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grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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Possible SSL connectivity problems detected. #44

Open evareisinger opened 3 years ago

evareisinger commented 3 years ago

Can not load biomart:

library(biomaRt) 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) : schannel: next InitializeSecurityContext failed: SEC_E_UNTRUSTED_ROOT (0x80090325) - Die Zertifikatkette wurde von einer nicht vertrauenswürdigen Zertifizierungsstelle ausgest

grimbough commented 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?

hoondy commented 3 years ago

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

elcamb commented 2 years ago

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

grimbough commented 2 years ago

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.

elcamb commented 2 years ago

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.

grimbough commented 2 years ago

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.

elcamb commented 2 years ago

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

grimbough commented 2 years ago

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?

elcamb commented 2 years ago

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
grimbough commented 2 years ago

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.

elcamb commented 2 years ago

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