biomaRt error in converting mouse to hg gene orthologs · Issue #61 · grimbough/biomaRt

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Please take a look at the code and error messages. ` library(biomaRt) musGenes <- c("Hmmr", "Tlx3", "Cpeb4") mouse = useEnsembl("ensembl","mmusculus_gene_ensembl", mirror ..."> <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> <meta property="fb:app_id" content="1401488693436528"> <meta name="apple-itunes-app" content="app-id=1477376905, app-argument=https://github.com/_view_fragments/issues/show/grimbough/biomaRt/61/issue_layout" /> <meta name="twitter:image" content="https://opengraph.githubassets.com/4a888c4c77f995d18595706ea51ce5fc327cb4b721e5f58101f9b39045c39085/grimbough/biomaRt/issues/61" /><meta name="twitter:site" content="@github" /><meta name="twitter:card" content="summary_large_image" /><meta name="twitter:title" content="biomaRt error in converting mouse to hg gene orthologs · Issue #61 · grimbough/biomaRt" /><meta name="twitter:description" content="Hi, I have been trying to convert mouse genes to human orthologs. Please take a look at the code and error messages. ` library(biomaRt) musGenes &lt;- c(&quot;Hmmr&quot;, &quot;Tlx3&quot;, &quot;Cp..." /> <meta property="og:image" content="https://opengraph.githubassets.com/4a888c4c77f995d18595706ea51ce5fc327cb4b721e5f58101f9b39045c39085/grimbough/biomaRt/issues/61" /><meta property="og:image:alt" content="Hi, I have been trying to convert mouse genes to human orthologs. Please take a look at the code and error messages. ` library(biomaRt) musGenes <- c("Hmmr", "Tlx3", "Cpeb4") mouse = useEnsembl("en..." /><meta property="og:image:width" content="1200" /><meta property="og:image:height" content="600" /><meta property="og:site_name" content="GitHub" /><meta property="og:type" content="object" /><meta property="og:title" content="biomaRt error in converting mouse to hg gene orthologs · Issue #61 · grimbough/biomaRt" /><meta property="og:url" content="https://github.com/grimbough/biomaRt/issues/61" /><meta property="og:description" content="Hi, I have been trying to convert mouse genes to human orthologs. Please take a look at the code and error messages. ` library(biomaRt) musGenes <- c("Hmmr", "Tlx3", "Cpeb4") mouse = useEnsembl("en..." /><meta property="og:author:username" content="pallavisurana1" /> <meta name="hostname" content="github.com"> <meta name="expected-hostname" content="github.com"> <meta http-equiv="x-pjax-version" content="272935131c2027f789efabd5bf30904ffaea35908a22afd03d8f75128cee7e1b" data-turbo-track="reload"> <meta http-equiv="x-pjax-csp-version" content="ace39c3b6632770952207593607e6e0be0db363435a8b877b1f96abe6430f345" data-turbo-track="reload"> <meta http-equiv="x-pjax-css-version" content="8968ee26e93ec8c6d3c4e91c77fb9d206091689d451ebbcddeca3832587a5b30" data-turbo-track="reload"> <meta http-equiv="x-pjax-js-version" content="c4972ae1cf5d4607c47252349fc1b47a24ff0ea303e5a8fbbe18ec27725a87ee" data-turbo-track="reload"> <meta name="turbo-cache-control" content="no-preview" data-turbo-transient=""> <meta name="voltron-timing" value="345"> <meta name="go-import" 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class="HeaderMenu-link border-0 width-full width-lg-auto px-0 px-lg-2 py-lg-2 no-wrap d-flex flex-items-center flex-justify-between js-details-target" aria-expanded="false"> Resources <svg opacity="0.5" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-chevron-down HeaderMenu-icon ml-1"> <path d="M12.78 5.22a.749.749 0 0 1 0 1.06l-4.25 4.25a.749.749 0 0 1-1.06 0L3.22 6.28a.749.749 0 1 1 1.06-1.06L8 8.939l3.72-3.719a.749.749 0 0 1 1.06 0Z"></path> </svg> </button> <div class="HeaderMenu-dropdown dropdown-menu rounded m-0 p-0 pt-2 pt-lg-4 position-relative position-lg-absolute