GenomicFeatures 1.0.10
Biocore Team c/o BioC user list
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/GenomicFeatures | | Last Changed Rev: 48832 / Revision: 49923 | | Last Changed Date: 2010-08-16 11:38:04 -0700 (Mon, 16 Aug 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | [ ERROR ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | ERROR | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | ERROR | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/GenomicFeatures.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.0.10'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GenomicFeatures' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* 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 examples ... ERROR
Running examples in 'GenomicFeatures-Ex.R' failed.
The error most likely occurred in:
> ### * makeTranscriptDbFromBiomart
>
> flush(stderr()); flush(stdout())
>
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeTranscriptDbFromBiomart
> ### Title: Making a TranscriptDb object from annotations available on a
> ### BioMart database
> ### Aliases: makeTranscriptDbFromBiomart
>
> ### ** Examples
>
> ## Discover which datasets are available in the "ensembl" and
> ## "plant_mart_5" BioMart databases:
> library(biomaRt)
> listDatasets(useMart("ensembl"))
dataset description
1 oanatinus_gene_ensembl Ornithorhynchus anatinus genes (OANA5)
2 tguttata_gene_ensembl Taeniopygia guttata genes (taeGut3.2.4)
3 cporcellus_gene_ensembl Cavia porcellus genes (cavPor3)
4 gaculeatus_gene_ensembl Gasterosteus aculeatus genes (BROADS1)
5 lafricana_gene_ensembl Loxodonta africana genes (loxAfr3)
6 mlucifugus_gene_ensembl Myotis lucifugus genes (myoLuc1)
7 hsapiens_gene_ensembl Homo sapiens genes (GRCh37)
8 choffmanni_gene_ensembl Choloepus hoffmanni genes (choHof1)
9 csavignyi_gene_ensembl Ciona savignyi genes (CSAV2.0)
10 fcatus_gene_ensembl Felis catus genes (CAT)
11 rnorvegicus_gene_ensembl Rattus norvegicus genes (RGSC3.4)
12 ggallus_gene_ensembl Gallus gallus genes (WASHUC2)
13 tbelangeri_gene_ensembl Tupaia belangeri genes (tupBel1)
14 xtropicalis_gene_ensembl Xenopus tropicalis genes (JGI4.1)
15 ecaballus_gene_ensembl Equus caballus genes (EquCab2)
16 cjacchus_gene_ensembl Callithrix jacchus genes (calJac3)
17 drerio_gene_ensembl Danio rerio genes (Zv8)
18 stridecemlineatus_gene_ensembl Spermophilus tridecemlineatus genes (speTri1)
19 tnigroviridis_gene_ensembl Tetraodon nigroviridis genes (TETRAODON8.0)
20 ttruncatus_gene_ensembl Tursiops truncatus genes (turTru1)
21 scerevisiae_gene_ensembl Saccharomyces cerevisiae genes (SGD1.01)
22 celegans_gene_ensembl Caenorhabditis elegans genes (WS210)
23 mmulatta_gene_ensembl Macaca mulatta genes (MMUL_1.0)
24 pvampyrus_gene_ensembl Pteropus vampyrus genes (pteVam1)
25 mdomestica_gene_ensembl Monodelphis domestica genes (monDom5)
26 vpacos_gene_ensembl Vicugna pacos genes (vicPac1)
27 acarolinensis_gene_ensembl Anolis carolinensis genes (AnoCar1.0)
28 tsyrichta_gene_ensembl Tarsius syrichta genes (tarSyr1)
29 ogarnettii_gene_ensembl Otolemur garnettii genes (otoGar1)
30 trubripes_gene_ensembl Takifugu rubripes genes (FUGU4.0)
31 dmelanogaster_gene_ensembl Drosophila melanogaster genes (BDGP5.13)
32 eeuropaeus_gene_ensembl Erinaceus europaeus genes (eriEur1)
33 mmurinus_gene_ensembl Microcebus murinus genes (micMur1)
34 olatipes_gene_ensembl Oryzias latipes genes (HdrR)
35 etelfairi_gene_ensembl Echinops telfairi genes (TENREC)
36 cintestinalis_gene_ensembl Ciona intestinalis genes (JGI2)
37 ptroglodytes_gene_ensembl Pan troglodytes genes (CHIMP2.1)
38 oprinceps_gene_ensembl Ochotona princeps genes (OchPri2.0)
39 ggorilla_gene_ensembl Gorilla gorilla genes (gorGor3)
40 dordii_gene_ensembl Dipodomys ordii genes (dipOrd1)
41 ppygmaeus_gene_ensembl Pongo pygmaeus abelii genes (PPYG2)
42 sscrofa_gene_ensembl Sus scrofa genes (Sscrofa9)
43 mmusculus_gene_ensembl Mus musculus genes (NCBIM37)
44 ocuniculus_gene_ensembl Oryctolagus cuniculus genes (oryCun2.0)
45 mgallopavo_gene_ensembl Meleagris gallopavo genes (UMD2)
46 saraneus_gene_ensembl Sorex araneus genes (sorAra1)
47 dnovemcinctus_gene_ensembl Dasypus novemcinctus genes (dasNov2)
48 pcapensis_gene_ensembl Procavia capensis genes (proCap1)
49 btaurus_gene_ensembl Bos taurus genes (Btau_4.0)
50 meugenii_gene_ensembl Macropus eugenii genes (Meug_1.0)
51 cfamiliaris_gene_ensembl Canis familiaris genes (CanFam_2.0)
version
1 OANA5
2 taeGut3.2.4
3 cavPor3
4 BROADS1
5 loxAfr3
6 myoLuc1
7 GRCh37
8 choHof1
9 CSAV2.0
10 CAT
11 RGSC3.4
12 WASHUC2
13 tupBel1
14 JGI4.1
15 EquCab2
16 calJac3
17 Zv8
18 speTri1
19 TETRAODON8.0
20 turTru1
21 SGD1.01
22 WS210
23 MMUL_1.0
24 pteVam1
25 monDom5
26 vicPac1
27 AnoCar1.0
28 tarSyr1
29 otoGar1
30 FUGU4.0
31 BDGP5.13
32 eriEur1
33 micMur1
34 HdrR
35 TENREC
36 JGI2
37 CHIMP2.1
38 OchPri2.0
39 gorGor3
40 dipOrd1
41 PPYG2
42 Sscrofa9
43 NCBIM37
44 oryCun2.0
45 UMD2
46 sorAra1
47 dasNov2
48 proCap1
49 Btau_4.0
50 Meug_1.0
51 CanFam_2.0
> listDatasets(useMart("plant_mart_5"))
Error in useMart("plant_mart_5") :
Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
Calls: listDatasets -> is -> useMart
Execution halted
* install options are ' --no-html'
* installing *source* package 'GenomicFeatures' ...
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
rbind, rep.int, table
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (GenomicFeatures)