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This page was generated on 2019-04-09 13:32:00 -0400 (Tue, 09 Apr 2019).
Package 62/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
AnnotationHubData 1.13.10 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: AnnotationHubData |
Version: 1.13.10 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AnnotationHubData_1.13.10.tar.gz |
StartedAt: 2019-04-08 23:14:33 -0400 (Mon, 08 Apr 2019) |
EndedAt: 2019-04-08 23:23:19 -0400 (Mon, 08 Apr 2019) |
EllapsedTime: 525.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AnnotationHubData.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AnnotationHubData_1.13.10.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AnnotationHubData.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AnnotationHubData/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AnnotationHubData’ version ‘1.13.10’ * 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 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 ... NOTE Missing object imported by a ':::' call: ‘AnnotationHub:::.db_connection’ Unexported object imported by a ':::' call: ‘OrganismDbi:::.packageTaxIds’ 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’ trackWithAuxiliaryTablesToGRanges: no visible binding for global variable ‘seqname’ Undefined global functions or variables: results seqname specData * 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 include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed validationFunctions 71.403 1.724 73.692 * 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 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/AnnotationHubData.Rcheck/00check.log’ for details.
AnnotationHubData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AnnotationHubData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘AnnotationHubData’ ... ** 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 * DONE (AnnotationHubData)
AnnotationHubData.Rcheck/tests/AnnotationHubData_unit_tests.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit) 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:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, append, as.data.frame, basename, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid INFO [2019-04-08 23:20:39] Preparer Class: ChEAImportPreparer complete! INFO [2019-04-08 23:20:40] 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 [2019-04-08 23:20:41] Preparer Class: EnsemblGtfImportPreparer ftp://ftp.ensembl.org/pub/release-84/gtf/ailuropoda_melanoleuca/ ftp://ftp.ensembl.org/pub/release-84/gtf/anas_platyrhynchos/ complete! INFO [2019-04-08 23:20:56] Preparer Class: EnsemblTwoBitPreparer complete! INFO [2019-04-08 23:21:18] Preparer Class: EpigenomeRoadMapPreparer trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/RRBS/FractionalMethylation_bigwig/' downloaded 13 KB trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/FractionalMethylation_bigwig/' downloaded 10 KB trying URL 'https://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/mCRF/FractionalMethylation_bigwig/' Content type 'text/html;charset=UTF-8' length 5015 bytes ================================================== downloaded 5015 bytes getting file info: E002_RRBS_FractionalMethylation.bigwig getting file info: E003_RRBS_FractionalMethylation.bigwig complete! INFO [2019-04-08 23:21:20] Preparer Class: GencodeFastaImportPreparer getting file info: gencode.v23.chr_patch_hapl_scaff.transcripts.fa.gz getting file info: gencode.v23.lncRNA_transcripts.fa.gz complete! INFO [2019-04-08 23:21:27] Preparer Class: GencodeGffImportPreparer getting file info: gencode.v23.2wayconspseudos.gff3.gz getting file info: gencode.v23.annotation.gff3.gz complete! INFO [2019-04-08 23:21:33] Preparer Class: Grasp2ImportPreparer complete! INFO [2019-04-08 23:21:33] Preparer Class: NCBIImportPreparer looking up value for: 3708 looking up value for: 3818 looking up value for: 90675 looking up value for: 3469 looking up value for: 7957 looking up value for: 4232 complete! INFO [2019-04-08 23:21:41] Preparer Class: RefNetImportPreparer complete! INFO [2019-04-08 23:21:42] 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://ftp1.nci.nih.gov/pub/PID/BioPAX/ ftp://ftp1.nci.nih.gov/pub/PID/BioPAX/ ftp://ftp1.nci.nih.gov/pub/PID/BioPAX/ RUNIT TEST PROTOCOL -- Mon Apr 8 23:23:13 2019 *********************************************** Number of test functions: 25 Number of errors: 0 Number of failures: 0 1 Test Suite : AnnotationHubData RUnit Tests - 25 test functions, 0 errors, 0 failures Number of test functions: 25 Number of errors: 0 Number of failures: 0 Warning message: In value[[3L]](cond) : chea-background.zip: Service Unavailable > > proc.time() user system elapsed 152.058 3.375 201.582
AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings
name | user | system | elapsed | |
AnnotationHubMetadata-class | 0.003 | 0.001 | 0.004 | |
ImportPreparer-class | 0.000 | 0.000 | 0.001 | |
makeAnnotationHubMetadata | 0.005 | 0.000 | 0.004 | |
makeEnsemblFasta | 0.000 | 0.000 | 0.001 | |
makeGencodeFasta | 0.001 | 0.001 | 0.001 | |
makeStandardOrgDbs | 0.001 | 0.000 | 0.000 | |
updateResources | 0.001 | 0.001 | 0.001 | |
upload_to_S3 | 0.001 | 0.000 | 0.000 | |
validationFunctions | 71.403 | 1.724 | 73.692 | |