Cannot open connection to

[ReubenMcG]

Hi, thanks for making this package, can't wait to use the full functionality.

I have tried to do the simplest id conversion: ConvertID(signifgenename,ID_from = "GENENAME", ID_to = "ACC+ID")

and continually get the error: Internet connection problem occurs and the function will return the original error cannot open the connection to 'https://www.uniprot.org/uploadlists/?query=Lyn A&format=tab&from=GENENAME&to=ACC+ID'

I am definitely connected to the internet and can access the Uniprot website...

I am using a MacBook pro (macOS Bit Sur ver 11.2.1)

`R version 4.0.4 (2021-02-15) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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

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

other attached packages: [1] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.4 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2
[7] tibble_3.1.0 ggplot2_3.3.3 tidyverse_1.3.0 UniprotR_2.0.4

loaded via a namespace (and not attached): [1] nlme_3.1-152 fs_1.5.0 bitops_1.0-6
[4] matrixStats_0.58.0 lubridate_1.7.10 progress_1.2.2
[7] httr_1.4.2 GenomeInfoDb_1.24.2 data.tree_1.0.0
[10] tools_4.0.4 backports_1.2.1 utf8_1.1.4
[13] R6_2.5.0 airr_1.3.0 DBI_1.1.1
[16] lazyeval_0.2.2 BiocGenerics_0.34.0 colorspace_2.0-0
[19] ade4_1.7-16 withr_2.4.1 gridExtra_2.3
[22] tidyselect_1.1.0 prettyunits_1.1.1 curl_4.3
[25] compiler_4.0.4 cli_2.3.1 rvest_0.3.6
[28] Biobase_2.48.0 xml2_1.3.2 DelayedArray_0.14.1
[31] plotly_4.9.3 scales_1.1.1 digest_0.6.27
[34] Rsamtools_2.4.0 foreign_0.8-81 rio_0.5.26
[37] XVector_0.28.0 pkgconfig_2.0.3 htmltools_0.5.1.1
[40] dbplyr_2.1.0 htmlwidgets_1.5.3 rlang_0.4.10
[43] readxl_1.3.1 rstudioapi_0.13 generics_0.1.0
[46] jsonlite_1.7.2 BiocParallel_1.22.0 qdapRegex_0.7.2
[49] zip_2.1.1 car_3.0-10 RCurl_1.98-1.2
[52] magrittr_2.0.1 GenomeInfoDbData_1.2.3 Matrix_1.3-2
[55] Rcpp_1.0.6 munsell_0.5.0 S4Vectors_0.26.1
[58] fansi_0.4.2 abind_1.4-5 ape_5.4-1
[61] lifecycle_1.0.0 stringi_1.5.3 yaml_2.2.1
[64] carData_3.0-4 MASS_7.3-53.1 SummarizedExperiment_1.18.2 [67] zlibbioc_1.34.0 plyr_1.8.6 grid_4.0.4
[70] parallel_4.0.4 alakazam_1.1.0 crayon_1.4.1
[73] lattice_0.20-41 Biostrings_2.56.0 haven_2.3.1
[76] hms_1.0.0 magick_2.6.0 pillar_1.5.0
[79] ggpubr_0.4.0 igraph_1.2.6 GenomicRanges_1.40.0
[82] ggsignif_0.6.1 seqinr_4.2-5 stats4_4.0.4
[85] reprex_1.0.0 glue_1.4.2 gprofiler2_0.2.0
[88] data.table_1.14.0 modelr_0.1.8 vctrs_0.3.6
[91] networkD3_0.4 cellranger_1.1.0 gtable_0.3.0
[94] assertthat_0.2.1 openxlsx_4.2.3 xfun_0.21
[97] broom_0.7.5 rstatix_0.7.0 viridisLite_0.3.0
[100] GenomicAlignments_1.24.0 tinytex_0.29 IRanges_2.22.2
[103] ellipsis_0.3.1 `

[MohmedSoudy]

Hi @ReubenMcG
Thank you for your interest in our package, To convert from gene name to UniProt accession number you can use the following command Accs <- ConvertID(signifgenename, ID_from = "GENENAME", ID_to = "ACC") and to get information about the accession's organism you can use Accs <- ConvertID(signifgenename, ID_from = "GENENAME", ID_to = "ID"). Hope this solves your problem.

[ReubenMcG]

That is exactly the code I ran in my post above, I am still getting the error stated above: cannot open the connection to 'https://www.uniprot.org/uploadlists/?query=CLPP&format=tab&from=GENENAME&to=ACC'Internet connection problem occurs and the function will return the original error

[MohmedSoudy]

Hi @ReubenMcG
I post the URL to the browser and I get an output. Could we organize a meeting based on your availability to figure out what is the problem?

[shimin-chen]

Hello, I am running into the same issue. I was wondering if you could share the solution to this problem?

[MohmedSoudy]

Hi @shimin-chen, Did you tried to change the network to to another network to validate that it's not related to your internet connection?

[shimin-chen]

I can use other functions such as GetProteinFunctions() without any issues, so I don't think it is a network problem. Actually, the error message I saw is similar to the one in issue #22 .

Here is the code and error I got > UniprotR::ConvertID("P08670", ID_to = "ENSEMBL_ID", ID_from = "ACC")

Internet connection problem occurs and the function will return the original error cannot open the connection to 'https://www.uniprot.org/uploadlists/?query=P08670&format=tab&from=ACC&to=ENSEMBL_ID' From_UniProtKB_AC_ID To ENSEMBL_ID 1 P08670 Warning message: In file(file, "rt") : cannot open URL 'https://rest.uniprot.org/uploadlists/query=P08670&format=tab&from=ACC&to=ENSEMBL_ID': HTTP status was '404 Not Found'

[MohmedSoudy]

Hi @shimin-chen , The problem is similar to #22. Can you use the solution provided there and let us know if it works for you?