Entering edit mode
Last seen 14 months ago
United States

Hi Team,

I am trying to run orthologue mapping of species in R. Since last Thursday I am not able to execute the function successfully before it was working fine. When I contacted the ENSEMBL helpdesk they were able to connect to BioMart using the web interface but not using R indicating a potential problem with the BioMart interface and not ensembl servers. Can you please help me with the same? Following is the error I am getting. I tried different mirror sites to make it work still I am getting the same error.

Ensembl site unresponsive, trying uswest mirror Error in curl::curl_fetch_memory(url, handle = handle) : Peer's Certificate issuer is not recognized. Called from: curl::curl_fetch_memory(url, handle = handle) Browse[1]>

convertRatGeneList <- function(x){
  human = useMart("ensembl", dataset = "hsapiens_gene_ensembl",host = "https://www.ensembl.org")
  rat = useMart("ensembl", dataset = "rnorvegicus_gene_ensembl",host = "https://www.ensembl.org")
  genesV2 = getLDS(attributes = c("rgd_symbol"), filters = "rgd_symbol", values = x , mart = rat, attributesL = c("hgnc_symbol"), martL = human, uniqueRows=T)
  humanx <- unique(genesV2[, 2])
  # Print the first 6 genes found to the screen

Ensembl site unresponsive, trying uswest mirror
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Peer's Certificate issuer is not recognized.
Called from: curl::curl_fetch_memory(url, handle = handle)

> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/prog/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib/libopenblas_haswellp-r0.2.20.so

 [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                  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       LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8          

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] orthogene_0.99.9        httr_1.4.2              corrplot_0.90           ensembldb_2.17.4        AnnotationFilter_1.17.1
 [6] GenomicFeatures_1.45.2  GenomicRanges_1.45.0    GenomeInfoDb_1.29.10    fgsea_1.19.4            AUCell_1.15.0          
[11] ComplexHeatmap_2.9.4    circlize_0.4.13         plyr_1.8.6              lattice_0.20-45         RColorBrewer_1.1-2     
[16] Matrix_1.3-4            cowplot_1.1.1           EnhancedVolcano_1.11.5  hciR_1.5                reshape2_1.4.4         
[21] splitstackshape_1.4.8   gplots_3.1.1            gtools_3.9.2            edgeR_3.35.3            msigdbr_7.4.1          
[26] clusterProfiler_4.1.4   qusage_2.27.5           limma_3.49.5            biomaRt_2.49.7          org.Hs.eg.db_3.14.0    
[31] AnnotationDbi_1.55.2    IRanges_2.27.2          S4Vectors_0.31.5        Biobase_2.53.0          BiocGenerics_0.39.2    
[36] ReactomePA_1.37.0       enrichR_3.0             annotables_0.1.91       forcats_0.5.1           stringr_1.4.0          
[41] dplyr_1.0.7             purrr_0.3.4             readr_2.0.2             tidyr_1.1.4             tibble_3.1.4           
[46] tidyverse_1.3.1         xlsx_0.6.5              SeuratObject_4.0.2      Seurat_4.0.5            ggrepel_0.9.1          
[51] ggplot2_3.3.5          

