GenomicFeatures 1.28.5
Bioconductor Package Maintainer
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/GenomicFeatures | | Branch: RELEASE_3_5 | | Last Commit: ba92381 | | Last Changed Date: 2017-09-19 02:07:55 -0400 (Tue, 19 Sep 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | TIMEOUT | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |  |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.28.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GenomicFeatures.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 ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.28.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’
‘AnnotationDbi’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GenomicFeatures’ 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 objects imported by ':::' calls:
‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
‘rtracklayer:::resourceDescription’ ‘rtracklayer:::ucscTableOutputs’
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
.writeMetadataFeatureTable: no visible global function definition for
‘packageDescription’
.write_metadata_table: no visible global function definition for
‘packageDescription’
Undefined global functions or variables:
packageDescription
Consider adding
importFrom("utils", "packageDescription")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘exonicParts’ ‘intronicParts’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ‘GenomicFeatures-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeTxDbFromBiomart
> ### Title: Make a TxDb object from annotations available on a BioMart
> ### database
> ### Aliases: makeTxDbFromBiomart getChromInfoFromBiomart
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## A. BASIC USAGE
> ## ---------------------------------------------------------------------
>
> ## We can use listDatasets() from the biomaRt package to list the
> ## datasets available in the "ENSEMBL_MART_ENSEMBL" BioMart database:
> library(biomaRt)
> listMarts(host="www.ensembl.org")
biomart version
1 ENSEMBL_MART_ENSEMBL Ensembl Genes 90
2 ENSEMBL_MART_MOUSE Mouse strains 90
3 ENSEMBL_MART_SNP Ensembl Variation 90
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 90
> mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
> datasets <- listDatasets(mart)
> head(datasets)
dataset description
1 amexicanus_gene_ensembl Cave fish genes (AstMex102)
2 oaries_gene_ensembl Sheep genes (Oar_v3.1)
3 pmarinus_gene_ensembl Lamprey genes (Pmarinus_7.0)
4 cjacchus_gene_ensembl Marmoset genes (C_jacchus3.2.1)
5 pformosa_gene_ensembl Amazon molly genes (Poecilia_formosa-5.1.2)
6 lafricana_gene_ensembl Elephant genes (Loxafr3.0)
version
1 AstMex102
2 Oar_v3.1
3 Pmarinus_7.0
4 C_jacchus3.2.1
5 Poecilia_formosa-5.1.2
6 Loxafr3.0
> subset(datasets, grepl("elegans", dataset, ignore.case=TRUE))
dataset description version
69 celegans_gene_ensembl Caenorhabditis elegans genes (WBcel235) WBcel235
>
> ## Retrieve the full transcript dataset for Worm:
> txdb1 <- makeTxDbFromBiomart(dataset="celegans_gene_ensembl")
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
> txdb1
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Caenorhabditis elegans
# Taxonomy ID: 6239
# Resource URL: www.ensembl.org:80
# BioMart database: ENSEMBL_MART_ENSEMBL
# BioMart database version: Ensembl Genes 90
# BioMart dataset: celegans_gene_ensembl
# BioMart dataset description: Caenorhabditis elegans genes (WBcel235)
# BioMart dataset version: WBcel235
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 58941
# exon_nrow: 175281
# cds_nrow: 131674
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2017-10-17 23:39:52 -0400 (Tue, 17 Oct 2017)
# GenomicFeatures version at creation time: 1.28.5
# RSQLite version at creation time: 2.0
# DBSCHEMAVERSION: 1.1
>
> ## Retrieve an incomplete transcript dataset for Human:
> transcript_ids <- c(
+ "ENST00000013894",
+ "ENST00000268655",
+ "ENST00000313243",
+ "ENST00000435657",
+ "ENST00000384428",
+ "ENST00000478783"
+ )
>
> if (interactive()) {
+ txdb2 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl",
+ transcript_ids=transcript_ids)
+ txdb2 # note that these annotations match the GRCh38 genome assembly
+ }
>
> ## ---------------------------------------------------------------------
> ## B. ACCESSING THE EnsemblGenomes MARTS
> ## ---------------------------------------------------------------------
>
> library(biomaRt)
>
> ## Note that BioMart is not currently available for Ensembl Bacteria.