left-0 left-lg-n3 pb-2 pb-lg-4 d-lg-flex flex-wrap dropdown-menu-wide"> <div class="HeaderMenu-column px-lg-4 border-lg-right mb-4 mb-lg-0 pr-lg-7"> <div class="border-bottom pb-3 pb-lg-0 border-lg-bottom-0"> <span class="d-block h4 color-fg-default my-1" id="resources-topics-heading">Topics</span> <ul class="list-style-none f5" 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class="HeaderMenu-dropdown dropdown-menu rounded m-0 p-0 pt-2 pt-lg-4 position-relative position-lg-absolute left-0 left-lg-n3 pb-2 pb-lg-4 px-lg-4"> <div class="HeaderMenu-column"> <div class="border-bottom pb-3 pb-lg-0 pb-lg-3 mb-3 mb-lg-0 mb-lg-3"> <ul class="list-style-none f5" > <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description" data-analytics-event="{"location":"navbar","action":"github_sponsors","context":"open_source","tag":"link","label":"github_sponsors_link_open_source_navbar"}" href="/sponsors"> <div> <div class="color-fg-default h4">GitHub Sponsors</div> Fund open source developers </div> </a></li> </ul> </div> <div class="border-bottom pb-3 pb-lg-0 pb-lg-3 mb-3 mb-lg-0 mb-lg-3"> <ul class="list-style-none f5" > <li> <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary d-flex flex-items-center Link--has-description" 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data-action=" combobox-commit:query-builder#comboboxCommit mousedown:query-builder#resultsMousedown " data-target="query-builder.resultsList" data-persist-list=false id="query-builder-test-results" ></ul> </div> <div class="FormControl-inlineValidation" id="validation-dcf9d7ef-c2cd-46c1-bb87-daae0370c69d" hidden="hidden"> <span class="FormControl-inlineValidation--visual"> <svg aria-hidden="true" height="12" viewBox="0 0 12 12" version="1.1" width="12" data-view-component="true" class="octicon octicon-alert-fill"> <path d="M4.855.708c.5-.896 1.79-.896 2.29 0l4.675 8.351a1.312 1.312 0 0 1-1.146 1.954H1.33A1.313 1.313 0 0 1 .183 9.058ZM7 7V3H5v4Zm-1 3a1 1 0 1 0 0-2 1 1 0 0 0 0 2Z"></path> </svg> </span> <span></span> </div> </div> <div data-target="query-builder.screenReaderFeedback" aria-live="polite" aria-atomic="true" class="sr-only"></div> </query-builder></form> <div class="d-flex flex-row color-fg-muted px-3 text-small color-bg-default search-feedback-prompt"> <a target="_blank" href="https://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax" data-view-component="true" class="Link color-fg-accent text-normal ml-2"> Search syntax tips </a> <div class="d-flex flex-1"></div> </div> </div> </div> </div> </modal-dialog></div> </div> <div data-action="click:qbsearch-input#retract" class="dark-backdrop position-fixed" hidden data-target="qbsearch-input.darkBackdrop"></div> <div class="color-fg-default"> <dialog-helper> <dialog data-target="qbsearch-input.feedbackDialog" data-action="close:qbsearch-input#handleDialogClose cancel:qbsearch-input#handleDialogClose" id="feedback-dialog" aria-modal="true" aria-labelledby="feedback-dialog-title" aria-describedby="feedback-dialog-description" data-view-component="true" class="Overlay Overlay-whenNarrow Overlay--size-medium Overlay--motion-scaleFade Overlay--disableScroll"> <div data-view-component="true" class="Overlay-header"> <div class="Overlay-headerContentWrap"> <div class="Overlay-titleWrap"> <h1 class="Overlay-title " id="feedback-dialog-title"> Provide feedback </h1> </div> <div class="Overlay-actionWrap"> <button data-close-dialog-id="feedback-dialog" aria-label="Close" type="button" data-view-component="true" class="close-button Overlay-closeButton"><svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x"> <path d="M3.72 3.72a.75.75 0 0 1 1.06 0L8 6.94l3.22-3.22a.749.749 0 0 1 1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path> </svg></button> </div> </div> </div> <scrollable-region data-labelled-by="feedback-dialog-title"> <div data-view-component="true" class="Overlay-body"> </option></form><form id="code-search-feedback-form" data-turbo="false" action="/search/feedback" accept-charset="UTF-8" method="post"><input type="hidden" data-csrf="true" name="authenticity_token" value="woLHEnZpaA8mzEFufeNioJc+/a30FPbPXSHh4A4hIG4Oknq1z5/u7WSyn+IK5CTqnHYswMnTcv2hkbivvkcD1w==" /> <p>We read every piece of feedback, and take your input very seriously.