| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:37 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1032/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| kebabs 1.35.0 (landing page) Ulrich Bodenhofer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: kebabs |
| Version: 1.35.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings kebabs_1.35.0.tar.gz |
| StartedAt: 2023-05-30 10:39:00 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 10:49:49 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 649.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: kebabs.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings kebabs_1.35.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/kebabs.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘kebabs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘kebabs’ version ‘1.35.0’
* 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 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking installed package size ... NOTE
installed size is 9.5Mb
sub-directories of 1Mb or more:
R 1.6Mb
data 1.2Mb
libs 6.2Mb
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
performModelSelection 17.149 0.128 17.279
performGridSearch 7.981 0.748 8.730
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘kebabs.Rnw’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/kebabs.Rcheck/00check.log’
for details.
kebabs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL kebabs ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘kebabs’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c ByteStringVector.c -o ByteStringVector.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c ExplicitRepC.cpp -o ExplicitRepC.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c GappyPairC.cpp -o GappyPairC.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c KernelUtils.cpp -o KernelUtils.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c MismatchC.cpp -o MismatchC.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c MotifC.cpp -o MotifC.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c PredictionC.cpp -o PredictionC.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c PredictionProfileC.cpp -o PredictionProfileC.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c R_init_kebabs.cpp -o R_init_kebabs.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c Rsvm.c -o Rsvm.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c SparseMatrixHash.cpp -o SparseMatrixHash.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c SpectrumC.cpp -o SpectrumC.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c SymmetricPairC.cpp -o SymmetricPairC.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c Utils.cpp -o Utils.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c XVector_stubs.c -o XVector_stubs.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.3.0/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.0/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/site-library/S4Vectors/include' -I/usr/local/include -fPIC -g -O2 -c svm.cpp -o svm.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o kebabs.so Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o Rsvm.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o svm.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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 | 0.055 | 0.009 | 0.064 | |
| CrossValidationResultAccessors | 0.002 | 0.000 | 0.002 | |
| KBModelAccessors | 0.002 | 0.000 | 0.002 | |
| KernelMatrixAccessors | 0.001 | 0.000 | 0.001 | |
| LinearKernel | 4.770 | 0.031 | 4.802 | |
| ModelSelectionResultAccessors | 0.001 | 0.000 | 0.001 | |
| PredictionProfileAccessors | 0.002 | 0.000 | 0.002 | |
| ROCDataAccessors | 0.001 | 0.000 | 0.001 | |
| SVMAccess | 0.082 | 0.004 | 0.086 | |
| annotationSpecificKernel | 0.166 | 0.004 | 0.169 | |
| computeROCandAUC | 0.975 | 0.016 | 0.991 | |
| evaluatePrediction | 1.363 | 0.004 | 1.366 | |
| explicitRepresentation | 0.207 | 0.000 | 0.208 | |
| featureWeights | 0.270 | 0.008 | 0.279 | |
| gappyPairKernel | 0.009 | 0.000 | 0.009 | |
| genRandBioSeqs | 0.063 | 0.000 | 0.063 | |
| getPredProfMixture-methods | 3.174 | 0.168 | 3.342 | |
| getPredictionProfile-methods | 0.754 | 0.060 | 0.813 | |
| heatmap-methods | 0.539 | 0.068 | 0.607 | |
| kbsvm-methods | 0.176 | 0.060 | 0.236 | |
| kebabsCollectInfo | 0.025 | 0.001 | 0.155 | |
| kebabsOverview | 0.303 | 0.024 | 0.326 | |
| mismatchKernel | 0.01 | 0.00 | 0.01 | |
| motifKernel | 0.008 | 0.000 | 0.009 | |
| performCrossValidation-methods | 0.230 | 0.000 | 0.231 | |
| performGridSearch | 7.981 | 0.748 | 8.730 | |
| performModelSelection | 17.149 | 0.128 | 17.279 | |
| plot-methods | 0.583 | 0.006 | 0.590 | |
| positionDependentKernel | 0.010 | 0.004 | 0.014 | |
| predict-methods | 0.272 | 0.004 | 0.275 | |
| sequenceKernel | 0.053 | 0.002 | 0.055 | |
| show-methods | 0.033 | 0.000 | 0.032 | |
| spectrumKernel | 0.008 | 0.000 | 0.008 | |
| symmetricPairKernel | 0.114 | 0.004 | 0.118 | |