>
> ## -------------
> ## Ensembl Fungi
> ## -------------
> mart <- useMart(biomart="fungal_mart", host="fungi.ensembl.org")
> datasets <- listDatasets(mart)
> datasets$dataset
[1] "pstriiformis_eg_gene" "aterreus_eg_gene"
[3] "vdahliaejr2_eg_gene" "ffujikuroi_eg_gene"
[5] "mlaricipopulina_eg_gene" "treesei_eg_gene"
[7] "cneoformans_eg_gene" "pgraminis_eg_gene"
[9] "fculmorum_eg_gene" "corbiculare_eg_gene"
[11] "ssclerotiorum_eg_gene" "mviolaceum_eg_gene"
[13] "aflavus_eg_gene" "sreilianum_eg_gene"
[15] "umaydis_eg_gene" "ggraminis_eg_gene"
[17] "bbassiana_eg_gene" "aclavatus_eg_gene"
[19] "anidulans_eg_gene" "soctosporus_eg_gene"
[21] "bgraminis_eg_gene" "agossypii_eg_gene"
[23] "afumigatus_eg_gene" "kpastoris_eg_gene"
[25] "afumigatusa1163_eg_gene" "scryophilus_eg_gene"
[27] "ztritici_eg_gene" "ncrassa_eg_gene"
[29] "ptriticirepentis_eg_gene" "vdahliae_eg_gene"
[31] "cgraminicola_eg_gene" "scerevisiae_eg_gene"
[33] "fpseudograminearum_eg_gene" "pgraminisug99_eg_gene"
[35] "ptriticina_eg_gene" "fsolani_eg_gene"
[37] "moryzae_eg_gene" "foxysporum_eg_gene"
[39] "tvirens_eg_gene" "fverticillioides_eg_gene"
[41] "pnodorum_eg_gene" "bcinerea_eg_gene"
[43] "fgraminearum_eg_gene" "mpoae_eg_gene"
[45] "chigginsianum_eg_gene" "ylipolytica_eg_gene"
[47] "aniger_eg_gene" "pteres_eg_gene"
[49] "sjaponicus_eg_gene" "lmaculans_eg_gene"
[51] "spombe_eg_gene" "cgloeosporioides_eg_gene"
[53] "dseptosporum_eg_gene" "tmelanosporum_eg_gene"
[55] "aoryzae_eg_gene" "nfischeri_eg_gene"
> yeast_txdb <- makeTxDbFromBiomart(biomart="fungal_mart",
+ dataset="scerevisiae_eg_gene",
+ host="fungi.ensembl.org")
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
> yeast_txdb
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Saccharomyces cerevisiae
# Taxonomy ID: 4932
# Resource URL: fungi.ensembl.org:80
# BioMart database: fungal_mart
# BioMart database version: Ensembl Fungi Genes 37
# BioMart dataset: scerevisiae_eg_gene
# BioMart dataset description: Saccharomyces cerevisiae genes (R64-1-1)
# BioMart dataset version: R64-1-1
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 7445
# exon_nrow: 7872
# cds_nrow: 7034
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2017-10-17 23:40:14 -0400 (Tue, 17 Oct 2017)
# GenomicFeatures version at creation time: 1.28.5
# RSQLite version at creation time: 2.0
# DBSCHEMAVERSION: 1.1
>
> ## Note that the dataset for Yeast on Ensembl Fungi is not necessarily
> ## the same as on the main Ensembl database:
> yeast_txdb0 <- makeTxDbFromBiomart(dataset="scerevisiae_gene_ensembl")
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
> all(transcripts(yeast_txdb0) %in% transcripts(yeast_txdb))
[1] TRUE
> all(transcripts(yeast_txdb) %in% transcripts(yeast_txdb0))
[1] FALSE
>
> ## ---------------
> ## Ensembl Metazoa
> ## ---------------
> mart <- useMart(biomart="metazoa_mart", host="metazoa.ensembl.org")
> datasets <- listDatasets(mart)
> datasets$dataset
[1] "tcastaneum_eg_gene" "dgrimshawi_eg_gene"
[3] "rprolixus_eg_gene" "sratti_eg_gene"
[5] "aqueenslandica_eg_gene" "phumanus_eg_gene"
[7] "bmori_eg_gene" "cjaponica_eg_gene"
[9] "dpulex_eg_gene" "turticae_eg_gene"
[11] "dwillistoni_eg_gene" "iscapularis_eg_gene"
[13] "apisum_eg_gene" "dyakuba_eg_gene"
[15] "celegans_eg_gene" "bantarctica_eg_gene"
[17] "acephalotes_eg_gene" "aaegypti_eg_gene"
[19] "tadhaerens_eg_gene" "obimaculoides_eg_gene"
[21] "ppacificus_eg_gene" "tkitauei_eg_gene"