</p> <textarea name="feedback" class="form-control width-full mb-2" style="height: 120px" id="feedback"></textarea> <input name="include_email" id="include_email" aria-label="Include my email address so I can be contacted" class="form-control mr-2" type="checkbox"> <label for="include_email" style="font-weight: normal">Include my email address so I can be contacted</label> </form></div> </scrollable-region> <div data-view-component="true" class="Overlay-footer Overlay-footer--alignEnd"> <button data-close-dialog-id="feedback-dialog" type="button" data-view-component="true" class="btn"> Cancel </button> <button form="code-search-feedback-form" data-action="click:qbsearch-input#submitFeedback" type="submit" data-view-component="true" class="btn-primary btn"> Submit feedback </button> </div> </dialog></dialog-helper> <custom-scopes data-target="qbsearch-input.customScopesManager"> <dialog-helper> <dialog data-target="custom-scopes.customScopesModalDialog" data-action="close:qbsearch-input#handleDialogClose cancel:qbsearch-input#handleDialogClose" id="custom-scopes-dialog" aria-modal="true" aria-labelledby="custom-scopes-dialog-title" aria-describedby="custom-scopes-dialog-description" data-view-component="true" class="Overlay Overlay-whenNarrow Overlay--size-medium Overlay--motion-scaleFade Overlay--disableScroll"> <div data-view-component="true" class="Overlay-header Overlay-header--divided"> <div class="Overlay-headerContentWrap"> <div class="Overlay-titleWrap"> <h1 class="Overlay-title " id="custom-scopes-dialog-title"> Saved searches </h1> <h2 id="custom-scopes-dialog-description" class="Overlay-description">Use saved searches to filter your results more quickly</h2> </div> <div class="Overlay-actionWrap"> <button data-close-dialog-id="custom-scopes-dialog" aria-label="Close" type="button" data-view-component="true" class="close-button Overlay-closeButton"><svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x"> <path d="M3.72 3.72a.75.75 0 0 1 1.06 0L8 6.94l3.22-3.22a.749.749 0 0 1 1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path> </svg></button> </div> </div> </div> <scrollable-region data-labelled-by="custom-scopes-dialog-title"> <div data-view-component="true" class="Overlay-body"> <div data-target="custom-scopes.customScopesModalDialogFlash"></div> <div hidden class="create-custom-scope-form" data-target="custom-scopes.createCustomScopeForm"> </option></form><form id="custom-scopes-dialog-form" data-turbo="false" action="/search/custom_scopes" 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class="d-block comment-body markdown-body js-comment-body"> <p dir="auto">Hi, I have been trying to convert mouse genes to human orthologs. Please take a look at the code and error messages.