Ulrich Bodenhofer
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/kebabs |
| git_branch: RELEASE_3_15 |
| git_last_commit: 90d8024 |
| git_last_commit_date: 2022-04-26 11:22:32 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:20:26 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
To the developers/maintainers of the kebabs package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1003/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| kebabs 1.30.0 (landing page) Ulrich Bodenhofer
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: kebabs |
| Version: 1.30.0 |
| Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings kebabs_1.30.0.tar.gz |
| StartedAt: 2022-10-18 20:17:48 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 20:20:33 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 165.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: kebabs.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings kebabs_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/kebabs.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘kebabs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘kebabs’ version ‘1.30.0’
* 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
* checking installed package size ... NOTE
installed size is 7.3Mb
sub-directories of 1Mb or more:
R 1.3Mb
data 1.2Mb
libs 4.3Mb
* 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 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 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 11.955 0.015 11.969
performGridSearch 5.561 0.016 5.577
* 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-3.15-bioc/meat/kebabs.Rcheck/00check.log’
for details.
kebabs.Rcheck/00install.out
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###
### Running command:
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### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL kebabs
###
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c ByteStringVector.c -o ByteStringVector.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c ExplicitRepC.cpp -o ExplicitRepC.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c GappyPairC.cpp -o GappyPairC.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c KernelUtils.cpp -o KernelUtils.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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 in this function [-Wmaybe-uninitialized]
432 | km(i,j) = kernelVal / currValSqrt;
| ~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c PredictionC.cpp -o PredictionC.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c PredictionProfileC.cpp -o PredictionProfileC.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Rsvm.c -o Rsvm.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c SpectrumC.cpp -o SpectrumC.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c SymmetricPairC.cpp -o SymmetricPairC.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Utils.cpp -o Utils.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c svm.cpp -o svm.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-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-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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 | 0.032 | 0.012 | 0.043 | |
| CrossValidationResultAccessors | 0.000 | 0.001 | 0.002 | |
| KBModelAccessors | 0.001 | 0.000 | 0.001 | |
| KernelMatrixAccessors | 0.000 | 0.001 | 0.001 | |
| LinearKernel | 4.563 | 0.297 | 4.867 | |
| ModelSelectionResultAccessors | 0.002 | 0.000 | 0.002 | |
| PredictionProfileAccessors | 0.003 | 0.000 | 0.003 | |
| ROCDataAccessors | 0.000 | 0.002 | 0.002 | |
| SVMAccess | 0.106 | 0.017 | 0.124 | |
| annotationSpecificKernel | 0.120 | 0.044 | 0.164 | |
| computeROCandAUC | 1.962 | 0.332 | 2.296 | |
| evaluatePrediction | 0.625 | 0.008 | 0.634 | |
| explicitRepresentation | 0.143 | 0.000 | 0.143 | |
| featureWeights | 0.279 | 0.004 | 0.283 | |
| gappyPairKernel | 0.003 | 0.004 | 0.008 | |
| genRandBioSeqs | 0.045 | 0.004 | 0.049 | |
| getPredProfMixture-methods | 2.805 | 0.204 | 3.009 | |
| getPredictionProfile-methods | 0.557 | 0.060 | 0.617 | |
| heatmap-methods | 0.835 | 0.064 | 0.899 | |
| kbsvm-methods | 0.184 | 0.012 | 0.196 | |
| kebabsCollectInfo | 0.04 | 0.00 | 0.04 | |
| kebabsOverview | 0.264 | 0.036 | 0.300 | |
| mismatchKernel | 0.004 | 0.003 | 0.008 | |
| motifKernel | 0.005 | 0.001 | 0.006 | |
| performCrossValidation-methods | 0.227 | 0.014 | 0.241 | |
| performGridSearch | 5.561 | 0.016 | 5.577 | |
| performModelSelection | 11.955 | 0.015 | 11.969 | |
| plot-methods | 0.447 | 0.012 | 0.460 | |
| positionDependentKernel | 0.011 | 0.002 | 0.013 | |
| predict-methods | 0.248 | 0.021 | 0.270 | |
| sequenceKernel | 0.042 | 0.000 | 0.042 | |
| show-methods | 0.018 | 0.004 | 0.022 | |
| spectrumKernel | 0.004 | 0.001 | 0.006 | |
| symmetricPairKernel | 0.091 | 0.010 | 0.101 | |