| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:09 -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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:kebabs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings kebabs_1.30.0.tar.gz |
| StartedAt: 2022-10-19 03:53:52 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 03:59:20 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 328.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: kebabs.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:kebabs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings kebabs_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/kebabs.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
performModelSelection 16.197 2.009 19.081
performGridSearch 7.753 0.908 8.670
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.15-bioc/meat/kebabs.Rcheck/00check.log’
for details.
kebabs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL kebabs ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘kebabs’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ByteStringVector.c -o ByteStringVector.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ExplicitRepC.cpp -o ExplicitRepC.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c GappyPairC.cpp -o GappyPairC.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c KernelUtils.cpp -o KernelUtils.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MismatchC.cpp -o MismatchC.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MotifC.cpp -o MotifC.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PredictionC.cpp -o PredictionC.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PredictionProfileC.cpp -o PredictionProfileC.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_kebabs.cpp -o R_init_kebabs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Rsvm.c -o Rsvm.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c SparseMatrixHash.cpp -o SparseMatrixHash.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c SpectrumC.cpp -o SpectrumC.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c SymmetricPairC.cpp -o SymmetricPairC.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Utils.cpp -o Utils.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c svm.cpp -o svm.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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 | 0.081 | 0.007 | 0.089 | |
| CrossValidationResultAccessors | 0.003 | 0.000 | 0.004 | |
| KBModelAccessors | 0.002 | 0.000 | 0.002 | |
| KernelMatrixAccessors | 0.002 | 0.000 | 0.002 | |
| LinearKernel | 4.798 | 0.035 | 4.841 | |
| ModelSelectionResultAccessors | 0.001 | 0.000 | 0.002 | |
| PredictionProfileAccessors | 0.002 | 0.000 | 0.002 | |
| ROCDataAccessors | 0.001 | 0.000 | 0.002 | |
| SVMAccess | 0.135 | 0.006 | 0.142 | |
| annotationSpecificKernel | 0.199 | 0.009 | 0.208 | |
| computeROCandAUC | 3.328 | 0.675 | 4.007 | |
| evaluatePrediction | 1.581 | 0.121 | 1.705 | |
| explicitRepresentation | 0.295 | 0.004 | 0.300 | |
| featureWeights | 0.447 | 0.031 | 0.477 | |
| gappyPairKernel | 0.013 | 0.001 | 0.013 | |
| genRandBioSeqs | 0.076 | 0.001 | 0.077 | |
| getPredProfMixture-methods | 3.438 | 0.227 | 3.668 | |
| getPredictionProfile-methods | 1.060 | 0.018 | 1.080 | |
| heatmap-methods | 1.054 | 0.060 | 1.115 | |
| kbsvm-methods | 0.341 | 0.006 | 0.347 | |
| kebabsCollectInfo | 0.073 | 0.005 | 0.079 | |
| kebabsOverview | 0.489 | 0.025 | 0.513 | |
| mismatchKernel | 0.013 | 0.001 | 0.014 | |
| motifKernel | 0.011 | 0.001 | 0.012 | |
| performCrossValidation-methods | 0.410 | 0.020 | 0.431 | |
| performGridSearch | 7.753 | 0.908 | 8.670 | |
| performModelSelection | 16.197 | 2.009 | 19.081 | |
| plot-methods | 0.778 | 0.081 | 0.860 | |
| positionDependentKernel | 0.018 | 0.002 | 0.020 | |
| predict-methods | 0.474 | 0.016 | 0.490 | |
| sequenceKernel | 0.065 | 0.001 | 0.066 | |
| show-methods | 0.043 | 0.009 | 0.052 | |
| spectrumKernel | 0.011 | 0.001 | 0.011 | |
| symmetricPairKernel | 0.195 | 0.010 | 0.207 | |