</p> <p dir="auto">`</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="library(biomaRt) musGenes <- c("Hmmr", "Tlx3", "Cpeb4") mouse = useEnsembl("ensembl","mmusculus_gene_ensembl", mirror = "uswest") human = useEnsembl("ensembl","hsapiens_gene_ensembl", mirror = "uswest") genesV2 = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = musGenes , mart = mouse, attributesL = c("hgnc_symbol"), martL = human, uniqueRows=T) "><pre class="notranslate"><code class="notranslate">library(biomaRt) musGenes <- c("Hmmr", "Tlx3", "Cpeb4") mouse = useEnsembl("ensembl","mmusculus_gene_ensembl", mirror = "uswest") human = useEnsembl("ensembl","hsapiens_gene_ensembl", mirror = "uswest") genesV2 = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = musGenes , mart = mouse, attributesL = c("hgnc_symbol"), martL = human, uniqueRows=T) </code></pre></div> <p dir="auto">`</p> <p dir="auto"><code class="notranslate"># ERROR messages Error in .createErrorMessage(error_code = status_code(res), host = host) : object 'err_msg' not found </code></p> <p dir="auto">`</p> <blockquote> <p dir="auto">sessionInfo()<br> R version 4.1.0 (2021-05-18)<br> Platform: x86_64-apple-darwin17.0 (64-bit)<br> Running under: macOS Big Sur 10.16</p> </blockquote> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="biomaRt_2.48.3 loaded via a namespace (and not attached): [1] httr_1.4.2 vroom_1.5.7 bit64_4.0.5 foreach_1.5.2 assertthat_0.2.1 [6] BiocManager_1.30.16 stats4_4.1.0 BiocFileCache_2.0.0 blob_1.2.3 GenomeInfoDbData_1.2.6 [11] progress_1.2.2 pillar_1.7.0 RSQLite_2.2.12 glue_1.6.2 digest_0.6.29 [16] RColorBrewer_1.1-3 XVector_0.32.0 colorspace_2.0-3 plyr_1.8.7 XML_3.99-0.9 [21] pkgconfig_2.0.3 zlibbioc_1.38.0 purrr_0.3.4 xtable_1.8-4 scales_1.2.0 [26] tzdb_0.3.0 tibble_3.1.6 KEGGREST_1.32.0 generics_0.1.2 IRanges_2.26.0 [31] ggplot2_3.3.5 ellipsis_0.3.2 cachem_1.0.6 withr_2.5.0 cli_3.2.0 [36] magrittr_2.0.3 crayon_1.5.1 memoise_2.0.1 fansi_1.0.3 doParallel_1.0.17 [41] xml2_1.3.3 tools_4.1.0 prettyunits_1.1.1 hms_1.1.1 lifecycle_1.0.1 [46] gridBase_0.4-7 stringr_1.4.0 S4Vectors_0.30.2 munsell_0.5.0 AnnotationDbi_1.54.1 [51] Biostrings_2.60.2 compiler_4.1.0 GenomeInfoDb_1.28.4 tinytex_0.38 rlang_1.0.2 [56] grid_4.1.0 RCurl_1.98-1.6 iterators_1.0.14 rstudioapi_0.13 rappdirs_0.3.3 [61] bitops_1.0-7 gtable_0.3.0 codetools_0.2-18 DBI_1.1.2 curl_4.3.2 [66] reshape2_1.4.4 R6_2.5.1 fastmap_1.1.0 bit_4.0.4 utf8_1.2.2 [71] filelock_1.0.2 stringi_1.7.6 Rcpp_1.0.8.3 vctrs_0.4.1 png_0.1-7 [76] dbplyr_2.1.1 tidyselect_1.1.2 xfun_0.30 `"><pre class="notranslate"><code class="notranslate">biomaRt_2.48.3 loaded via a namespace (and not attached): [1] httr_1.4.2 vroom_1.5.7 bit64_4.0.5 foreach_1.5.2 assertthat_0.2.1 [6] BiocManager_1.30.16 stats4_4.1.0 BiocFileCache_2.0.0 blob_1.2.3 GenomeInfoDbData_1.2.6 [11] progress_1.2.2 pillar_1.7.0 RSQLite_2.2.12 glue_1.6.2 digest_0.6.29 [16] RColorBrewer_1.1-3 XVector_0.32.0 colorspace_2.0-3 plyr_1.8.7 XML_3.99-0.9 [21] pkgconfig_2.0.3 zlibbioc_1.38.0 purrr_0.3.4 xtable_1.8-4 scales_1.2.0 [26] tzdb_0.3.0 tibble_3.1.6 KEGGREST_1.32.0 generics_0.1.2 IRanges_2.26.0 [31] ggplot2_3.3.5 ellipsis_0.3.2 cachem_1.0.6 withr_2.5.0 cli_3.2.0 [36] magrittr_2.0.3 crayon_1.5.1 memoise_2.0.1 fansi_1.0.3 doParallel_1.0.17 [41] xml2_1.3.3 tools_4.1.0 prettyunits_1.1.1 hms_1.1.1 lifecycle_1.0.1 [46] gridBase_0.4-7 stringr_1.4.0 S4Vectors_0.30.2 munsell_0.5.0 AnnotationDbi_1.54.1 [51] Biostrings_2.60.2 compiler_4.1.0 GenomeInfoDb_1.28.4 tinytex_0.38 rlang_1.0.2 [56] grid_4.1.0 RCurl_1.98-1.6 iterators_1.0.14 rstudioapi_0.13 rappdirs_0.3.3 [61] bitops_1.0-7 gtable_0.3.0 codetools_0.2-18 DBI_1.1.2 curl_4.3.2 [66] reshape2_1.4.4 R6_2.5.1 fastmap_1.1.0 bit_4.0.4 utf8_1.2.2 [71] filelock_1.0.2 stringi_1.7.6 Rcpp_1.0.8.3 vctrs_0.4.1 png_0.1-7 [76] dbplyr_2.1.1 tidyselect_1.1.2 xfun_0.30 ` </code></pre></div> </td> </tr> <tr class="d-block pl-3 pr-3 pb-3 js-comment-body-error" hidden> <td class="d-block"> <div class="flash flash-warn" role="alert"> <p class="mb-1"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-info"> <path d="M0 8a8 8 0 1 1 16 0A8 8 0 0 1 0 8Zm8-6.5a6.5 6.5 0 1 0 0 13 6.5 6.5 0 0 0 0-13ZM6.5 7.75A.75.75 0 0 1 7.25 7h1a.75.75 0 0 1 .75.75v2.75h.25a.75.75 0 0 1 0 1.5h-2a.75.75 0 0 1 0-1.5h.25v-2h-.25a.75.75 0 0 1-.75-.75ZM8 6a1 1 0 1 1 0-2 1 1 0 0 1 