[23] "dsechellia_eg_gene" "dsimulans_eg_gene"
[25] "spurpuratus_eg_gene" "amellifera_eg_gene"
[27] "aglabripennis_eg_gene" "dmelanogaster_eg_gene"
[29] "dplexippus_eg_gene" "cbriggsae_eg_gene"
[31] "mscalaris_eg_gene" "dananassae_eg_gene"
[33] "ovolvulus_eg_gene" "smansoni_eg_gene"
[35] "agambiae_eg_gene" "cquinquefasciatus_eg_gene"
[37] "smimosarum_eg_gene" "dvirilis_eg_gene"
[39] "tspiralis_eg_gene" "bmalayi_eg_gene"
[41] "lanatina_eg_gene" "bimpatiens_eg_gene"
[43] "hmelpomene_eg_gene" "cbrenneri_eg_gene"
[45] "mdestructor_eg_gene" "znevadensis_eg_gene"
[47] "cgigas_eg_gene" "dpersimilis_eg_gene"
[49] "derecta_eg_gene" "cremanei_eg_gene"
[51] "adarlingi_eg_gene" "cteleta_eg_gene"
[53] "nvitripennis_eg_gene" "lloa_eg_gene"
[55] "sinvicta_eg_gene" "lcuprina_eg_gene"
[57] "hrobusta_eg_gene" "dpseudoobscura_eg_gene"
[59] "mcinxia_eg_gene" "mleidyi_eg_gene"
[61] "smaritima_eg_gene" "sscabiei_eg_gene"
[63] "nvectensis_eg_gene" "lsalmonis_eg_gene"
[65] "lgigantea_eg_gene" "avaga_eg_gene"
[67] "dmojavensis_eg_gene" "dponderosae_eg_gene"
> worm_txdb <- makeTxDbFromBiomart(biomart="metazoa_mart",
+ dataset="celegans_eg_gene",
+ host="metazoa.ensembl.org")
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
> worm_txdb
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Caenorhabditis elegans
# Taxonomy ID: 6239
# Resource URL: metazoa.ensembl.org:80
# BioMart database: metazoa_mart
# BioMart database version: Ensembl Metazoa Genes 37
# BioMart dataset: celegans_eg_gene
# BioMart dataset description: Caenorhabditis elegans genes (WBcel235)
# BioMart dataset version: WBcel235
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 58941
# exon_nrow: 175281
# cds_nrow: 131674
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2017-10-17 23:41:42 -0400 (Tue, 17 Oct 2017)
# GenomicFeatures version at creation time: 1.28.5
# RSQLite version at creation time: 2.0
# DBSCHEMAVERSION: 1.1
>
> ## Note that even if the dataset for Worm on Ensembl Metazoa contains
> ## the same transcript as on the main Ensembl database, the transcript
> ## type might be annotated with slightly different terms (e.g. antisense
> ## vs antisense_RNA):
> filter <- list(tx_name="Y71G12B.44")
> transcripts(worm_txdb, filter=filter, columns=c("tx_name", "tx_type"))
GRanges object with 1 range and 2 metadata columns:
seqnames ranges strand | tx_name tx_type
<Rle> <IRanges> <Rle> | <character> <character>
[1] I [1692352, 1693675] + | Y71G12B.44 antisense
-------
seqinfo: 7 sequences (1 circular) from an unspecified genome
> transcripts(txdb1, filter=filter, columns=c("tx_name", "tx_type"))
GRanges object with 1 range and 2 metadata columns:
seqnames ranges strand | tx_name tx_type
<Rle> <IRanges> <Rle> | <character> <character>
[1] I [1692352, 1693675] + | Y71G12B.44 antisense_RNA
-------
seqinfo: 7 sequences (1 circular) from an unspecified genome
>
> ## --------------
> ## Ensembl Plants
> ## --------------
> mart <- useMart(biomart="plants_mart", host="plants.ensembl.org")
> datasets <- listDatasets(mart)
> datasets[ , 1:2]
dataset description
1 atauschii_eg_gene Aegilops tauschii genes (ASM34733v1)
2 obrachyantha_eg_gene Oryza brachyantha genes (Oryza_brachyantha.v1.4b)
3 ptrichocarpa_eg_gene Populus trichocarpa genes (JGI2.0)
4 ppersica_eg_gene Prunus persica genes (Prupe1_0)
5 stuberosum_eg_gene Solanum tuberosum genes (SolTub_3.0)
6 sitalica_eg_gene Setaria italica genes (JGIv2.0)
7 slycopersicum_eg_gene Solanum lycopersicum genes (SL2.50)
