Failure when receiving data from the peer

[polya18]

Hello, I used to produce results smoothy by multimir. However, I got the error msg. last night (copied below). I have no idea to figure out. I test the same code on mac and linux. Both of them reported the same error.

Error in map(): ℹ In index: 1. Caused by error in load(): ! cannot open the connection to 'http://multimir.org/multimir_cutoffs_2.3.rda' Run rlang::last_trace() to see where the error occurred. Warning message: In load(url.file) : URL 'http://multimir.org/multimir_cutoffs_2.3.rda': status was 'Failure when receiving data from the peer'

[smahaffey]

@polya18 is the issue persisting? I've tested it this morning and checked the URL and everything seems to be working. Please provide any additional details unless it's working. It may have been a short term connection or server issue. Thank you!

[polya18]

Hi Multimir,

Thanks for asking. The error is still there. It happened when table='predicted'. For table='validated', I can get results after ran the code many times. The following showed detailed error msg from R terminal. And attachment is the session info on my Mac.

Thanks again. All the Best.

rlang::last_trace(drop = FALSE) <error/purrr_error_indexed> Error in map(): ℹ In index: 1. Caused by error in load(): ! cannot open the connection to 'http://multimir.org/multimir_cutoffs_2.3.rda'

Backtrace: ▆

1. ├─multiMiR::get_multimir(...)
2. │ └─purrr::map(...)
3. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
4. │ ├─purrr:::with_indexed_errors(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ ├─purrr:::call_with_cleanup(...)
7. │ └─multiMiR (local) .f(.x[[i]], ...)
8. │ └─multiMiR:::sql_predicted(...)
9. │ └─multiMiR:::cutoff_to_score(...)
10. │ └─multiMiR:::get.multimir.cutoffs()
11. │ └─base::load(url.file)
12. └─base::.handleSimpleError(...)
13. └─purrr (local) h(simpleError(msg, call))
14. └─cli::cli_abort(...)
15. └─rlang::abort(...)

-----原始邮件----- 发件人:"Spencer Mahaffey" @.> 发送时间:2023-04-05 00:11:38 (星期三) 收件人: KechrisLab/multiMiR @.> 抄送: polya18 @.>, Mention @.> 主题: Re: [KechrisLab/multiMiR] Failure when receiving data from the peer (Issue #46)

@polya18 is the issue persisting? I've tested it this morning and checked the URL and everything seems to be working. Please provide any additional details unless it's working. It may have been a short term connection or server issue. Thank you!

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***> R version 4.2.2 (2022-10-31) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] stats4 stats graphics grDevices utils datasets [7] methods base

other attached packages: [1] org.Mm.eg.db_3.16.0 ggVennDiagram_1.2.2
[3] biomaRt_2.54.1 ReactomePA_1.42.0
[5] org.Hs.eg.db_3.16.0 clusterProfiler_4.6.2
[7] DOSE_3.24.2 enrichplot_1.18.3
[9] seqinr_4.2-23 mirTarRnaSeq_1.6.0
[11] multiMiR_1.20.0 EnhancedVolcano_1.16.0
[13] ggrepel_0.9.3 pheatmap_1.0.12
[15] RColorBrewer_1.1-3 ggplot2_3.4.1
[17] DESeq2_1.38.3 SummarizedExperiment_1.28.0 [19] MatrixGenerics_1.10.0 matrixStats_0.63.0
[21] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[23] gdtools_0.3.3 phylotools_0.2.2
[25] ape_5.7-1 scales_1.2.1
[27] dplyr_1.1.1 eoffice_0.2.2
[29] stringr_1.5.0 data.table_1.14.8
[31] KEGG.db_1.0 AnnotationDbi_1.60.2
[33] IRanges_2.32.0 S4Vectors_0.36.2
[35] Biobase_2.58.0 BiocGenerics_0.44.0