0 2Z"></path> </svg> The text was updated successfully, but these errors were encountered: </p> <ol class="mb-0 pl-4 ml-4"> </ol> </div> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container 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</span> </details-menu> </details> </div> <div class="d-none d-sm-flex"> </div> <h3 class="f5 text-normal" style="flex: 1 1 auto"> <div> <strong> <a class="author Link--primary text-bold css-overflow-wrap-anywhere " show_full_name="false" data-hovercard-type="user" data-hovercard-url="/users/whywhowhat/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/whywhowhat">whywhowhat</a> </strong> commented <a href="#issuecomment-1108507971" id="issuecomment-1108507971-permalink" class="Link--secondary js-timestamp"><relative-time datetime="2022-04-25T12:28:40Z" class="no-wrap">Apr 25, 2022</relative-time></a> </div> </h3> </div> <div class="edit-comment-hide"> <task-lists disabled sortable> <table class="d-block user-select-contain" data-paste-markdown-skip> <tbody class="d-block"> <tr class="d-block"> <td class="d-block comment-body markdown-body js-comment-body"> <p dir="auto">does <a href="https://github.com/grimbough/biomaRt/issues/59#issuecomment-1099737317" data-hovercard-type="issue" data-hovercard-url="/grimbough/biomaRt/issues/59/hovercard">this</a> help?</p> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container d-none"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" name="authenticity_token" value="cANZhvacJO9-l5f_WywCt4nodK-mMLlz0bmnpnpwi9kZl1BoIZ0Q_Gm_YkXJPocCX-Ki9XzJiZ8EVSZMM75lXg" autocomplete="off" /> <input type="hidden" name="input[subjectId]" value="IC_kwDOBgs-bM5CEn1D"> <input type="hidden" name="input[context]" value="" > <div class="js-comment-reactions-options d-flex 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src="https://avatars.githubusercontent.com/u/104420082?s=80&v=4" width="40" height="40" alt="@tt342400" /></a> </div> <div class=" timeline-comment-group js-minimizable-comment-group js-targetable-element TimelineItem-body my-0 " id="issuecomment-1109470157"> <div class="ml-n3 timeline-comment unminimized-comment comment previewable-edit js-task-list-container js-comment timeline-comment--caret" data-body-version="c8591b979beddbc39f13e388f119ff3c0097dd8abc47f80db27327a6656c1832"> <div class="timeline-comment-header clearfix d-flex" data-morpheus-enabled="false"> <div class="timeline-comment-actions flex-shrink-0 d-flex flex-items-center"> <details class="details-overlay details-reset position-relative d-inline-block"> <summary data-view-component="true" class="timeline-comment-action Link--secondary Button--link Button--medium Button"> <span class="Button-content"> <span class="Button-label"><svg aria-label="Show options" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-kebab-horizontal"> <path d="M8 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3ZM1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Zm13 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Z"></path> </svg></span> </span> </summary> <details-menu class="dropdown-menu dropdown-menu-sw show-more-popover color-fg-default" style="width:185px" src="" preload > <span data-view-component="true"> <clipboard-copy aria-label="Copy link" for="issuecomment-1109470157-permalink" role="menuitem" data-view-component="true" class="dropdown-item btn-link"> Copy link </clipboard-copy> <div aria-live="polite" aria-atomic="true" class="sr-only" data-clipboard-copy-feedback></div> </span> </details-menu> </details> </div> <div class="d-none d-sm-flex"> </div> <h3 class="f5 text-normal" style="flex: 1 1 auto"> <div> <strong> <a class="author Link--primary text-bold css-overflow-wrap-anywhere " show_full_name="false" data-hovercard-type="user" data-hovercard-url="/users/tt342400/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/tt342400">tt342400</a> </strong> commented <a href="#issuecomment-1109470157" id="issuecomment-1109470157-permalink" class="Link--secondary js-timestamp"><relative-time datetime="2022-04-26T07:55:39Z" class="no-wrap">Apr 26, 2022</relative-time></a> </div> </h3> </div> <div class="edit-comment-hide"> <task-lists disabled sortable> <table class="d-block user-select-contain" data-paste-markdown-skip> <tbody class="d-block"> <tr class="d-block"> <td class="d-block comment-body markdown-body js-comment-body"> <p dir="auto">Others have solved this problem, please use this code:</p> <p dir="auto">human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "<a href="https://dec2021.archive.ensembl.org/" rel="nofollow">https://dec2021.archive.ensembl.org/</a>")<br> mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = "<a href="https://dec2021.archive.ensembl.org/" rel="nofollow">https://dec2021.archive.ensembl.org/</a>")</p> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container has-reactions d-flex"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" name="authenticity_token" value="KHB984cpPj1aHsMek5XUeZhDBAx_Ll-q0srUPat8651B5HQdUCgKLk02NqQBh1HMTknSVqXXb0YHJlXX4rIFGg" autocomplete="off" /> <input type="hidden" name="input[subjectId]" value="IC_kwDOBgs-bM5CISvN"> <input type="hidden" name="input[context]" value="" > <div class="js-comment-reactions-options d-flex flex-items-center flex-row flex-wrap"> <button name="input[content]" 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Button--link Button--medium Button"> <span class="Button-content"> <span class="Button-label"><svg aria-label="Show options" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-kebab-horizontal"> <path d="M8 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3ZM1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Zm13 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Z"></path> </svg></span> </span> </summary> <details-menu class="dropdown-menu dropdown-menu-sw show-more-popover color-fg-default" style="width:185px" src="" preload > <span data-view-component="true"> <clipboard-copy aria-label="Copy link" for="issuecomment-1109499394-permalink" role="menuitem" data-view-component="true" class="dropdown-item btn-link"> Copy link </clipboard-copy> <div aria-live="polite" aria-atomic="true" class="sr-only" data-clipboard-copy-feedback></div> </span> </details-menu> </details> </div> <div class="d-none d-sm-flex"> <span aria-label="This user is the owner of the biomaRt repository." data-view-component="true" class="tooltipped tooltipped-n"> <span data-view-component="true" class="Label ml-1">Owner</span> </span> </div> <h3 class="f5 text-normal" style="flex: 1 1 auto"> <div> <strong> <a class="author Link--primary text-bold css-overflow-wrap-anywhere " show_full_name="false" data-hovercard-type="user" data-hovercard-url="/users/grimbough/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/grimbough">grimbough</a> </strong> commented <a href="#issuecomment-1109499394" id="issuecomment-1109499394-permalink" class="Link--secondary js-timestamp"><relative-time datetime="2022-04-26T08:22:27Z" class="no-wrap">Apr 26, 2022</relative-time></a> </div> </h3> </div> <div class="edit-comment-hide"> <task-lists disabled sortable> <table class="d-block user-select-contain" data-paste-markdown-skip> <tbody class="d-block"> <tr class="d-block"> <td class="d-block comment-body markdown-body js-comment-body"> <p dir="auto">There seems to be an issue with the link dataset queries after the latest update to Ensembl version 106. I've reported this to the Ensembl help desk, hopefully there will be a fix soon.