############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.15-data-experiment/R/library --no-vignettes --timings scRNAseq_2.9.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/scRNAseq.Rcheck’ * using R Under development (unstable) (2022-01-05 r81451) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scRNAseq/DESCRIPTION’ ... OK * this is package ‘scRNAseq’ version ‘2.9.2’ * package encoding: UTF-8 * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scRNAseq’ 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 ... WARNING Problems with news in ‘inst/NEWS.Rd’: inst/NEWS.Rd:35: unexpected section header '\section' inst/NEWS.Rd:51: unexpected section header '\section' inst/NEWS.Rd:59: unexpected section header '\section' inst/NEWS.Rd:67: unexpected section header '\section' inst/NEWS.Rd:70: unexpected END_OF_INPUT ' ' * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed HeOrganAtlasData 78.297 14.219 95.704 BhaduriOrganoidData 40.009 4.530 45.188 ZeiselNervousData 39.231 2.973 43.447 BacherTCellData 27.547 4.684 32.742 ErnstSpermatogenesisData 25.908 3.032 29.963 StoeckiusHashingData 25.875 1.453 31.743 JessaBrainData 23.268 3.818 28.467 GiladiHSCData 22.403 3.594 27.024 LunSpikeInData 18.113 1.513 22.417 LaMannoBrainData 17.408 0.928 20.479 BachMammaryData 16.499 1.325 19.203 ZhaoImmuneLiverData 15.303 1.420 17.367 BuettnerESCData 14.604 0.725 16.914 BunisHSPCData 13.659 1.352 15.862 TasicBrainData 12.828 0.941 16.578 NestorowaHSCData 12.374 1.368 15.740 ZilionisLungData 12.862 0.705 14.456 MessmerESCData 12.227 0.989 15.824 AztekinTailData 11.488 1.288 13.384 SegerstolpePancreasData 10.223 0.741 12.749 ReprocessedData 9.619 0.517 10.954 ShekharRetinaData 9.615 0.447 11.972 CampbellBrainData 9.005 0.600 10.064 KolodziejczykESCData 8.683 0.891 10.782 BaronPancreasData 8.595 0.824 10.351 KotliarovPBMCData 8.455 0.665 9.644 ZeiselBrainData 8.682 0.424 10.019 RichardTCellData 8.281 0.576 10.090 ChenBrainData 7.672 0.567 8.689 NowakowskiCortexData 7.793 0.407 9.198 HuCortexData 6.951 1.176 8.840 UsoskinBrainData 7.742 0.366 9.515 FletcherOlfactoryData 6.941 0.806 8.351 MairPBMCData 6.930 0.623 8.418 GrunPancreasData 6.735 0.395 7.868 XinPancreasData 6.827 0.192 7.870 MuraroPancreasData 5.913 0.673 8.414 MacoskoRetinaData 5.754 0.485 6.690 LedergorMyelomaData 5.596 0.304 6.345 HermannSpermatogenesisData 5.205 0.398 6.158 PaulHSCData 4.703 0.403 5.555 * 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: 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::NestorowaHSCData(remove.htseq = FALSE) 6. └─scRNAseq:::.define_location_from_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. └─scRNAseq:::.AnnotationHub() 9. └─AnnotationHub::AnnotationHub() 10. └─AnnotationHub::.Hub(...) 11. └─AnnotationHub:::.db_create_index(hub) 12. └─base::readRDS(index_path) [ FAIL 1 | WARN 37 | SKIP 0 | PASS 118 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection Execution halted * 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 ERROR, 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.15-data-experiment/meat/scRNAseq.Rcheck/00check.log’ for details.