Error running makeOrgPackage

[joonhoon]

Hello, The change from .lookupSpeciesFromTaxId() to lookup_organism_by_tax_id() in 18a9f8dec4f9e462976b1eb889c099c2d1aa137b is causing an error when running makeOrgPackage.

library("AnnotationForge") makeOrgPackage(version = '1.0', maintainer = 'maintainer', author = 'author', tax_id = 1)

Error in .makeOrgPackage(data, version = version, maintainer = maintainer, : 'tax_id' must be a single string Traceback:

1. makeOrgPackage(version = "1.0", maintainer = "maintainer", author = "author", . tax_id = 1)
2. .makeOrgPackage(data, version = version, maintainer = maintainer, . author = author, outputDir = outputDir, tax_id = tax_id, . genus = genus, species = species, goTable = goTable, verbose = verbose)
3. stop("'tax_id' must be a single string")

makeOrgPackage(version = '1.0', maintainer = 'maintainer', author = 'author', tax_id = '1')

Error in GenomeInfoDb:::lookup_organism_by_tax_id(tax_id): isSingleNumber(tax_id) is not TRUE Traceback:

1. makeOrgPackage(version = "1.0", maintainer = "maintainer", author = "author", . tax_id = "1")
2. .makeOrgPackage(data, version = version, maintainer = maintainer, . author = author, outputDir = outputDir, tax_id = tax_id, . genus = genus, species = species, goTable = goTable, verbose = verbose)
3. GenomeInfoDb:::lookup_organism_by_tax_id(tax_id)
4. stopifnot(isSingleNumber(tax_id))

sessionInfo()

R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.6

Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] AnnotationForge_1.22.1 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 bit_1.1-14
[4] uuid_0.1-2 blob_1.1.1 stringr_1.3.1
[7] tools_3.5.1 DBI_1.0.0 htmltools_0.3.6
[10] bit64_0.9-7 digest_0.6.15 crayon_1.3.4
[13] IRdisplay_0.5.0 repr_0.15.0 bitops_1.0-6
[16] base64enc_0.1-3 RCurl_1.95-4.11 IRkernel_0.8.12.9000 [19] memoise_1.1.0 evaluate_0.11 RSQLite_2.1.1
[22] pbdZMQ_0.3-3 stringi_1.2.4 compiler_3.5.1
[25] XML_3.98-1.12 jsonlite_1.5

Thank you. Joonhoon

[hpages]

Hi Joonhoon,

Thanks for the reproducible example. This should be addressed in AnnotationForge 1.22.2 (BioC release) and 1.23.3 (BioC devel). Here is the change.

H.

[lshep]

Hopefully this has been addressed; @joonhoon if this is still an issue please let us know and we can reopen the issue.

[joonhoon]

It works for me. Thank you!