8 onivara_eg_gene Oryza nivara genes (AWHD00000000)
9 ppatens_eg_gene Physcomitrella patens genes (ASM242v1)
10 gmax_eg_gene Glycine max genes (V1.0)
11 sbicolor_eg_gene Sorghum bicolor genes (Sorghum_bicolor_v2)
12 bdistachyon_eg_gene Brachypodium distachyon genes (v1.0)
13 lperrieri_eg_gene Leersia perrieri genes (Lperr_V1.4)
14 opunctata_eg_gene Oryza punctata genes (AVCL00000000)
15 oindica_eg_gene Oryza sativa Indica genes (ASM465v1)
16 smoellendorffii_eg_gene Selaginella moellendorffii genes (v1.0)
17 gsulphuraria_eg_gene Galdieria sulphuraria genes (ASM34128v1)
18 oglumaepatula_eg_gene Oryza glumaepatula genes (ALNU02000000)
19 obarthii_eg_gene Oryza barthii genes (O.barthii_v1)
20 osativa_eg_gene Oryza sativa Japonica genes (IRGSP-1.0)
21 olucimarinus_eg_gene Ostreococcus lucimarinus genes (ASM9206v1)
22 hvulgare_eg_gene Hordeum vulgare genes (IBSC v2)
23 boleracea_eg_gene Brassica oleracea genes (v2.1)
24 bnapus_eg_gene Brassica napus genes (AST_PRJEB5043_v1)
25 omeridionalis_eg_gene Oryza meridionalis genes (Oryza_meridionalis_v1.3)
26 alyrata_eg_gene Arabidopsis lyrata genes (v.1.0)
27 ccrispus_eg_gene Chondrus crispus genes (ASM35022v2)
28 orufipogon_eg_gene Oryza rufipogon genes (OR_W1943)
29 taestivum_eg_gene Triticum aestivum genes (TGACv1)
30 brapa_eg_gene Brassica rapa genes (IVFCAASv1)
31 vvinifera_eg_gene Vitis vinifera genes (IGGP_12x)
32 zmays_eg_gene Zea mays genes (B73 RefGen_v4)
33 mtruncatula_eg_gene Medicago truncatula genes (MedtrA17_4.0)
34 atrichopoda_eg_gene Amborella trichopoda genes (AMTR1.0)
35 bvulgaris_eg_gene Beta vulgaris subsp. vulgaris genes (RefBeet-1.2.2)
36 creinhardtii_eg_gene Chlamydomonas reinhardtii genes (v3.1)
37 ccapsularis_eg_gene Corchorus capsularis genes (CCACVL1_1.0)
38 olongistaminata_eg_gene Oryza longistaminata genes (O_longistaminata_v1.0)
39 tpratense_eg_gene Trifolium pratense genes (Trpr)
40 cmerolae_eg_gene Cyanidioschyzon merolae genes (ASM9120v1)
41 oglaberrima_eg_gene Oryza glaberrima genes (AGI1.1)
42 tcacao_eg_gene Theobroma cacao genes (Theobroma_cacao_20110822)
43 macuminata_eg_gene Musa acuminata genes (MA1)
44 turartu_eg_gene Triticum urartu genes (ASM34745v1)
45 athaliana_eg_gene Arabidopsis thaliana genes (TAIR10)
> athaliana_txdb <- makeTxDbFromBiomart(biomart="plants_mart",
+ dataset="athaliana_eg_gene",
+ host="plants.ensembl.org")
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
> athaliana_txdb
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Arabidopsis thaliana
# Taxonomy ID: 3702
# Resource URL: plants.ensembl.org:80
# BioMart database: plants_mart
# BioMart database version: Ensembl Plants Genes 37
# BioMart dataset: athaliana_eg_gene
# BioMart dataset description: Arabidopsis thaliana genes (TAIR10)
# BioMart dataset version: TAIR10
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 55157
# exon_nrow: 198031
# cds_nrow: 156751
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2017-10-17 23:43:09 -0400 (Tue, 17 Oct 2017)
# GenomicFeatures version at creation time: 1.28.5
# RSQLite version at creation time: 2.0
# DBSCHEMAVERSION: 1.1
>
> ## ----------------
> ## Ensembl Protists
> ## ----------------
> mart <- useMart(biomart="protist_mart", host="protists.ensembl.org")
> datasets <- listDatasets(mart)
> datasets$dataset
[1] "pramorum_eg_gene" "pvivax_eg_gene"
[3] "piwayamai_eg_gene" "ddiscoideum_eg_gene"
[5] "glamblia_eg_gene" "lmajor_eg_gene"
