getURL() failed
Closed this issue · 4 comments
Hi,
Thanks for a great resource! I am using the import_OmniPath_annotations method for human genes, but for some selections of genes, the URL is not responding, and I recieve and error, e.g.:
cannot open URL 'https://omnipathdb.org/annotations?&proteins=YTHDF3,YTHDF2,YTHDF1,YTHDC2,YTHDC1,YRDC,YPEL5,YPEL4,YPEL3,YPEL2,YPEL1,YOD1,YME1L1,YLPM1,YKT6,YJU2,YJEFN3,YIPF7,YIPF6,YIPF5,YIPF4,YIPF3,YIPF2,YIPF1,YIF1B,YIF1A,YES1,YEATS4,YEATS2,YDJC,YBX3,YBX2,YBX1,YBEY,YARS2,YARS1,YAP1,YAF2,YAE1,XYLT2,XYLT1,XXYLT1,XRRA1,XRN2,XRN1,XRCC6,XRCC5,XRCC4,XRCC3,XRCC2
Not sure why this fails, got any idea?
On beforehand, thanks!
regards,
Sigve
Hi Sigve,
Thanks for your report. We know about this issue, it is a server side error, it happens if for some resource the license is unknown. We will fix it still today, I will close this issue once fixed.
Best wishes,
Denes
Hi @deeenes,
I am getting a similar error with this code in the vignette. Hope you can help me figure that out.
HPA_small <- import_omnipath_annotations(
proteins = c('TP53', 'LMNA'),
resources = c('HPA_tissue'),
wide = TRUE
)
Error in (function (URL, FUN, ..., N.TRIES = 1L) :
omnipath_download() failed:
URL: https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=TP53,LMNA&license=academic
error: cannot open the connection to 'https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=TP53,LMNA&license=academic'
In addition: Warning message:
In file(file, "rt") :
cannot open URL 'https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=TP53,LMNA&license=academic': HTTP status was '500 Internal Server Error'
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] OmnipathR_2.0.0 jsonlite_1.7.2 tidyr_1.1.2 qgraph_1.6.9 igraph_1.2.6 openxlsx_4.2.3
[7] purrr_0.3.4 tibble_3.0.6 dplyr_1.0.4
loaded via a namespace (and not attached):
[1] splines_4.0.2 tmvnsim_1.0-2 gtools_3.8.2 Formula_1.2-4
[5] assertthat_0.2.1 BiocManager_1.30.10 stats4_4.0.2 latticeExtra_0.6-29
[9] yaml_2.2.1 remotes_2.2.0 pbivnorm_0.6.0 pillar_1.4.7
[13] backports_1.2.1 lattice_0.20-41 glue_1.4.2 digest_0.6.27
[17] RColorBrewer_1.1-2 checkmate_2.0.0 colorspace_2.0-0 htmltools_0.5.1.1
[21] Matrix_1.3-2 plyr_1.8.6 psych_2.0.12 pkgconfig_2.0.3
[25] corpcor_1.6.9 scales_1.1.1 glasso_1.11 jpeg_0.1-8.1
[29] fdrtool_1.2.16 htmlTable_2.1.0 generics_0.1.0 ggplot2_3.3.3
[33] ellipsis_0.3.1 pbapply_1.4-3 nnet_7.3-15 cli_2.3.0
[37] mnormt_2.0.2 survival_3.2-7 magrittr_2.0.1 crayon_1.4.0
[41] fansi_0.4.2 nlme_3.1-152 foreign_0.8-81 tools_4.0.2
[45] data.table_1.13.6 lifecycle_0.2.0 stringr_1.4.0 munsell_0.5.0
[49] cluster_2.1.0 zip_2.1.1 packrat_0.5.0 compiler_4.0.2
[53] rlang_0.4.10 grid_4.0.2 rstudioapi_0.13 htmlwidgets_1.5.3
[57] lavaan_0.6-7 base64enc_0.1-3 gtable_0.3.0 curl_4.3
[61] abind_1.4-5 DBI_1.1.1 reshape2_1.4.4 R6_2.5.0
[65] gridExtra_2.3 knitr_1.31 utf8_1.1.4 Hmisc_4.4-2
[69] stringi_1.5.3 parallel_4.0.2 Rcpp_1.0.6 vctrs_0.3.6
[73] rpart_4.1-15 png_0.1-7 tidyselect_1.1.0 xfun_0.20
All the best,
Asuman
Hi Asuman,
Looks like it was a temporary disruption, probably the server was overloaded.
The same query was successful for me. Let me know if you are still experiencing this issue.
Best,
Denes
Works perfectly now, many thanks!