Error in bmRequest: Internal Server Error (HTTP 500) when calling markeOrgPackageFromNCBI()

[janstrauss1]

Hi, I'm still trying to build a custom annotation package for Plasmodium falciparum using makeOrgPackageFromNCBI() as follows:

makeOrgPackageFromNCBI(version = "0.0.1",
                       author = "Some One <so@someplace.org>",
                       maintainer = "Some One <so@someplace.org>",
                       tax_id = "36329",
                       genus = "Plasmodium", species = "falciparum.3d7"
                       )

Unfortunately, I keep receiving an Error in bmRequest: Internal Server Error (HTTP 500), which I think may relate to issues when connecting to the biomart server as raised previously here: https://stackoverflow.com/questions/60032266/internal-server-errors-when-querying-biomart https://www.gitmemory.com/issue/grimbough/biomaRt/19/511884641

Below the full output of my makeOrgPackageFromNCBI() call and sessionInfo().

Many thanks in advance for your help.

Jan

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
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
extracting data for our organism from : gene_info
getting data for gene2go.gz
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 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: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
3: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
4: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
5: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] AnnotationForge_1.28.0  GenomeInfoDb_1.22.1     biomaRt_2.42.1          GO.db_3.10.0           
 [5] org.Pf.plasmo.db_3.10.0 pkgconfig_2.0.3         AnnotationDbi_1.48.0    IRanges_2.20.2         
 [9] S4Vectors_0.24.4        Biobase_2.46.0          BiocGenerics_0.32.0    

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6           BiocManager_1.30.10    pillar_1.4.3           compiler_3.6.3        
 [5] dbplyr_1.4.3           bitops_1.0-6           prettyunits_1.1.1      tools_3.6.3           
 [9] progress_1.2.2         digest_0.6.25          bit_1.1-15.2           lifecycle_0.2.0       
[13] tibble_3.0.0           RSQLite_2.2.0          memoise_1.1.0          BiocFileCache_1.10.2  
[17] rlang_0.4.5            cli_2.0.2              DBI_1.1.0              rstudioapi_0.11       
[21] curl_4.3               GenomeInfoDbData_1.2.2 stringr_1.4.0          httr_1.4.1            
[25] dplyr_0.8.5            rappdirs_0.3.1         vctrs_0.2.4            askpass_1.1           
[29] hms_0.5.3              tidyselect_1.0.0       bit64_0.9-7            glue_1.4.0            
[33] R6_2.4.1               fansi_0.4.1            XML_3.99-0.3           purrr_0.3.4           
[37] blob_1.2.1             magrittr_1.5           ellipsis_0.3.0         assertthat_0.2.1      
[41] stringi_1.4.6          RCurl_1.98-1.2         openssl_1.4.1          crayon_1.3.4          

[lshep]

Yes this ERROR is related to biomart serve connectivity. I am looking into both this and your other issue #11

[lshep]

We believe this is truly intermittent. Currently we wouldn't be able to change the code to a mirror since we wouldn't know the location of the user. We will consider other code alternatives in the future (perhaps an environment variable setting) but for now closing.