[7] "pknowlesi_eg_gene" "tgondii_eg_gene"
[9] "plateralis_eg_gene" "alaibachii_eg_gene"
[11] "pchabaudi_eg_gene" "harabidopsidis_eg_gene"
[13] "pultimum_eg_gene" "paphanidermatum_eg_gene"
[15] "tthermophila_eg_gene" "pkernoviae_eg_gene"
[17] "pfalciparum_eg_gene" "pberghei_eg_gene"
[19] "parrhenomanes_eg_gene" "ehistolytica_eg_gene"
[21] "bnatans_eg_gene" "psojae_eg_gene"
[23] "ptetraurelia_eg_gene" "tpseudonana_eg_gene"
[25] "pirregulare_eg_gene" "gtheta_eg_gene"
[27] "ptricornutum_eg_gene" "pinfestans_eg_gene"
[29] "pvexans_eg_gene" "ehuxleyi_eg_gene"
[31] "pparasitica_eg_gene" "tbrucei_eg_gene"
> tgondii_txdb <- makeTxDbFromBiomart(biomart="protist_mart",
+ dataset="tgondii_eg_gene",
+ host="protists.ensembl.org")
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning in .normarg_makeTxDb_chrominfo(chrominfo, transcripts$tx_chrom, :
chromosome lengths and circularity flags are not available for this TxDb object
OK
> tgondii_txdb
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Toxoplasma gondii
# Taxonomy ID: 5811
# Resource URL: protists.ensembl.org:80
# BioMart database: protist_mart
# BioMart database version: Ensembl Protists Genes 37
# BioMart dataset: tgondii_eg_gene
# BioMart dataset description: Toxoplasma gondii genes (ToxoDB-7.1)
# BioMart dataset version: ToxoDB-7.1
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 8172
# exon_nrow: 43027
# cds_nrow: 42491
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2017-10-17 23:43:33 -0400 (Tue, 17 Oct 2017)
# GenomicFeatures version at creation time: 1.28.5
# RSQLite version at creation time: 2.0
# DBSCHEMAVERSION: 1.1
>
> ## ---------------------------------------------------------------------
> ## C. USING AN Ensembl MIRROR
> ## ---------------------------------------------------------------------
>
> ## You can use the 'host' argument to access the "ENSEMBL_MART_ENSEMBL"
> ## BioMart database at a mirror (e.g. at uswest.ensembl.org). A gotcha
> ## when doing this is that the name of the database on the mirror might
> ## be different! We can check this with listMarts() from the biomaRt
> ## package:
> listMarts(host="useast.ensembl.org")
biomart version
1 ENSEMBL_MART_ENSEMBL Ensembl Genes 90
2 ENSEMBL_MART_MOUSE Mouse strains 90
3 ENSEMBL_MART_SNP Ensembl Variation 90
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 90
>
> ## Therefore in addition to setting 'host' to "uswest.ensembl.org" we
> ## might also need to specify the 'biomart' argument:
> if (interactive()) {
+ txdb3 <- makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
+ dataset="hsapiens_gene_ensembl",
+ transcript_ids=transcript_ids,
+ host="useast.ensembl.org")
+ txdb3
+ }
>
> ## ---------------------------------------------------------------------
> ## D. USING FILTERS
> ## ---------------------------------------------------------------------
>
> ## We can use listFilters() from the biomaRt package to get valid filter
> ## names:
> mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",
+ dataset="hsapiens_gene_ensembl",
+ host="www.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://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Error in if (!grepl(x = registry, pattern = "^\n*<MartRegistry>")) { :
argument is of length zero
Calls: useMart -> listMarts
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.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 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.