loaded via a namespace (and not attached): [1] utf8_1.2.3 R.utils_2.12.2
[3] tidyselect_1.2.0 RSQLite_2.3.0
[5] htmlwidgets_1.6.2 grid_4.2.2
[7] BiocParallel_1.32.6 scatterpie_0.1.8
[9] munsell_0.5.0 units_0.8-1
[11] codetools_0.2-19 ragg_1.2.5
[13] withr_2.5.0 colorspace_2.1-0
[15] GOSemSim_2.24.0 filelock_1.0.2
[17] knitr_1.42 uuid_1.1-0
[19] rstudioapi_0.14 pscl_1.5.5
[21] officer_0.6.2 fontLiberation_0.1.0
[23] labeling_0.4.2 GenomeInfoDbData_1.2.9 [25] polyclip_1.10-4 bit64_4.0.5
[27] farver_2.1.1 downloader_0.4
[29] vctrs_0.6.1 treeio_1.22.0
[31] generics_0.1.3 gson_0.1.0
[33] xfun_0.38 BiocFileCache_2.6.1
[35] fontquiver_0.2.1 R6_2.5.1
[37] graphlayouts_0.8.4 RVenn_1.1.0
[39] locfit_1.5-9.7 bitops_1.0-7
[41] cachem_1.0.7 fgsea_1.24.0
[43] gridGraphics_0.5-1 DelayedArray_0.24.0
[45] assertthat_0.2.1 promises_1.2.0.1
[47] ggraph_2.1.0 gtable_0.3.3
[49] Cairo_1.6-0 tidygraph_1.2.3
[51] rlang_1.1.0 systemfonts_1.0.4
[53] splines_4.2.2 lazyeval_0.2.2
[55] broom_1.0.4 yaml_2.3.7
[57] BiocManager_1.30.20 reshape2_1.4.4
[59] backports_1.4.1 httpuv_1.6.9
[61] qvalue_2.30.0 tools_4.2.2
[63] ggplotify_0.1.0 ellipsis_0.3.2
[65] proxy_0.4-27 devEMF_4.2
[67] Rcpp_1.0.10 plyr_1.8.8
[69] progress_1.2.2 base64enc_0.1-3
[71] zlibbioc_1.44.0 classInt_0.4-9
[73] purrr_1.0.1 RCurl_1.98-1.12
[75] prettyunits_1.1.1 openssl_2.0.6
[77] viridis_0.6.2 cowplot_1.1.1
[79] crul_1.3 magrittr_2.0.3
[81] magick_2.7.4 flextable_0.9.0
[83] reactome.db_1.82.0 hms_1.1.3
[85] patchwork_1.1.2 mime_0.12
[87] evaluate_0.20 xtable_1.8-4
[89] HDO.db_0.99.1 XML_3.99-0.14
[91] gridExtra_2.3 compiler_4.2.2
[93] fontBitstreamVera_0.1.1 tibble_3.2.1
[95] KernSmooth_2.23-20 shadowtext_0.1.2
[97] crayon_1.5.2 R.oo_1.25.0
[99] htmltools_0.5.5 ggfun_0.0.9
[101] later_1.3.0 tidyr_1.3.0
[103] geneplotter_1.76.0 aplot_0.1.10
[105] DBI_1.1.3 tweenr_2.0.2
[107] corrplot_0.92 dbplyr_2.3.2
[109] rappdirs_0.3.3 MASS_7.3-58.3
[111] sf_1.0-12 Matrix_1.5-3
[113] ade4_1.7-22 cli_3.6.1
[115] R.methodsS3_1.8.2 parallel_4.2.2
[117] igraph_1.4.1 pkgconfig_2.0.3
[119] plotly_4.10.1 xml2_1.3.3
[121] ggtree_3.6.2 annotate_1.76.0
[123] XVector_0.38.0 rvg_0.3.2
[125] yulab.utils_0.0.6 digest_0.6.31
[127] graph_1.76.0 httpcode_0.3.0
[129] Biostrings_2.66.0 rmarkdown_2.21
[131] fastmatch_1.1-3 tidytree_0.4.2
[133] curl_5.0.0 graphite_1.44.0
[135] shiny_1.7.4 lifecycle_1.0.3
[137] nlme_3.1-162 jsonlite_1.8.4
[139] viridisLite_0.4.1 askpass_1.1
[141] fansi_1.0.4 pillar_1.9.0
[143] lattice_0.20-45 R.devices_2.17.1
[145] KEGGREST_1.38.0 fastmap_1.1.1
[147] httr_1.4.5 GO.db_3.16.0
[149] glue_1.6.2 zip_2.2.2
[151] png_0.1-8 bit_4.0.5
[153] class_7.3-21 ggforce_0.4.1
[155] stringi_1.7.12 blob_1.2.4
[157] textshaping_0.3.6 gfonts_0.2.0
[159] caTools_1.18.2 memoise_2.0.1
[161] e1071_1.7-13

[polya18]

Hello, The problem is still happened. Is there any way to resolve it? Thanks

[smahaffey]

@polya18 I haven't been able to replicate the problem. Where are you located? It seems more like a network problem.

[polya18]

Thanks. I locate in China. I asked someone to test at Shanghai, but it was not work. Also use VPN loacted in Japan and Korea. I asked someone in US to run the code, it works fine. Hope I can get results in the future.

Thanks again.

All the best.

-----原始邮件----- 发件人:"Spencer Mahaffey" @.> 发送时间:2023-05-05 23:54:32 (星期五) 收件人: KechrisLab/multiMiR @.> 抄送: polya18 @.>, Mention @.> 主题: Re: [KechrisLab/multiMiR] Failure when receiving data from the peer (Issue #46)

@polya18 I haven't been able to replicate the problem. Where are you located? It seems more like a network problem.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

[smahaffey]

@polya18 Ok let me see if I can change any of the configuration to make the website available. Nothing specifically should be blocking it on our side however.

[artnasamran]

Hi @smahaffey, I'm encountering a similar issue when running get_multimir() with table = "predicted" or "disease.drug" ("validated" works fine).

Error in map(): ℹ In index: 1. Caused by error in load(): ! cannot open the connection to 'http://multimir.org/multimir_cutoffs_2.3.rda' Run rlang::last_trace() to see where the error occurred.

[smahaffey]

I have tried to extend the global timeout in R once the package is loaded. I'm hoping this will help with this issue when users are located outside the US. I will close this for now, but please update me if the new Bioconductor 3.20 release doesn't fix the issue. It is scheduled for 10/30/24 and fixes have been implemented in the current development branch for inclusion.