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Question: Error:object 'lookup_tax_id_by_organism' not found with makeOrgPackageFromNCBI
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gravatar for sbbinfo90
3 months ago by
sbbinfo900
sbbinfo900 wrote:

 

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!

 

 

ADD COMMENTlink modified 3 months ago by James W. MacDonald48k • written 3 months ago by sbbinfo900
1
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald48k wrote:

The function you are missing comes from the GenomeInfoDb package, which evidently hasn't been installed by anaconda. I presume there is a way to tell anaconda to install that package.

ADD COMMENTlink written 3 months ago by James W. MacDonald48k

Thanks for the reply.

Do you mean by this package installation https://anaconda.org/bioconda/bioconductor-genomeinfodb ?

or shall I contact anaconda?

 

 

ADD REPLYlink written 3 months ago by sbbinfo900

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.

ADD REPLYlink written 3 months ago by James W. MacDonald48k

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

ADD REPLYlink written 3 months ago by sbbinfo900

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_2.0.2      
ADD REPLYlink written 3 months ago by James W. MacDonald48k

Hello James,

Can you comment on this thread Vidger library error ?

ADD REPLYlink written 3 months ago by sbbinfo900

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!

 

ADD REPLYlink written 3 months ago by sbbinfo900
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