downloadChemblDb(31)

[hyojin0912]

Hello, Thank you for creating and maintaining such a great package.

I tried to download the latest chembl database using the "downloadChemblDb" function. But I got the following error: > db <- downloadChemblDb(31) trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_31_sqlite.tar.gz' Content type 'unknown' length 4505413744 bytes (4296.7 MB) Error in download.file(url, tarFile) : cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_31_sqlite.tar.gz' In addition: Warning messages: 1: In download.file(url, tarFile) : downloaded length 623933920 != reported length 4505413744 2: In download.file(url, tarFile) : URL 'ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_31_sqlite.tar.gz': Timeout of 60 seconds was reached

Could you please tell me how to solve this problem?

Also my R session info is below.

sessionInfo() R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043)

other attached packages: [1] drugTargetInteractions_1.4.0

... AnnotationDbi_1.58.0
[66] ensembldb_2.20.2 Biostrings_2.64.1 compiler_4.2.1 GenomeInfoDb_1.32.4 rlang_1.0.5
[71] grid_4.2.1 RCurl_1.98-1.9 rstudioapi_0.14 rjson_0.2.21 rappdirs_0.3.3
[76] htmlwidgets_1.5.4 bitops_1.0-7 restfulr_0.0.15 codetools_0.2-18 DBI_1.1.3
[81] curl_4.3.2 R6_2.5.1 GenomicAlignments_1.32.1 dplyr_1.0.10 rtracklayer_1.56.1
[86] fastmap_1.1.0 bit_4.0.4 utf8_1.2.2 filelock_1.0.2 ProtGenerics_1.28.0
[91] stringi_1.7.8 parallel_4.2.1 Rcpp_1.0.9 vctrs_0.4.1 png_0.1-7
[96] dbplyr_2.2.1 tidyselect_1.1.2

Thanks,

Sincerely,

Hyojin Son

[tgirke]

The path on ChEMBL has changed from "ftp..." to "https://ftp...". We can fix this in the function. In the meantime you can just download from here directly: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/, but make to extract the downloaded chembl_31_sqlite.tar.gz file.

[tgirke]

You can just download https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_31_sqlite.tar.gz in your web browser, then uncompress the file. That's all. Since the file is large the download will take some time. If this doesn't work for you then you would need to wait some time until the package is updated. After this you can reinstall it.

T. Girke

On Tue, Oct 4, 2022 at 8:13 AM Sonhyojin @.***> wrote:

Thanks for the quick reply. Professor

I'm not used to this kind of thing, so I'm sorry.

The url variable of the "downloadChemblDb" function was rewritten by adding "https://". But I got the following error:

trying URL 'https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_31_sqlite.tar.gz' Content type 'application/x-gzip' length 4505413744 bytes (4296.7 MB) downloaded 496.6 MB

Error in download.file(url, tarFile) : download from https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_31_sqlite.tar.gz' failed In addition: Warning messages: 1: In download.file(url, tarFile) : downloaded length 520695808 != reported length 4505413744 2: In download.file(url, tarFile) : URL 'https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_31_sqlite.tar.gz': Timeout of 60 seconds was reached

It could be a ChEMBL server issue.

For the 2nd method, after directly downloading "chembl_31_sqlite.tar.gz", could you guide how to parse that file using your package?

— Reply to this email directly, view it on GitHub https://github.com/girke-lab/drugTargetInteractions/issues/4#issuecomment-1267162567, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKGMVCL4IGYWRFPWXKC6IDWBRCR5ANCNFSM6AAAAAAQ4T3I2U . You are receiving this because you modified the open/close state.Message ID: @.***>

-- Thomas Girke, Ph.D. Professor of Bioinformatics Director of High-Performance Computing Center (HPCC) Director of Graduate Program in Genetics, Genomics and Bioinformatics (GGB) 1207F Genomics Building University of California Riverside, CA 92521

E-mail: @.*** URL: https://girke.bioinformatics.ucr.edu Phone/Cell/Text: 951-732-7072 Fax: 951-827-4437