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This page was generated on 2018-10-17 08:27:59 -0400 (Wed, 17 Oct 2018).
| Package 56/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AnnotationHubData 1.10.3 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: AnnotationHubData |
| Version: 1.10.3 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings AnnotationHubData_1.10.3.tar.gz |
| StartedAt: 2018-10-15 22:27:20 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 22:33:02 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 342.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AnnotationHubData.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings AnnotationHubData_1.10.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/AnnotationHubData.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (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 ‘1.10.3’ * 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 ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘BiocInstaller’ A package should be listed in only one of these fields. * 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 'library' or 'require' call to ‘BiocInstaller’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘GEOquery’ All declared Imports should be used. 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’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘Title’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘Description’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘BiocVersion’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘Genome’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘SourceType’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘SourceUrl’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘SourceVersion’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘Species’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘TaxonomyId’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘Coordinate_1_based’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘DataProvider’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘Maintainer’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘RDataClass’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘RDataDateAdded’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘RDataPath’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘DispatchClass’ makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible binding for global variable ‘Location_Prefix’ test_BioPaxImportPreparer_recipe: no visible binding for global variable ‘ahroot’ test_BioPaxImportPreparer_recipe: no visible binding for global variable ‘BiocVersion’ test_BioPaxImportPreparer_recipe: no visible global function definition for ‘checkTrue’ test_Inparanoid8ImportPreparer_recipe: no visible global function definition for ‘suppresWarnings’ test_Inparanoid8ImportPreparer_recipe: no visible binding for global variable ‘ahroot’ test_Inparanoid8ImportPreparer_recipe: no visible binding for global variable ‘BiocVersion’ test_Inparanoid8ImportPreparer_recipe: no visible global function definition for ‘checkTrue’ trackWithAuxiliaryTablesToGRanges: no visible binding for global variable ‘seqname’ Undefined global functions or variables: BiocVersion Coordinate_1_based DataProvider Description DispatchClass Genome Location_Prefix Maintainer RDataClass RDataDateAdded RDataPath SourceType SourceUrl SourceVersion Species TaxonomyId Title ahroot checkTrue results seqname specData suppresWarnings * 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 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.7-bioc/meat/AnnotationHubData.Rcheck/00check.log’ for details.
AnnotationHubData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL AnnotationHubData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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 version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, lengths, 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 [2018-10-15 22:30:52] Preparer Class: ChEAImportPreparer
complete!
INFO [2018-10-15 22:30:52] 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 [2018-10-15 22:30:57] Preparer Class: EnsemblGtfImportPreparer
complete!
INFO [2018-10-15 22:31:16] Preparer Class: EnsemblTwoBitPreparer
complete!
INFO [2018-10-15 22:32:18] 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 [2018-10-15 22:32:25] 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 [2018-10-15 22:32:32] Preparer Class: GencodeGffImportPreparer
getting file info: gencode.v23.2wayconspseudos.gff3.gz
getting file info: gencode.v23.annotation.gff3.gz
complete!
INFO [2018-10-15 22:32:39] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2018-10-15 22:32:39] Preparer Class: NCBIImportPreparer
looking up value for: 3708
looking up value for: 90675
looking up value for: 4232
looking up value for: 3635
looking up value for: 4097
looking up value for: 7962
complete!
INFO [2018-10-15 22:32:45] Preparer Class: RefNetImportPreparer
complete!
INFO [2018-10-15 22:32:46] Preparer Class: dbSNPVCFPreparer
complete!
RUNIT TEST PROTOCOL -- Mon Oct 15 22:33:00 2018
***********************************************
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
Warning message:
In value[[3L]](cond) : chea-background.zip: Service Unavailable
>
> proc.time()
user system elapsed
46.000 0.732 158.324
AnnotationHubData.Rcheck/AnnotationHubData-Ex.timings
| name | user | system | elapsed | |
| AnnotationHubMetadata-class | 0.004 | 0.000 | 0.004 | |
| ImportPreparer-class | 0.000 | 0.000 | 0.003 | |
| makeAnnotationHubMetadata | 0.000 | 0.004 | 0.006 | |
| makeEnsemblFasta | 0.000 | 0.000 | 0.001 | |
| makeGencodeFasta | 0.004 | 0.000 | 0.002 | |
| makeStandardOrgDbs | 0.000 | 0.004 | 0.004 | |
| updateResources | 0.004 | 0.000 | 0.004 | |
| upload_to_S3 | 0.000 | 0.000 | 0.001 | |