Open evareisinger opened 3 years ago
Thank you for the report. Could you also include the output of sessionInfo()
so I can see which operating system and package versions you're running?
I am also getting the same error message:
Possible SSL connectivity problems detected. Please report this issue at https://github.com/grimbough/biomaRt/issues Error in curl::curl_fetch_memory(url, handle = handle) : error:1408F10B:SSL routines:ssl3_get_record:wrong version number
sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS: /sc/arion/projects/CommonMind/leed62/conda/envs/r403/lib/libblas.so.3.8.0 LAPACK: /sc/arion/projects/CommonMind/leed62/conda/envs/r403/lib/liblapack.so.3.8.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base
other attached packages:
[1] dplyr_1.0.4 reshape2_1.4.4 S4Vectors_0.28.1
[4] BiocGenerics_0.36.0 patchwork_1.1.1 cowplot_1.1.1
[7] ggplot2_3.3.3 harmony_1.0 Rcpp_1.0.6
[10] Signac_1.1.1.9001 SeuratObject_4.0.0 Seurat_4.0.0
loaded via a namespace (and not attached):
[1] reticulate_1.18 tidyselect_1.1.0
[3] RSQLite_2.2.3 AnnotationDbi_1.52.0
[5] htmlwidgets_1.5.3 grid_4.0.3
[7] BiocParallel_1.24.1 Rtsne_0.15
[9] munsell_0.5.0 codetools_0.2-18
[11] ica_1.0-2 pbdZMQ_0.3-4
[13] future_1.21.0 miniUI_0.1.1.1
[15] withr_2.4.1 colorspace_2.0-0
[17] OrganismDbi_1.32.0 Biobase_2.50.0
[19] knitr_1.31 uuid_0.1-4
[21] rstudioapi_0.13 ROCR_1.0-11
[23] tensor_1.5 listenv_0.8.0
[25] MatrixGenerics_1.2.1 repr_1.1.3
[27] GenomeInfoDbData_1.2.4 polyclip_1.10-0
[29] farver_2.0.3 bit64_4.0.5
[31] parallelly_1.23.0 vctrs_0.3.6
[33] generics_0.1.0 xfun_0.20
[35] biovizBase_1.38.0 BiocFileCache_1.14.0
[37] lsa_0.73.2 ggseqlogo_0.1
[39] R6_2.5.0 GenomeInfoDb_1.26.2
[41] AnnotationFilter_1.14.0 reshape_0.8.8
[43] bitops_1.0-6 spatstat.utils_2.0-0
[45] cachem_1.0.3 DelayedArray_0.16.1
[47] assertthat_0.2.1 promises_1.1.1
[49] scales_1.1.1 nnet_7.3-15
[51] gtable_0.3.0 globals_0.14.0
[53] goftest_1.2-2 ggbio_1.38.0
[55] ensembldb_2.14.0 rlang_0.4.10
[57] RcppRoll_0.3.0 splines_4.0.3
[59] rtracklayer_1.50.0 lazyeval_0.2.2
[61] dichromat_2.0-0 checkmate_2.0.0
[63] BiocManager_1.30.10 abind_1.4-5
[65] GenomicFeatures_1.42.1 backports_1.2.1
[67] httpuv_1.5.5 Hmisc_4.4-2
[69] RBGL_1.66.0 tools_4.0.3
[71] ellipsis_0.3.1 RColorBrewer_1.1-2
[73] ggridges_0.5.3 plyr_1.8.6
[75] base64enc_0.1-3 progress_1.2.2
[77] zlibbioc_1.36.0 purrr_0.3.4
[79] RCurl_1.98-1.2 prettyunits_1.1.1
[81] rpart_4.1-15 openssl_1.4.3
[83] deldir_0.2-9 pbapply_1.4-3
[85] zoo_1.8-8 SummarizedExperiment_1.20.0
[87] ggrepel_0.9.1 cluster_2.1.0
[89] magrittr_2.0.1 data.table_1.13.6
[91] scattermore_0.7 lmtest_0.9-38
[93] RANN_2.6.1 SnowballC_0.7.0
[95] ProtGenerics_1.22.0 fitdistrplus_1.1-3
[97] matrixStats_0.58.0 hms_1.0.0
[99] mime_0.9 evaluate_0.14
[101] xtable_1.8-4 XML_3.99-0.5
[103] jpeg_0.1-8.1 IRanges_2.24.1
[105] gridExtra_2.3 compiler_4.0.3
[107] biomaRt_2.46.2 tibble_3.0.6
[109] KernSmooth_2.23-18 crayon_1.4.1
[111] htmltools_0.5.1.1 mgcv_1.8-33
[113] later_1.1.0.1 Formula_1.2-4
[115] tidyr_1.1.2 DBI_1.1.1
[117] tweenr_1.0.1 dbplyr_2.1.0
[119] MASS_7.3-53 rappdirs_0.3.3
[121] Matrix_1.3-2 igraph_1.2.6
[123] GenomicRanges_1.42.0 pkgconfig_2.0.3
[125] GenomicAlignments_1.26.0 foreign_0.8-81
[127] IRdisplay_1.0 plotly_4.9.3
[129] xml2_1.3.2 XVector_0.30.0
[131] stringr_1.4.0 VariantAnnotation_1.36.0
[133] digest_0.6.27 sctransform_0.3.2
[135] RcppAnnoy_0.0.18 graph_1.68.0
[137] spatstat.data_1.7-0 Biostrings_2.58.0
[139] leiden_0.3.7 fastmatch_1.1-0
[141] htmlTable_2.1.0 uwot_0.1.10
[143] curl_4.3 shiny_1.6.0
[145] Rsamtools_2.6.0 lifecycle_0.2.0
[147] nlme_3.1-152 jsonlite_1.7.2
[149] viridisLite_0.3.0 askpass_1.1
[151] BSgenome_1.58.0 pillar_1.4.7
[153] lattice_0.20-41 GGally_2.1.0
[155] fastmap_1.1.0 httr_1.4.2
[157] survival_3.2-7 glue_1.4.2
[159] spatstat_1.64-1 png_0.1-7
[161] bit_4.0.4 ggforce_0.3.2
[163] stringi_1.5.3 blob_1.2.1
[165] latticeExtra_0.6-29 memoise_2.0.0
[167] IRkernel_1.1.1 irlba_2.3.3
[169] future.apply_1.7.0
Hello,
I also have a similar issue. It looks like the package is using http instead of https, causing the request to be blocked at the server level.
