############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:pRoloc.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings pRoloc_1.47.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/pRoloc.Rcheck’ * using R Under development (unstable) (2024-11-14 r87333) * 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 ‘pRoloc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pRoloc’ version ‘1.47.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 27 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘pRoloc’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... INFO installed size is 5.0Mb sub-directories of 1Mb or more: R 1.2Mb libs 2.3Mb * 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 ... NOTE ':::' calls which should be '::': ‘MLInterfaces:::.macroF1’ ‘MLInterfaces:::.precision’ ‘MLInterfaces:::.recall’ ‘MLInterfaces:::es2df’ See the note in ?`:::` about the use of this operator. Unexported object imported by a ':::' call: ‘caret:::predict.plsda’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘getAttributesOfInterest0’ ‘getAttributesOfInterestX’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘pRoloc/R/annotation.R’: unlockBinding("params", .pRolocEnv) * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: GenRegRes-class.Rd: MSnSet-class MLearn-methods.Rd: MSnSet-class, xvalSpec, MLearn QSep-class.Rd: MSnSet-class, Versioned-class SpatProtVis-class.Rd: MSnSet-class clustDist.Rd: MSnSet-class getMarkerClasses.Rd: MSnSet-class getMarkers.Rd: MSnSet-class getPredictions.Rd: MSnSet-class highlightOnPlot.Rd: FeaturesOfInterest-class knnClassification.Rd: MSnSet-class, knn knnOptimisation.Rd: MSnSet-class, knn knntlClassification.Rd: MSnSet-class knntlOptimisation.Rd: MSnSet-class ksvmClassification.Rd: MSnSet-class, ksvm ksvmOptimisation.Rd: MSnSet-class, ksvm makeGoSet.Rd: MSnSet-class minMarkers.Rd: MSnSet-class move2Ds.Rd: MSnSetList nbClassification.Rd: MSnSet-class, naiveBayes nbOptimisation.Rd: MSnSet-class, naiveBayes nnetClassification.Rd: MSnSet-class, nnet nnetOptimisation.Rd: MSnSet-class, nnet orgQuants.Rd: MSnSet-class perTurboClassification.Rd: MSnSet-class, ginv perTurboOptimisation.Rd: MSnSet-class, ginv phenoDisco.Rd: filterNA plot2Ds.Rd: MSnSet-class, MSnSetList plsdaClassification.Rd: MSnSet-class, plsda plsdaOptimisation.Rd: MSnSet-class, plsda rfClassification.Rd: MSnSet-class, randomForest rfOptimisation.Rd: MSnSet-class, randomForest sampleMSnSet.Rd: MSnSet-class svmClassification.Rd: MSnSet-class, svm svmOptimisation.Rd: MSnSet-class, svm testMSnSet.Rd: MSnSet-class testMarkers.Rd: MSnSet-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 perTurboClassification 7.450 0.005 7.460 plot2D 6.818 0.128 6.211 ClustDist-class 2.303 0.063 6.442 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 5. └─biomaRt:::.listMarts(...) ── Error ('test_goannotations.R:9:1'): (code run outside of `test_that()`) ───── Error: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable. Look at ?useEnsembl for details on how to try a mirror site. Backtrace: ▆ 1. └─pRoloc::setAnnotationParams(inputs = c("Mouse genes", "UniProtKB/Swiss-Prot ID")) at test_goannotations.R:9:1 2. └─pRoloc:::getFilterList(m[spidx, "dataset"]) 3. └─biomaRt::useMart(...) 4. └─biomaRt:::.useMart(...) 5. └─biomaRt:::.listMarts(...) [ FAIL 3 | WARN 5 | SKIP 0 | PASS 133 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘v01-pRoloc-tutorial.Rmd’ using rmarkdown --- finished re-building ‘v01-pRoloc-tutorial.Rmd’ --- re-building ‘v02-pRoloc-ml.Rmd’ using rmarkdown --- finished re-building ‘v02-pRoloc-ml.Rmd’ --- re-building ‘v03-pRoloc-bayesian.Rmd’ using rmarkdown --- finished re-building ‘v03-pRoloc-bayesian.Rmd’ --- re-building ‘v04-pRoloc-goannotations.Rmd’ using rmarkdown --- finished re-building ‘v04-pRoloc-goannotations.Rmd’ --- re-building ‘v05-pRoloc-transfer-learning.Rmd’ using rmarkdown Quitting from lines 213-247 [hparprep] (v05-pRoloc-transfer-learning.Rmd) Error: processing vignette 'v05-pRoloc-transfer-learning.Rmd' failed with diagnostics: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable. Look at ?useEnsembl for details on how to try a mirror site. --- failed re-building ‘v05-pRoloc-transfer-learning.Rmd’ SUMMARY: processing the following file failed: ‘v05-pRoloc-transfer-learning.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 4 NOTEs See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/pRoloc.Rcheck/00check.log’ for details.