Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 |
Package 75/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AnnotationHubData 1.36.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the AnnotationHubData package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnnotationHubData.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: AnnotationHubData |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AnnotationHubData_1.36.0.tar.gz |
StartedAt: 2024-12-20 11:13:09 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 11:25:06 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 717.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: AnnotationHubData.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AnnotationHubData_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/AnnotationHubData.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AnnotationHubData/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AnnotationHubData’ version ‘1.36.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘AnnotationHubData’ 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 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘AzureStor’ ‘stringr’ 'loadNamespace' or 'requireNamespace' call not declared from: ‘AzureStor’ Missing objects imported by ':::' calls: ‘AnnotationHub:::.db_connection’ ‘GenomicFeatures:::.makeUCSCChrominfo’ ‘GenomicFeatures:::lookup_organism_by_UCSC_genome’ Unexported objects imported by ':::' calls: ‘BiocCheck:::getParent’ ‘GenomeInfoDb:::check_tax_id’ ‘GenomeInfoDb:::fetch_species_index_from_Ensembl_FTP’ ‘GenomeInfoDb:::lookup_organism_by_tax_id’ ‘GenomeInfoDb:::lookup_tax_id_by_organism’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .NCBIMetadataFromUrl: no visible binding for global variable ‘results’ .NCBIMetadataFromUrl: no visible binding for global variable ‘specData’ .makeComplexGR: no visible binding for global variable ‘seqname’ needToRerunNonStandardOrgDb: no visible binding for global variable ‘results’ needToRerunNonStandardOrgDb: no visible binding for global variable ‘specData’ oldAWSS3_needToRerunNonStandardOrgDb: no visible binding for global variable ‘results’ oldAWSS3_needToRerunNonStandardOrgDb: no visible binding for global variable ‘specData’ trackWithAuxiliaryTablesToGRanges: no visible binding for global variable ‘seqname’ Undefined global functions or variables: results seqname specData * checking Rd files ... NOTE checkRd: (-1) makeAnnotationHubMetadata.Rd:31-36: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAnnotationHubMetadata.Rd:40-187: Lost braces in \itemize; meant \describe ? * 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 include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed validationFunctions 98.761 1.172 100.097 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘AnnotationHubData_unit_tests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/AnnotationHubData.Rcheck/00check.log’ for details.
AnnotationHubData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AnnotationHubData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘AnnotationHubData’ ... ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (AnnotationHubData)
AnnotationHubData.Rcheck/tests/AnnotationHubData_unit_tests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("AnnotationHubData") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname INFO [2024-12-20 11:20:58] Preparer Class: ChEAImportPreparer complete! INFO [2024-12-20 11:20:58] Preparer Class: EncodeImportPreparer getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878CellTotal.broadPeak.gz getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongnonpolya.broadPeak.gz getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongpolya.broadPeak.gz getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878NucleolusTotal.broadPeak.gz getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878NucleusLongnonpolya.broadPeak.gz complete! INFO [2024-12-20 11:21:05] Preparer Class: Grasp2ImportPreparer complete! INFO [2024-12-20 11:21:05] Preparer Class: NCBIImportPreparer looking up value for: 495146 looking up value for: 4565 looking up value for: 214697 looking up value for: 3708 looking up value for: 3818 looking up value for: 106335 AZURE_SAS_TOKEN environment variable is not set. Regenerating all files. Processing 8 files. complete! INFO [2024-12-20 11:21:16] Preparer Class: RefNetImportPreparer complete! INFO [2024-12-20 11:21:17] Preparer Class: dbSNPVCFPreparer ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_1.0/2016/ complete! Found invalid DispatchClass. [1] "somethingNotThere" For currently available DispatchClass run 'AnnotationHub::DispatchClassList()' Found invalid DispatchClass. [1] "somethingNotThere" For currently available DispatchClass run 'AnnotationHub::DispatchClassList()' Loading valid species information. ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/ ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/ ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/ RUNIT TEST PROTOCOL -- Fri Dec 20 11:24:54 2024 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 0 1 Test Suite : AnnotationHubData RUnit Tests - 20 test functions, 0 errors, 0 failures Number of test functions: 20 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 184.325 2.742 299.377
AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings
name | user | system | elapsed | |
AnnotationHubMetadata-class | 0.002 | 0.001 | 0.004 | |
ImportPreparer-class | 0.000 | 0.001 | 0.001 | |
makeAnnotationHubMetadata | 0.004 | 0.000 | 0.004 | |
makeEnsemblFasta | 0.000 | 0.000 | 0.001 | |
makeGencodeFasta | 0.000 | 0.001 | 0.000 | |
makeStandardOrgDbs | 0.000 | 0.001 | 0.001 | |
updateResources | 0.001 | 0.001 | 0.001 | |
upload_to_S3 | 0.000 | 0.000 | 0.001 | |
upload_to_azure | 0.001 | 0.000 | 0.000 | |
validationFunctions | 98.761 | 1.172 | 100.097 | |