Entering edit mode
I do not know how to install the end product. I also do not know how to interpret the warning message. Hoping for some insight as to where to go from here. Thanks
library(AnnotationForge)
# https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=32201\
org<-makeOrgPackageFromNCBI(version = "0.1",author ="MT",maintainer = "netname@aol.com",outputDir = "C:\\Users\\mat14\\OneDrive\\Desktop\\wd\\C-ill-Pawnee\\db",tax_id = 32201,genus ="Carya",species ="illinoinensis")
If files are not cached locally this may take awhile to assemble a 33 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.Please also see AnnotationHub for some pre-builtOrgDb downloads
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
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
table metadata filled
Creating package in C:\Users\mat14\OneDrive\Desktop\wd\C-ill-Pawnee\db/org.Cillinoinensis.eg.db
Now deleting temporary database file
complete!
Warning message:
**In file.remove(dbFileName) :
cannot remove file 'C:\Users\mat14\OneDrive\Desktop\wd\C-ill-Pawnee\db/org.Cillinoinensis.eg.sqlite', reason 'Permission denied'**
I tried the code you provided, but it is still having issues. Do you know of any potential work-arounds?
...
Installing package into 'C:/Users/mat14/AppData/Local/R/win-library/4.3' (as 'lib' is unspecified)
Malformed maintainer field.
See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. ERROR: installing package DESCRIPTION failed for package 'org.Cillinoinensis.eg.db'
You got this error:
Error : Invalid DESCRIPTION file. Malformed maintainer field.You used:
maintainer = "netname@aol.com"(andauthor ="MT").AFAIK it should be:
maintainer = "Net Name <netname@aol.com>"(andauthor ="MT <netname@aol.com>").Thus add your name, and email should be between
<>. To be sure, also do this at the author field.I also struggled with this a bit before...: problem with makeOrgPackageFromNCBI when making an annotation package
Thanks for pointing it out - this was the solution. Silly mistake on my end, you saved me from walking in (more) circles
FWIW, it's only the maintainer field that requires the bracketed email. Including in the author field won't cause an error, but is not necessary.