library(biomaRt) listMarts() Ensembl site unresponsive, trying asia mirror Error in curl::curl_fetch_memory(url, handle = handle) : SSL certificate problem: self signed certificate in certificate chain sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux 8.3 (Ootpa)
Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.12.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] biomaRt_2.50.3
loaded via a namespace (and not attached):
[1] KEGGREST_1.34.0 progress_1.2.2 tidyselect_1.1.2 xfun_0.30
[5] purrr_0.3.4 vctrs_0.4.0 generics_0.1.2 htmltools_0.5.2
[9] stats4_4.1.2 BiocFileCache_2.2.1 yaml_2.3.5 utf8_1.2.2
[13] blob_1.2.2 XML_3.99-0.9 rlang_1.0.2 pillar_1.7.0
[17] glue_1.6.2 DBI_1.1.2 rappdirs_0.3.3 BiocGenerics_0.40.0
[21] bit64_4.0.5 dbplyr_2.1.1 GenomeInfoDbData_1.2.7 lifecycle_1.0.1
[25] stringr_1.4.0 zlibbioc_1.40.0 Biostrings_2.62.0 memoise_2.0.1
[29] evaluate_0.15 Biobase_2.54.0 knitr_1.38 IRanges_2.28.0
[33] fastmap_1.1.0 GenomeInfoDb_1.30.1 curl_4.3.2 fansi_1.0.2
[37] AnnotationDbi_1.56.2 Rcpp_1.0.8.3 filelock_1.0.2 cachem_1.0.6
[41] S4Vectors_0.32.3 XVector_0.34.0 bit_4.0.4 hms_1.1.1
[45] png_0.1-7 digest_0.6.29 stringi_1.7.6 dplyr_1.0.8
[49] cli_3.2.0 tools_4.1.2 bitops_1.0-7 magrittr_2.0.3
[53] tibble_3.1.6 RCurl_1.98-1.6 RSQLite_2.2.11 pacman_0.5.1
[57] crayon_1.5.0 pkgconfig_2.0.3 ellipsis_0.3.2 xml2_1.3.3
[61] prettyunits_1.1.1 assertthat_0.2.1 rmarkdown_2.13 httr_1.4.2
[65] rstudioapi_0.13 R6_2.5.1
Hello,
I also have a similar issue. It looks like the package is using http instead of https, causing the request to be blocked at the server level.
library(biomaRt) listMarts() Ensembl site unresponsive, trying asia mirror Error in curl::curl_fetch_memory(url, handle = handle) : SSL certificate problem: self signed certificate in certificate chain
What happens if you try listEnsembl()
which should use ensembl specific settings like https.
Hi, Thanks for the suggestion:
library(biomaRt) listEnsembl() Possible SSL connectivity problems detected. Please report this issue at https://github.com/grimbough/biomaRt/issues Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 104
Ensembl site unresponsive, trying asia mirror Error in curl::curl_fetch_memory(url, handle = handle) : SSL certificate problem: self signed certificate in certificate chain
Emanuele
Hello,
I also have a similar issue. It looks like the package is using http instead of https, causing the request to be blocked at the server level.
library(biomaRt) listMarts() Ensembl site unresponsive, trying asia mirror Error in curl::curl_fetch_memory(url, handle = handle) : SSL certificate problem: self signed certificate in certificate chain
What happens if you try listEnsembl() which should use ensembl specific settings like https.
Thanks for the extra info. I don't think I've seen the "self signed certificate" issue before. I'll report this to the Ensembl server team and see if they have any details.
Hi, just checking if there was any update on this, or if there's something else I could try? I'm still getting the same error Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 104 Thanks,
Emanuele
Hi @elcamb
Could you try running the following code before doing anything with biomaRt:
httr::config(ssl_verifypeer = FALSE)
then try
library(biomaRt)
listEnsembl()
Does that make any difference?
Hi @grimbough I seem to get the same error:
httr::config(ssl_verifypeer = FALSE)
Options: * ssl_verifypeer: FALSE library(biomaRt) listEnsembl() Ensembl site unresponsive, trying uswest mirror Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 104
Sorry, my bad. That should have been:
httr::set_config(httr::config(ssl_verifypeer = FALSE))
then
library(biomaRt)
listEnsembl()
The first version didn't actually make any configuration changes.
Same thing:
httr::set_config(httr::config(ssl_verifypeer = FALSE)) library(biomaRt) listEnsembl() Possible SSL connectivity problems detected. Please report this issue at https://github.com/grimbough/biomaRt/issues Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 104
Ensembl site unresponsive, trying asia mirror Error in curl::curl_fetch_memory(url, handle = handle) : OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 104
Can not load biomart: