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Package 159/389HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: GenomicFeatures
Version: 1.0.10
Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings GenomicFeatures_1.0.10.tar.gz
StartedAt: 2010-10-04 17:01:50 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 17:05:59 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 249.2 seconds
RetCode: 1
Status:  ERROR  
CheckDir: GenomicFeatures.Rcheck
Warnings: NA

Command output

* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/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 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

GenomicFeatures.Rcheck/00install.out:

* 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)

GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings:

nameusersystemelapsed
TranscriptDb-class0.680.210.91
extractTranscriptsFromGenome 68.39 5.37114.50
makeTranscriptDb0.190.020.20