I am having problems getting makeOrgPackageFromNCBI to complete. Note that this downloads about 12Gb of data from the NCBI. There is an SQL error when uploading/parsing the GO terms.
Any help would be appreciated.
Here is the code I run:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("AnnotationForge")
BiocManager::install("biomaRt")
BiocManager::install("GenomeInfoDbData")
BiocManager::install("GO.db")
library(AnnotationForge)
library(biomaRt)
tx_id <- "568703"
makeOrgPackageFromNCBI(version = "0.1",
author = "placeholder@domain",
maintainer = "placeholder@domain",
outputDir = ".",
tax_id = tx_id,
genus = "Lactobacullis",
species = "rhamnosus")
And the error (eventually):
processing gene2pubmed
processing gene_info: chromosomes
processing gene_info: description
processing alias data
processing refseq data
processing accession data
processing GO data
Error in bmRequest(request = request, verbose = verbose) :
Internal Server Error (HTTP 500).
In addition: Warning messages:
1: In result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
2: call dbDisconnect() when finished working with a connection
3: In result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
And my session. I tried it with R4.0 as well, and get a similar error message.
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /bifo/itmp/lactobacillus_rhamnosus_gg/LactobacillusRhamnosusGG/NCBI/R-env/lib/libopenblasp-r0.3.9.so
locale:
[1] C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] biomaRt_2.42.1 AnnotationForge_1.28.0 AnnotationDbi_1.48.0
[4] IRanges_2.20.2 S4Vectors_0.24.4 Biobase_2.46.0
[7] BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 GenomeInfoDb_1.22.1 compiler_3.6.3
[4] pillar_1.4.4 dbplyr_1.4.3 prettyunits_1.1.1
[7] bitops_1.0-6 tools_3.6.3 progress_1.2.2
[10] digest_0.6.25 bit_1.1-15.2 RSQLite_2.2.0
[13] memoise_1.1.0 BiocFileCache_1.10.2 tibble_3.0.1
[16] lifecycle_0.2.0 pkgconfig_2.0.3 rlang_0.4.6
[19] DBI_1.1.0 curl_4.3 GenomeInfoDbData_1.2.2
[22] dplyr_0.8.5 stringr_1.4.0 httr_1.4.1
[25] rappdirs_0.3.1 vctrs_0.3.0 askpass_1.1
[28] hms_0.5.3 tidyselect_1.1.0 bit64_0.9-7
[31] glue_1.4.0 R6_2.4.1 XML_3.99-0.3
[34] purrr_0.3.4 blob_1.2.1 magrittr_1.5
[37] ellipsis_0.3.0 assertthat_0.2.1 stringi_1.4.6
[40] RCurl_1.98-1.2 openssl_1.4.1 crayon_1.3.4
That's an orthogonal issue, but I'm happy it worked for you.