Entering edit mode
I can not download the 9606 interactions, is the server down? I also tried using http.
# include your problematic code here with any corresponding output
# please also include the results of running the following in an R session
# instantiate stringdb
string_db <- STRINGdb$new( version="11.5", species=9606,
score_threshold=0, input_directory="")
# get interactions
string_db_interactions = string_db$get_interactions(string_db$get_aliases()$STRING_id)
#trying URL 'https://stringdb-static.org/download/protein.links.v11.5/9606.protein.links.v11.5.txt.gz'
#Warning: URL 'https://stringdb-static.org/download/protein.links.v11.5/9606.protein.links.v11.5.txt.gz': Timeout of 60 #seconds was reachedError in download.file(urlStr, temp) :
# cannot open URL 'https://stringdb-static.org/download/protein.links.v11.5/9606.protein.links.v11.5.txt.gz'
sessionInfo( )
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.24.0 AnnotationFilter_1.24.0
[4] GenomicFeatures_1.52.1 AnnotationDbi_1.62.2 STRINGdb_2.12.0
[7] biomaRt_2.56.1 dplyr_1.1.2 OmnipathR_3.9.6
[10] igraph_1.4.2 ClustMMDD_1.0.4 Rcpp_1.0.10
[13] SGS_1.0.0 bitops_1.0-7 TreeSummarizedExperiment_2.8.0
[16] Biostrings_2.68.1 XVector_0.40.0 SingleCellExperiment_1.22.0
[19] SummarizedExperiment_1.30.2 Biobase_2.60.0 GenomicRanges_1.52.0
[22] GenomeInfoDb_1.36.1 IRanges_2.34.1 S4Vectors_0.38.1
[25] MatrixGenerics_1.12.2 matrixStats_1.0.0 gRbase_1.8.9
[28] BiocGenerics_0.46.0
I take the liberty to ask about when the repair can be completed. I was unsuccessful installing version 1.2.9 of bioconductor-genomeinfodbdata.
The current timeline is that it will be fixed on Wednesday. Unfortunately, I'm not familiar with genomeinfodbdata versioning.
Really, sorry for the inconvenience, and thanks for your patience.
If you are ok with changing the source, in STRINGdb package, rstring.R script, change all occurrences of:
To
This should fix the issue immediately.
Best,
Thank you very much for your reply. Because I urgently need to download version 1.2.9 (not the latest version) of bioconductor-genomeinfodbdata through conda. I found that the three links provided in the bioconductor-genomeinfodbdata compressed package of version 1.2.9 submitted to conda are all invalid, so I cannot download it. Could you please restore this is three links, even one of them.
There is another easier way, can you help me upload GenomeInfoDbData_1.2.9.tar.gz to https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/ under this storage directory?
------------------------------------------------
package: name: bioconductor-genomeinfodbdata version: 1.2.9 source: md5: 7cc138cfb74665fdfa8d1c244eac4879 url:
ah... I think there is a misunderstanding. The original question and my answer had nothing to do with bioconductor-genomeinfodbdata.
Please create a new thread with the correct topic and tags. Hopefully, someone will be able to help you.
Best,
I'm so sorry. But I still want to ask if the old download server you mentioned in your first reply refers to storing only the STRINGdb R package, maybe I mistakenly thought that the server you mentioned is storing all old versions of R packages (including bioconductor-genomeinfodbdata 1.2.9)
The download server I have mentioned only stores data related to the STRINGdb package. Unfortunately, I don't have any information about bioconductor-genomeinfodbdata. These seem to be completely unrelated issues.
Good luck!