Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:13 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for kebabs on machv2


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.

raw results

Package 978/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kebabs 1.28.1  (landing page)
Ulrich Bodenhofer
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/kebabs
git_branch: RELEASE_3_14
git_last_commit: 1f83eb1
git_last_commit_date: 2022-01-25 04:54:59 -0400 (Tue, 25 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: kebabs
Version: 1.28.1
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_1.28.1.tar.gz
StartedAt: 2022-04-12 14:42:44 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 14:47:24 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 279.7 seconds
RetCode: 0
Status:   OK  
CheckDir: kebabs.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.28.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.28.1’
* 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 14.724  2.636  17.377
performGridSearch      6.956  1.040   8.002
* 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-3.14-bioc/meat/kebabs.Rcheck/00check.log’
for details.



Installation output

kebabs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL kebabs
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/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)

Tests output


Example timings

kebabs.Rcheck/kebabs-Ex.timings

nameusersystemelapsed
BioVector0.0530.0060.059
CrossValidationResultAccessors0.0020.0000.002
KBModelAccessors0.0010.0010.003
KernelMatrixAccessors0.0020.0010.002
LinearKernel4.3730.0384.416
ModelSelectionResultAccessors0.0020.0000.002
PredictionProfileAccessors0.0020.0000.004
ROCDataAccessors0.0020.0010.003
SVMAccess0.1240.0080.132
annotationSpecificKernel0.1980.0050.203
computeROCandAUC3.2800.7224.007
evaluatePrediction1.0010.0861.088
explicitRepresentation0.2800.0160.296
featureWeights0.4100.0330.443
gappyPairKernel0.0130.0020.055
genRandBioSeqs0.0960.0030.099
getPredProfMixture-methods3.1750.2193.401
getPredictionProfile-methods1.3840.0371.423
heatmap-methods0.5560.0390.595
kbsvm-methods0.3540.0160.370
kebabsCollectInfo0.0700.0060.076
kebabsOverview0.4410.0480.490
mismatchKernel0.0110.0020.013
motifKernel0.0120.0020.014
performCrossValidation-methods0.3760.0230.400
performGridSearch6.9561.0408.002
performModelSelection14.724 2.63617.377
plot-methods0.6860.1030.790
positionDependentKernel0.0160.0050.021
predict-methods0.4430.0220.465
sequenceKernel0.0690.0060.075
show-methods0.0420.0150.058
spectrumKernel0.0100.0020.013
symmetricPairKernel0.1400.0120.152