GenomicFeatures 1.20.6
Bioconductor Package Maintainer
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GenomicFeatures | | Last Changed Rev: 108989 / Revision: 109384 | | Last Changed Date: 2015-09-29 23:24:53 -0700 (Tue, 29 Sep 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | ERROR | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.20.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.20.6’
* 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 ... [16s/16s] 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
'library' or 'require' calls in package code:
‘FDb.UCSC.tRNAs’ ‘mirbase.db’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': ‘AnnotationDbi:::dbconn’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘AnnotationDbi:::.colsArgumentWarning’
‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.resort’
‘AnnotationDbi:::.testForValidKeytype’
‘AnnotationDbi:::.testSelectArgs’ ‘AnnotationDbi:::.valid.colnames’
‘AnnotationDbi:::.valid.metadata.table’
‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’
‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’
‘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
.microRNAs: no visible global function definition for ‘mirbase_dbconn’
supportedMiRBaseBuildValues: no visible global function definition for
‘toTable’
supportedMiRBaseBuildValues: no visible binding for global variable
‘mirbaseSPECIES’
* checking Rd files ... NOTE
prepare_Rd: makeTxDbFromGRanges.Rd:38-39: Dropping empty section \details
* 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 sizes of PDF files under ‘inst/doc’ ... 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
> ### makeTranscriptDbFromBiomart
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## A. BASIC USAGE
> ## ---------------------------------------------------------------------
>
> ## We can use listDatasets() from the biomaRt package to list the
> ## datasets available in the "ensembl" BioMart database:
> library(biomaRt)
> head(listDatasets(useMart("ensembl")))
dataset description
1 oanatinus_gene_ensembl Ornithorhynchus anatinus genes (OANA5)
2 cporcellus_gene_ensembl Cavia porcellus genes (cavPor3)
3 gaculeatus_gene_ensembl Gasterosteus aculeatus genes (BROADS1)
4 lafricana_gene_ensembl Loxodonta africana genes (loxAfr3)
5 itridecemlineatus_gene_ensembl Ictidomys tridecemlineatus genes (spetri2)
6 choffmanni_gene_ensembl Choloepus hoffmanni genes (choHof1)
version
1 OANA5
2 cavPor3
3 BROADS1
4 loxAfr3
5 spetri2
6 choHof1
>
> ## 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
# Resource URL: www.biomart.org:80
# BioMart database: ensembl
# BioMart database version: ENSEMBL GENES 81 (SANGER UK)
# 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: 57834
# exon_nrow: 173506
# cds_nrow: 131562
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-10-09 02:24:25 -0700 (Fri, 09 Oct 2015)
# GenomicFeatures version at creation time: 1.20.6
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
>
> ## Retrieve an incomplete transcript dataset for Human:
> transcript_ids <- c(
+ "ENST00000013894",
+ "ENST00000268655",
+ "ENST00000313243",
+ "ENST00000435657",
+ "ENST00000384428",
+ "ENST00000478783"
+ )
> txdb2 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl",
+ 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
> txdb2 # note that these annotations match the GRCh38 genome assembly
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Homo sapiens
# Resource URL: www.biomart.org:80
# BioMart database: ensembl
# BioMart database version: ENSEMBL GENES 81 (SANGER UK)
# BioMart dataset: hsapiens_gene_ensembl
# BioMart dataset description: Homo sapiens genes (GRCh38.p3)
# BioMart dataset version: GRCh38.p3
# Full dataset: no
# miRBase build ID: NA
# transcript_nrow: 6
# exon_nrow: 56
# cds_nrow: 48
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-10-09 02:24:41 -0700 (Fri, 09 Oct 2015)
# GenomicFeatures version at creation time: 1.20.6
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
>
> ## ---------------------------------------------------------------------
> ## B. USING A HOST OTHER THAN www.biomart.org
> ## ---------------------------------------------------------------------
>
> ## A typical use case is to access the "ensembl" BioMart database on a
> ## mirror e.g. on uswest.ensembl.org. A gotcha when doing this is that
> ## the name of the database on the mirror can be different! We can check
> ## this with listMarts() from the biomaRt package:
> listMarts(host="uswest.ensembl.org")
biomart version
1 ENSEMBL_MART_ENSEMBL Ensembl Genes 82
2 ENSEMBL_MART_SNP Ensembl Variation 82
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 82
4 ENSEMBL_MART_VEGA Vega 62
5 pride PRIDE (EBI UK)
>
> ## Therefore, in addition to setting 'host' to "uswest.ensembl.org" we
> ## must also change the name passed to the 'biomart' argument:
> txdb3 <- makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
+ dataset="hsapiens_gene_ensembl",
+ transcript_ids=transcript_ids,
+ host="uswest.ensembl.org")
Download and preprocess the 'transcripts' data frame ... Error in getBM(attributes, filters = bm_filters, values = bm_values, ...) :
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_82: DBI connect('database=ensembl_mart_82;host=martdb.local.cloud.local;port=3306','ensro',...) failed: Unknown database 'ensembl_mart_82' at /ensemblweb/www/www_82/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
Calls: makeTxDbFromBiomart -> .makeBiomartTranscripts -> .getBM2 -> getBM
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘GenomicFeatures_unit_tests.R’ [99s/113s]
[99s/114s] 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, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.
* installing *source* package ‘GenomicFeatures’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (GenomicFeatures)