Error in makeOrgPackageFromNCBI for Medicago truncatula
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Entering edit mode
@chiapellom-9116
Last seen 3.6 years ago
Italy

Dear all,

I did this:

makeOrgPackageFromNCBI(version = "0.1",
                       author = "Marco Chiapello <chiapello.m@gmail.com>",
                       maintainer = "Some One <so@someplace.org>",
                       outputDir = ".",
                       tax_id = "3880",
                       genus = "Medicago",
                       species = "truncatula")

And I get this output error:

If this is the 1st time you have run this function, it may take a long time (over an hour) to download needed files and assemble a 12 GB cache databse in the NCBIFilesDir directory.  Subsequent calls to this function should be faster (seconds).  The cache will try to rebuild once per day.
Getting data for gene2pubmed.gz
Loading required package: RCurl
Loading required package: bitops
extracting only data for our organism from : gene2pubmed
Getting data for gene2accession.gz
extracting only data for our organism from : gene2accession
Getting data for gene2refseq.gz
extracting only data for our organism from : gene2refseq
Getting data for gene2unigene
extracting only data for our organism from : gene2unigene
getting all data for our organism from : gene2unigene
Getting data for gene_info.gz
extracting only data for our organism from : gene_info
Getting data for gene2go.gz
extracting only data for our organism from : gene2go
Error in function (type, msg, asError = TRUE)  : FTP response timeout

Any idea how to fix it?

Thank you very much in advance,

Marco

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      tools     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] gridExtra_2.0.0 tidyr_0.3.1     ggplot2_1.0.1   HSAUR_1.3-7     cluster_2.0.3  
[6] mvtnorm_1.0-3   gss_2.1-5      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1      magrittr_1.5     MASS_7.3-44      munsell_0.4.2    colorspace_1.2-6
 [6] R6_2.1.1         stringr_1.0.0    plyr_1.8.3       dplyr_0.4.3      parallel_3.2.2  
[11] gtable_0.1.2     DBI_0.3.1        lazyeval_0.1.10  digest_0.6.8     assertthat_0.1  
[16] reshape2_1.4.1   labeling_0.3     stringi_1.0-1    scales_0.3.0     proto_0.3-10 
annotation annotationforge • 1.0k views
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Entering edit mode
@martin-morgan-1513
Last seen 7 days ago
United States

Not so much a fix (which looks like a network timeout issue), but for your version of Bioconductor (please edit your original post to include the output of sessionInfo()) this may be in AnnotationHub

> library(AnnotationHub)
> hub = AnnotationHub()
> query(hub, c("Medicago", "OrgDb"))
AnnotationHub with 1 record
# snapshotDate(): 2015-08-26 
# names(): AH48011
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Medicago truncatula
# $rdataclass: OrgDb
# $title: org.Medicago_truncatula.eg.sqlite
# $description: NCBI gene ID based annotations about Medicago_truncatula
# $taxonomyid: 3880
# $genome: NCBI genomes
# $sourcetype: NCBI/UniProt
# $sourceurl: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, ftp://ftp.uniprot.org/p...
# $sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: NCBI, Gene, Annotation 
# retrieve record with 'object[["AH48011"]]' 

and then

> orgdb = hub[["AH48011"]]
loading from cache '/home/mtmorgan/.AnnotationHub/54317'
> orgdb
OrgDb object:
| DBSCHEMAVERSION: 2.1
| DBSCHEMA: NOSCHEMA_DB
| ORGANISM: Medicago truncatula
| SPECIES: Medicago truncatula
| CENTRALID: GID
| Taxonomy ID: 3880
| Db type: OrgDb
| Supporting package: AnnotationDbi

Please see: help('select') for usage information

I'm not sure if there is a function to make this into a package; the underlying sqlite file is at AnnotationHub::cache(hub["AH48011"]).

 

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Entering edit mode

Dear Martin,

thank you for your comment.

My final goal is to use topGO package (or any other package) to do the functional enrichment. Do you know if I can use it after the way you suggested to me?

Thank you,

Marco

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