Hello,
I wanted to retrieve Annotation information of Ustilago maydis using the bioconductor package since it was not available at database list of AnnotationHub. But I came across with an Error such as:
processing gene2pubmed
processing gene_info: chromosomes
processing gene_info: description
processing alias data
processing refseq data
processing accession data
processing GO data
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'lookup_tax_id_by_organism' not found
Calls: makeOrgPackageFromNCBI ... unlist -> lapply -> lapply -> match.fun -> ::: -> get
In addition: Warning messages:
1: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
2: call dbDisconnect() when finished working with a connection
3: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
4: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
5: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
6: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
7: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
8: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
9: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Execution halted
The R script was:
#!/usr/bin/env Rscript
library("AnnotationForge", lib.loc="/scratch/lzeo/anaconda3/lib/R/library")
makeOrgPackageFromNCBI(version ="0.1", author ="Leo Zeo leozeo@gmail.com", maintainer="Leo Zeo", outputDir = "/scratch/lzeo/anaconda3/lib/R/library", tax_id = "237631",genus = "Ustilago", species = "maydis")
Looking for the positive solution from the author.
Thank You!
Thanks for the reply.
Do you mean by this package installation https://anaconda.org/bioconda/bioconductor-genomeinfodb ?
or shall I contact anaconda?
I don't know anything about bioconda, so can't help you there. If that's how you install GenomeInfoDb using bioconda, then yes, that's what I mean. Also you should ensure that you have the latest version of R/BioC, which again I have no idea how you divine that using bioconda. They are a completely different group, unaffiliated with Bioconductor, so really if you have questions about their stuff you should ask where ever one asks about that.
Hello James,
I did installed GenomeInfoDb and here is the error:
getting data for gene2pubmed.gz
extracting data for our organism from : gene2pubmed
getting data for gene2accession.gz
extracting data for our organism from : gene2accession
getting data for gene2refseq.gz
extracting data for our organism from : gene2refseq
getting data for gene_info.gz
rebuilding the cache
extracting data for our organism from : gene_info
getting data for gene2go.gz
rebuilding the cache
extracting data for our organism from : gene2go
processing gene2pubmed
processing gene_info: chromosomes
processing gene_info: description
processing alias data
processing refseq data
processing accession data
processing GO data
Error in result_create(conn@ptr, statement) : no such table: altGO_date
Calls: makeOrgPackageFromNCBI ... new -> initialize -> initialize -> result_create -> .Call
In addition: Warning messages:
1: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
2: call dbDisconnect() when finished working with a connection
3: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
4: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
5: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
6: In result_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Execution halted
As I mentioned above it seems you have an old R/Bioc installation. On a current version, this is what I get
> makeOrgPackageFromNCBI("0.0.1","me <me@mine.org>", "me", tax_id="237631", genus = "Ustilago",species = "maydis") If files are not cached locally this may take awhile to 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. preparing data from NCBI ... starting download for [1] gene2pubmed.gz [2] gene2accession.gz [3] gene2refseq.gz [4] gene_info.gz [5] gene2go.gz getting data for gene2pubmed.gz rebuilding the cache extracting data for our organism from : gene2pubmed getting data for gene2accession.gz rebuilding the cache extracting data for our organism from : gene2accession getting data for gene2refseq.gz rebuilding the cache extracting data for our organism from : gene2refseq getting data for gene_info.gz rebuilding the cache extracting data for our organism from : gene_info getting data for gene2go.gz rebuilding the cache extracting data for our organism from : gene2go processing gene2pubmed processing gene_info: chromosomes processing gene_info: description processing alias data processing refseq data processing accession data processing GO data Please be patient while we work out which organisms can be annotated with ensembl IDs. making the OrgDb package ... Populating genes table: genes table filled Populating pubmed table: pubmed table filled Populating chromosomes table: chromosomes table filled Populating gene_info table: gene_info table filled Populating entrez_genes table: entrez_genes table filled Populating alias table: alias table filled Populating refseq table: refseq table filled Populating accessions table: accessions table filled Populating go table: go table filled table metadata filled 'select()' returned many:1 mapping between keys and columns Dropping GO IDs that are too new for the current GO.db Populating go table: go table filled 'select()' returned many:1 mapping between keys and columns Populating go_all table: go_all table filled Creating package in /data/tmp2/org.Umaydis.eg.db Now deleting temporary database file complete! [1] "org.Umaydis.eg.sqlite" There were 50 or more warnings (use warnings() to see the first 50) > sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) Matrix products: default BLAS: /data/oldR/R-3.5.0/lib64/R/lib/libRblas.so LAPACK: /data/oldR/R-3.5.0/lib64/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] AnnotationForge_1.22.2 AnnotationDbi_1.42.1 IRanges_2.14.10 [4] S4Vectors_0.18.3 Biobase_2.40.0 BiocGenerics_0.26.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.18 magrittr_1.5 hms_0.4.2 [4] progress_1.2.0 bit_1.1-14 R6_2.2.2 [7] rlang_0.2.2 GenomeInfoDb_1.16.0 httr_1.3.1 [10] stringr_1.3.1 blob_1.1.1 tools_3.5.0 [13] DBI_1.0.0 assertthat_0.2.0 bit64_0.9-7 [16] digest_0.6.16 crayon_1.3.4 GenomeInfoDbData_1.1.0 [19] bitops_1.0-6 RCurl_1.95-4.11 biomaRt_2.36.1 [22] memoise_1.1.0 RSQLite_2.1.1 stringi_1.2.4 [25] GO.db_3.6.0 compiler_3.5.0 prettyunits_1.0.2 [28] XML_3.98-1.16 pkgconfig_2.0.2Hello James,
Can you comment on this thread Vidger library error ?
Hello Jim,
This thread A: Easy way to turn OrgDb object from AnnotationHub into package? was quite helpful for creating the package from AnnotationHub listed organisms.
Thanks!