| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:35 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the AnnotationHub package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnnotationHub.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 58/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AnnotationHub 3.7.1 (landing page) Bioconductor Package Maintainer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: AnnotationHub |
| Version: 3.7.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings AnnotationHub_3.7.1.tar.gz |
| StartedAt: 2023-02-27 20:20:49 -0000 (Mon, 27 Feb 2023) |
| EndedAt: 2023-02-27 20:31:48 -0000 (Mon, 27 Feb 2023) |
| EllapsedTime: 659.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: AnnotationHub.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings AnnotationHub_3.7.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/AnnotationHub.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘AnnotationHub/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHub’ version ‘3.7.1’
* 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 ‘AnnotationHub’ 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 ... WARNING
'::' or ':::' imports not declared from:
‘CompoundDb’ ‘ensembldb’ ‘keras’
Unexported objects imported by ':::' calls:
‘BiocFileCache:::.get_tbl_rid’ ‘S4Vectors:::selectSome’
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 ... OK
* checking Rd files ... WARNING
checkRd: (5) AnnotationHub-class.Rd:134-142: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:151-154: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:155-158: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:163-166: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:167-171: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:172-178: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:179-213: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:215-217: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:219-221: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:223-225: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:234-238: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:239-243: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:244-250: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:251-272: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:273-281: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:282-287: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:288-293: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:300-304: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:305-309: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:310-321: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:322-325: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:326-329: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:330-337: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:338-345: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:346-351: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:358-362: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:363-367: \item in \describe must have non-empty label
* 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 ... ERROR
Running examples in ‘AnnotationHub-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AnnotationHub-objects
> ### Title: AnnotationHub objects and their related methods and functions
> ### Aliases: class:AnnotationHub AnnotationHub-class class:Hub Hub-class
> ### .Hub AnnotationHub refreshHub mcols,Hub-method cache cache,Hub-method
> ### cache,AnnotationHub-method cache<- cache<-,Hub-method hubUrl
> ### hubUrl,Hub-method hubCache hubCache,Hub-method hubDate
> ### hubDate,Hub-method package package,Hub-method removeCache isLocalHub
> ### isLocalHub,Hub-method isLocalHub<- isLocalHub<-,Hub-method
> ### possibleDates snapshotDate snapshotDate,Hub-method snapshotDate<-
> ### snapshotDate<-,Hub-method removeResources
> ### removeResources,missing-method removeResources,character-method
> ### dbconn,Hub-method dbfile,Hub-method .db_close recordStatus
> ### recordStatus,Hub-method length,Hub-method names,Hub-method
> ### fileName,Hub-method $,Hub-method [[,Hub,character,missing-method
> ### [[,Hub,numeric,missing-method [,Hub,character,missing-method
> ### [,Hub,logical,missing-method [,Hub,numeric,missing-method
> ### [<-,Hub,character,missing,Hub-method
> ### [<-,Hub,logical,missing,Hub-method [<-,Hub,numeric,missing,Hub-method
> ### subset,Hub-method query query,Hub-method display display,Hub-method
> ### as.list.Hub as.list,Hub-method c,Hub-method show,Hub-method
> ### show,AnnotationHubResource-method
> ### Keywords: classes methods
>
> ### ** Examples
>
> ## create an AnnotationHub object
> library(AnnotationHub)
> ah = AnnotationHub()
snapshotDate(): 2022-12-16
>
> ## Summary of available records
> ah
AnnotationHub with 67944 records
# snapshotDate(): 2022-12-16
# $dataprovider: Ensembl, BroadInstitute, UCSC, ftp://ftp.ncbi.nlm.nih.gov/g...
# $species: Homo sapiens, Mus musculus, Drosophila melanogaster, Bos taurus,...
# $rdataclass: GRanges, TwoBitFile, BigWigFile, EnsDb, Rle, OrgDb, ChainFile...
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH5012"]]'
title
AH5012 | Chromosome Band
AH5013 | STS Markers
AH5014 | FISH Clones
AH5015 | Recomb Rate
AH5016 | ENCODE Pilot
... ...
