error while making database using Annotationforge package

Question

[Kritika]

Hello All,

Please bear with me i have one silly question. I using clusterprofiler package for gene ontology study. Because my sample database is not present in given package so i need to make it. For making database i am using annotationforge library this is my R command :

setwd(dir = "/home/Psuedo/tmp/") makeOrgPackageFromNCBI(version="NC_002516.2",author="[e-mail]",maintainer= "[e-mail]",outputDir = ".",tax_id = "208964", genus="Pseudomonas" ,species = "Pseudomonas aeruginosa PAO1" )

it will run 3-4 hours after that it will give me error saying

Creating package in ./org.PPseudomonas aeruginosa PAO1.eg.db chmod: cannot access ‘./org.PPseudomonas’: No such file or directory chmod: cannot access ‘aeruginosa’: No such file or directory chmod: cannot access ‘PAO1.eg.db/inst/extdata/org.PPseudomonas’: No such file or directory chmod: cannot access ‘aeruginosa’: No such file or directory chmod: cannot access ‘PAO1.eg.sqlite’: No such file or directory Now deleting temporary database file complete! [1] "org.PPseudomonas aeruginosa PAO1.eg.sqlite" Warning message: In .makeAnnDbPkg(x, dbfile, dest_dir = dest_dir, no.man = no.man, : chmod 444 ./org.PPseudomonas aeruginosa PAO1.eg.db/inst/extdata/org.PPseudomonas aeruginosa PAO1.eg.sqlite failed

my file have permission for allthings still it giving me error

and these are my output files which are generated

gene2accession.gz gene_info.gz gene2go.gz idmapping_selected.tab.gz gene2pubmed.gz NCBI.sqlite gene2refseq.gz org.PPseudomonas aeruginosa PAO1.eg.db

but it ends giving me error

please help me out as i need this urgently.

sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.4 LTS locale: [1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8
[4] LC_COLLATE=en_IN.UTF-8 LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8
[7] LC_PAPER=en_IN.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages: [1] GO.db_3.3.0 RSQLite_1.0.0 DBI_0.4-1 httr_1.2.1
[5] biomaRt_2.28.0 RCurl_1.95-4.8 bitops_1.0-6 AnnotationForge_1.14.2 [9] AnnotationDbi_1.34.4 IRanges_2.6.1 S4Vectors_0.10.2 Biobase_2.32.0
[13] BiocGenerics_0.18.0
loaded via a namespace (and not attached): [1] XML_3.98-1.4 GenomeInfoDb_1.8.3 R6_2.1.2 tools_3.3.1

Answer 1

[dschika]

I assume it's a problem of spaces in the species name.

Creating package in ./org.PPseudomonas aeruginosa PAO1.eg.db

chmod: cannot access ‘./org.PPseudomonas’: No such file or directory

chmod: cannot access ‘aeruginosa’:

The package './org.PPseudomonas aeruginosa PAO1.eg.db' is created, but then chmod tries to alter a file './org.PPseudomonas' and then 'aeruginosa'

You could try to replace the spaces in the species name with underscores...

[Kritika]

no i think its related to access actually in directory inside that this tool made subdirectory which was named as org.PPseudomonas aeruginosa PAO1.eg.db i went and check the permission mode it was read only. now i am running this again with chmod -R 777 pseudo/ if this doesnt work then i will try to change the name of my file as you mentioned

[dschika]

The permission mode of org.PPseudomonas aeruginosa PAO1.eg.db does not matter as long as the library tries to do chmod with ./org.PPseudomonas and not with org.PPseudomonas aeruginosa PAO1.eg.db

[Kritika]

the org.PPseudomonas aeroginso PA01.eg.db is automatically made at the last by package itself. and there is no option in command to specify file name

[dschika]

I bet it's based on the species name. That's why I suggested to remove spaces in the species name. I just checked the manual of AnnotationForge and it says:

species Single string indicating the species.

[Kritika]

yes it was species name

[Guangchuang Yu]

I think

makeOrgPackageFromNCBI(version="NC_002516.2",author="[e-mail]",maintainer= "[e-mail]",outputDir = ".",tax_id = "208964", genus="Pseudomonas" ,species = "PAO1" )

should be fine.

I am testing it.

[Kritika]

Yes even this works