loaded via a namespace (and not attached):
  [1] ica_1.0-2                   Rsamtools_2.9.1             foreach_1.5.1               lmtest_0.9-38              
  [5] crayon_1.4.1                spatstat.core_2.3-0         MASS_7.3-54                 nlme_3.1-153               
  [9] backports_1.3.0             reprex_2.0.1                GOSemSim_2.19.1             rlang_0.4.12               
 [13] XVector_0.33.0              ROCR_1.0-11                 readxl_1.3.1                irlba_2.3.3                
 [17] extrafontdb_1.0             filelock_1.0.2              extrafont_0.17              BiocParallel_1.27.17       
 [21] rjson_0.2.20                bit64_4.0.5                 glue_1.4.2                  sctransform_0.3.2          
 [25] vipor_0.4.5                 spatstat.sparse_2.0-0       DOSE_3.19.4                 spatstat.geom_2.3-0        
 [29] haven_2.4.3                 tidyselect_1.1.1            SummarizedExperiment_1.23.5 rio_0.5.27                 
 [33] fitdistrplus_1.1-6          XML_3.99-0.8                zoo_1.8-9                   ggpubr_0.4.0               
 [37] proj4_1.0-10.1              GenomicAlignments_1.29.0    xtable_1.8-4                magrittr_2.0.1             
 [41] cli_3.0.1                   zlibbioc_1.39.0             rstudioapi_0.13             miniUI_0.1.1.1             
 [45] rpart_4.1-15                fastmatch_1.1-3             treeio_1.17.2               maps_3.4.0                 
 [49] shiny_1.7.1                 clue_0.3-60                 cluster_2.1.2               caTools_1.18.2             
 [53] tidygraph_1.2.0             KEGGREST_1.33.0             ape_5.5                     listenv_0.8.0              
 [57] xlsxjars_0.6.1              Biostrings_2.61.2           png_0.1-7                   future_1.22.1              
 [61] withr_2.4.2                 bitops_1.0-7                ggforce_0.3.3               cellranger_1.1.0           
 [65] GSEABase_1.55.2             pillar_1.6.4                GlobalOptions_0.1.2         cachem_1.0.6               
 [69] fs_1.5.0                    GetoptLong_1.0.5            graphite_1.39.3             vctrs_0.3.8                
 [73] ellipsis_0.3.2              generics_0.1.1              tools_4.1.1                 foreign_0.8-81             
 [77] beeswarm_0.4.0              munsell_0.5.0               tweenr_1.0.2                emmeans_1.7.0              
 [81] DelayedArray_0.19.4         fastmap_1.1.0               compiler_4.1.1              abind_1.4-5                
 [85] httpuv_1.6.3                rtracklayer_1.53.1          plotly_4.10.0               rJava_1.0-5                
 [89] GenomeInfoDbData_1.2.7      gridExtra_2.3               deldir_1.0-6                fftw_1.0-6                 
 [93] utf8_1.2.2                  later_1.3.0                 BiocFileCache_2.1.1         jsonlite_1.7.2             
 [97] scales_1.1.1                graph_1.71.2                carData_3.0-4               tidytree_0.3.5             
[101] pbapply_1.5-0               estimability_1.3            lazyeval_0.2.2              promises_1.2.0.1           
[105] car_3.0-11                  doParallel_1.0.16           R.utils_2.11.0              goftest_1.2-3              
[109] spatstat.utils_2.2-0        reticulate_1.22             checkmate_2.0.0             openxlsx_4.2.4             
[113] ash_1.0-15                  Rtsne_0.15                  downloader_0.4              uwot_0.1.10                
[117] igraph_1.2.7                survival_3.2-13             yaml_2.2.1                  htmltools_0.5.2            
[121] memoise_2.0.0               BiocIO_1.3.0                locfit_1.5-9.4              graphlayouts_0.7.1         
[125] viridisLite_0.4.0           digest_0.6.28               assertthat_0.2.1            mime_0.12                  
[129] rappdirs_0.3.3              Rttf2pt1_1.3.9              RSQLite_2.2.8               yulab.utils_0.0.4          
[133] future.apply_1.8.1          data.table_1.14.2           blob_1.2.2                  R.oo_1.24.0                
[137] splines_4.1.1               ProtGenerics_1.25.1         RCurl_1.98-1.5              broom_0.7.9                
[141] hms_1.1.1                   gprofiler2_0.2.1            modelr_0.1.8                colorspace_2.0-2           
[145] ggbeeswarm_0.6.0            shape_1.4.6                 aplot_0.1.1                 ggrastr_0.2.3              
[149] Rcpp_1.0.7                  RANN_2.6.1                  mvtnorm_1.1-3               enrichplot_1.13.2          
[153] fansi_0.5.0                 tzdb_0.1.2                  parallelly_1.28.1           R6_2.5.1                   
[157] ggridges_0.5.3              lifecycle_1.0.1             zip_2.2.0                   ggsignif_0.6.3             
[161] curl_4.3.2                  leiden_0.3.9                DO.db_2.9                   qvalue_2.25.0              
[165] RcppAnnoy_0.0.19            iterators_1.0.13            htmlwidgets_1.5.4           polyclip_1.10-0            
[169] shadowtext_0.0.9            gridGraphics_0.5-1          reactome.db_1.77.0          rvest_1.0.2                
[173] mgcv_1.8-38                 globals_0.14.0              patchwork_1.1.1             codetools_0.2-18           
[177] matrixStats_0.60.1          lubridate_1.8.0             GO.db_3.14.0                prettyunits_1.1.1          
[181] dbplyr_2.1.1                R.methodsS3_1.8.1           gtable_0.3.0                DBI_1.1.1                  
[185] ggfun_0.0.4                 tensor_1.5                  KernSmooth_2.23-20          vroom_1.5.5                
[189] stringi_1.7.5               progress_1.2.2              farver_2.1.0                annotate_1.71.0            
[193] viridis_0.6.2               ggtree_3.1.6                xml2_1.3.2                  ggalt_0.4.0                
[197] restfulr_0.0.13             homologene_1.   ggplotify_0.1.0             scattermore_0.7            
[201] bit_4.0.4                   scatterpie_0.1.7            MatrixGenerics_1.5.4        spatstat.data_2.1-0        
[205] ggraph_2.0.5                pkgconfig_2.0.3             babelgene_21.4              rstatix_0.7.0
biomaRt • 449 views
Entering edit mode
Last seen 7 hours ago
United States

You are running a bunch of devel packages that are prior to the just released version 3.14 of Bioconductor. You should upgrade to the release version and try again.

Entering edit mode

To be clear, I have no problems connecting, so you should check your install first.

Entering edit mode
Mike Smith ★ 5.9k
Last seen 6 hours ago
EMBL Heidelberg

James is right that problems starting on Thursday would tie in with the release of Bioconductor 3.14. You can use BiocManager::valid() to check what version you're using (and if there are any package conflicts) and BiocManager::install(version = "3.14") to make sure if you're using the latest versions.

If that doesn't help, what happens if you replace your calls to useMart() with useEnsembl()? In this specific case, where you're using CentOS, I'd also advise setting the argument mirror = "www".

I've seen issue in the past with certain versions of Linux not accepting the SSL certificates that the Ensembl mirror sites have. useEnsembl() tries to detect if this is a problem and will change some settings in the background - however I don't think I've ever seen "Peer's Certificate issuer is not recognized", so it may not help here.


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