AH109476 | Ensembl 108 EnsDb for Xiphophorus couchianus
AH109477 | Ensembl 108 EnsDb for Xiphophorus maculatus
AH109478 | Ensembl 108 EnsDb for Xenopus tropicalis
AH109479 | Ensembl 108 EnsDb for Zonotrichia albicollis
AH109480 | Ensembl 108 EnsDb for Zalophus californianus
>
> ## Detail for a single record
> ah[1]
AnnotationHub with 1 record
# snapshotDate(): 2022-12-16
# names(): AH5012
# $dataprovider: UCSC
# $species: Homo sapiens
# $rdataclass: GRanges
# $rdatadateadded: 2013-03-26
# $title: Chromosome Band
# $description: GRanges object from UCSC track 'Chromosome Band'
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: UCSC track
# $sourceurl: rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/hg19/database...
# $sourcesize: NA
# $tags: c("cytoBand", "UCSC", "track", "Gene", "Transcript",
# "Annotation")
# retrieve record with 'object[["AH5012"]]'
>
> ## and what is the date we are using?
> snapshotDate(ah)
[1] "2022-12-16"
>
> ## how many resources?
> length(ah)
[1] 67944
>
> ## from which resources, is data available?
> head(sort(table(ah$dataprovider), decreasing=TRUE))
Ensembl
33054
BroadInstitute
18248
UCSC
11192
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
1871
Haemcode
945
FANTOM5,DLRP,IUPHAR,HPRD,STRING,SWISSPROT,TREMBL,ENSEMBL,CELLPHONEDB,BADERLAB,SINGLECELLSIGNALR,HOMOLOGENE
501
>
> ## from which species, is data available ?
> head(sort(table(ah$species),decreasing=TRUE))
Homo sapiens Mus musculus Drosophila melanogaster
26552 1796 458
Bos taurus Rattus norvegicus Pan troglodytes
331 325 317
>
> ## what web service and local cache does this AnnotationHub point to?
> hubUrl(ah)
[1] "https://annotationhub.bioconductor.org"
> hubCache(ah)
[1] "/home/biocbuild/.cache/R/AnnotationHub"
>
> ### Examples ###
>
> ## One can search the hub for multiple strings
> ahs2 <- query(ah, c("GTF", "77","Ensembl", "Homo sapiens"))
>
> ## information about the file can be retrieved using
> ahs2[1]
AnnotationHub with 1 record
# snapshotDate(): 2022-12-16
# names(): AH28812
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: GRanges
# $rdatadateadded: 2015-03-25
# $title: Homo_sapiens.GRCh38.77.gtf
# $description: Gene Annotation for Homo sapiens
# $taxonomyid: 9606
# $genome: GRCh38
# $sourcetype: GTF
# $sourceurl: ftp://ftp.ensembl.org/pub/release-77/gtf/homo_sapiens/Homo_sap...
# $sourcesize: 44454526
# $tags: c("GTF", "ensembl", "Gene", "Transcript", "Annotation")
# retrieve record with 'object[["AH28812"]]'
>
> ## one can further extract information from this show method
> ## like the sourceurl using:
> ahs2$sourceurl
[1] "ftp://ftp.ensembl.org/pub/release-77/gtf/homo_sapiens/Homo_sapiens.GRCh38.77.gtf.gz"
> ahs2$description
[1] "Gene Annotation for Homo sapiens"
> ahs2$title
[1] "Homo_sapiens.GRCh38.77.gtf"
>
> ## We can download a file by name like this (using a list semantic):
> gr <- ahs2[[1]]
loading from cache
require(“GenomicRanges”)
Error: failed to load resource
name: AH28812
title: Homo_sapiens.GRCh38.77.gtf
reason: error in evaluating the argument 'x' in selecting a method for function 'get': error reading from connection
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘AnnotationHub-HOWTO.Rmd’... OK
‘AnnotationHub.Rmd’ using ‘UTF-8’... OK
‘TroubleshootingTheCache.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/AnnotationHub.Rcheck/00check.log’
for details.
AnnotationHub.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL AnnotationHub ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘AnnotationHub’ ... ** 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 (AnnotationHub)
AnnotationHub.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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("AnnotationHub")
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, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
snapshotDate(): 2022-12-16
Using 'localHub=TRUE'
If offline, please also see BiocManager vignette section on offline use
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
require("xxx_foo")
RUNIT TEST PROTOCOL -- Mon Feb 27 20:28:28 2023
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 0
1 Test Suite :
AnnotationHub RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20
Number of errors: 0
Number of failures: 0
Warning messages:
1: call dbDisconnect() when finished working with a connection
2: download failed
hub path: 'bogus/url'
cache resource: 'AHInvalid : 5012'
reason: all(rtype == "web" | file.exists(fpath)) is not TRUE
>
> proc.time()
user system elapsed
52.641 5.819 295.467
AnnotationHub.Rcheck/AnnotationHub-Ex.timings
| name | user | system | elapsed |