | 0.000 | |
| LinearKernel | 4.459 | 0.550 | 5.029 | |
| ModelSelectionResultAccessors | 0 | 0 | 0 | |
| PredictionProfileAccessors | 0.001 | 0.000 | 0.001 | |
| ROCDataAccessors | 0.000 | 0.001 | 0.001 | |
| SVMAccess | 0.066 | 0.003 | 0.069 | |
| annotationSpecificKernel | 0.074 | 0.000 | 0.074 | |
| computeROCandAUC | 0.320 | 0.027 | 0.347 | |
| evaluatePrediction | 0.268 | 0.006 | 0.274 | |
| explicitRepresentation | 0.108 | 0.024 | 0.131 | |
| featureWeights | 0.102 | 0.009 | 0.110 | |
| gappyPairKernel | 0.005 | 0.001 | 0.005 | |
| genRandBioSeqs | 0.030 | 0.001 | 0.031 | |
| getPredProfMixture-methods | 3.357 | 0.268 | 3.626 | |
| getPredictionProfile-methods | 0.390 | 0.086 | 0.477 | |
| heatmap-methods | 0.255 | 0.076 | 0.331 | |
| kbsvm-methods | 0.108 | 0.015 | 0.123 | |
| kebabsCollectInfo | 0.013 | 0.009 | 0.026 | |
| kebabsOverview | 0.137 | 0.012 | 0.149 | |
| mismatchKernel | 0.005 | 0.000 | 0.007 | |
| motifKernel | 0.004 | 0.000 | 0.005 | |
| performCrossValidation-methods | 0.105 | 0.007 | 0.112 | |
| performGridSearch | 3.811 | 0.030 | 3.848 | |
| performModelSelection | 6.993 | 0.017 | 7.081 | |
| plot-methods | 0.155 | 0.005 | 0.161 | |
| positionDependentKernel | 0.006 | 0.001 | 0.006 | |
| predict-methods | 0.114 | 0.006 | 0.120 | |
| sequenceKernel | 0.02 | 0.00 | 0.02 | |
| show-methods | 0.014 | 0.001 | 0.015 | |
| spectrumKernel | 0.003 | 0.000 | 0.003 | |
| symmetricPairKernel | 0.072 | 0.006 | 0.078 | |