OrganismDbi 1.18.1
Biocore Data Team
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/OrganismDbi | | Branch: RELEASE_3_5 | | Last Commit: ba2d123 | | Last Changed Date: 2017-10-11 13:19:38 -0400 (Wed, 11 Oct 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK |  |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings OrganismDbi_1.18.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/OrganismDbi.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OrganismDbi/DESCRIPTION’ ... OK
* this is package ‘OrganismDbi’ version ‘1.18.1’
* 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 ‘OrganismDbi’ 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
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.biocAnnPackages’ ‘.extractPkgsAndCols’ ‘.gentlyExtractDbFiles’
‘.lookupDbNameFromKeytype’ ‘.mungeGraphData’ ‘.taxIdToOrgDb’
‘.taxIdToOrgDbName’ ‘.testGraphData’ ‘.testKeys’ ‘OrganismDb’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OrganismDbi-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeOrganismDbFromBiomart
> ### Title: Make a OrganismDb object from annotations available on a BioMart
> ### database
> ### Aliases: makeOrganismDbFromBiomart
>
> ### ** Examples
>
> ## Discover which datasets are available in the "ensembl" BioMart
> ## database:
> library(biomaRt)
> head(listDatasets(useMart("ensembl")))
dataset description
1 hfemale_gene_ensembl Naked mole-rat female genes (HetGla_female_1.0)
2 xtropicalis_gene_ensembl Xenopus genes (JGI 4.2)
3 cjacchus_gene_ensembl Marmoset genes (C_jacchus3.2.1)
4 cintestinalis_gene_ensembl C.intestinalis genes (KH)
5 jjaculus_gene_ensembl Lesser Egyptian jerboa genes (JacJac1.0)
6 tnigroviridis_gene_ensembl Tetraodon genes (TETRAODON 8.0)
version
1 HetGla_female_1.0
2 JGI 4.2
3 C_jacchus3.2.1
4 KH
5 JacJac1.0
6 TETRAODON 8.0
>
> ## Retrieving an incomplete transcript dataset for Human from the
> ## "ensembl" BioMart database:
> transcript_ids <- c(
+ "ENST00000013894",
+ "ENST00000268655",
+ "ENST00000313243",
+ "ENST00000435657",
+ "ENST00000384428",
+ "ENST00000478783"
+ )
> odb <- makeOrganismDbFromBiomart(transcript_ids=transcript_ids)
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> odb # note that these annotations match the GRCh38 genome assembly
OrganismDb Object:
# Includes GODb Object: GO.db
# With data about: Gene Ontology
# Includes OrgDb Object: org.Hs.eg.db
# Gene data about: Homo sapiens
# Taxonomy Id: 9606
# Includes TxDb Object: TxDb.Hsapiens.BioMart.ENSEMBLMARTENSEMBL.GRCh38.p10
# Transcriptome data about: Homo sapiens
# Based on genome:
# The OrgDb gene id ENSEMBL is mapped to the TxDb gene id GENEID .
>
> ## Now what if we want to use another mirror? We might make use of the
> ## new host argument. But wait! If we use biomaRt, we can see that
> ## this host has named the mart differently!
> listMarts(host="uswest.ensembl.org")
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://uswest.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Error in if (!grepl(x = registry, pattern = "^\n*<MartRegistry>")) { :
argument is of length zero
Calls: listMarts
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘OrganismDbi_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: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.5-bioc/meat/OrganismDbi.Rcheck/00check.log’
for details.