</p> <p dir="auto">For now using the 105 archive as suggested by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/tt342400/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/tt342400">@tt342400</a> is the best workaround solution.</p> <p dir="auto">I'll report back here if I hear anything more from the Ensembl team.</p> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container d-none"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" name="authenticity_token" value="_wkj-C4plimhCQaWdqxGBS8c4GcWHH239lK2WVpDGgaWnSoW-SiiOrYh8yzkvsOw-RY2PczlTVsjvjezE430gQ" autocomplete="off" /> <input type="hidden" name="input[subjectId]" value="IC_kwDOBgs-bM5CIZ4C"> <input type="hidden" name="input[context]" value="" > <div class="js-comment-reactions-options d-flex flex-items-center flex-row flex-wrap"> <div class="js-reactions-container"> <details class="dropdown details-reset details-overlay d-inline-block js-all-reactions-popover" hidden> <summary aria-haspopup="true" data-view-component="true" class="Button--link Button--medium Button"> <span class="Button-content"> <span class="Button-label">All reactions</span> </span> </summary> <ul class="dropdown-menu dropdown-menu-se"> </ul> </details> </div> </div> </form></div> </div> </div> </div> </option></form><form class="js-comment-update" id="issuecomment-1109499394-edit-form" data-turbo="false" action="/grimbough/biomaRt/issue_comments/1109499394" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" data-csrf="true" name="authenticity_token" value="TOIkPXLmCJZoLtxuvwx0MpN/pSX93t4yr/aQlosr3PPC4PDhBLg5QHYby4LM9EB8KIGgtr0dwPq3MVCcq0dajw==" /> <include-fragment loading="lazy" src="/grimbough/biomaRt/issue_comments/1109499394/edit_form?textarea_id=issuecomment-1109499394-body&comment_context=" class="previewable-comment-form js-comment-edit-form-deferred-include-fragment" > <p class="text-center mt-3" data-hide-on-error> <span data-view-component="true"> <svg aria-label="Loading..." style="box-sizing: content-box; 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z-index: 99;" src="/user_content_edits/show_edit_history_log/IC_kwDOBgs-bM5CrIAo" preload > <include-fragment class="my-3" style="min-width: 100px;" aria-label="Loading..."> <span data-view-component="true"> <svg style="box-sizing: content-box; color: var(--color-icon-primary);" width="32" height="32" viewBox="0 0 16 16" fill="none" aria-hidden="true" data-view-component="true" class="mx-auto d-block anim-rotate"> <circle cx="8" cy="8" r="7" stroke="currentColor" stroke-opacity="0.25" stroke-width="2" vector-effect="non-scaling-stroke" fill="none" /> <path d="M15 8a7.002 7.002 0 00-7-7" stroke="currentColor" stroke-width="2" stroke-linecap="round" vector-effect="non-scaling-stroke" /> </svg> <span class="sr-only">Loading</span> </span> </include-fragment> </details-menu> </details> </span> </div> </h3> </div> <div class="edit-comment-hide"> <task-lists disabled sortable> <table class="d-block user-select-contain" data-paste-markdown-skip> <tbody class="d-block"> <tr class="d-block"> <td class="d-block comment-body markdown-body js-comment-body"> <p dir="auto">Thank you for your reports. We are actively looking into this issue and can confirm we are seeing the same as you. The error message doesn't make much sense to us, though. I assume this is caused by an error in the error-handling code in biomaRt, so that the original cause is masked?</p> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container d-none"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" name="authenticity_token" value="tvn5bt6Sugl11JAeuXsoMWC36ACB7hGOG2l5U48_5aLfbfCACZOOGmL8ZaQraa2Etr0-WlsXIWLOhfi5xvELJQ" autocomplete="off" /> <input type="hidden" name="input[subjectId]" value="IC_kwDOBgs-bM5CrIAo"> <input type="hidden" name="input[context]" value="" > <div class="js-comment-reactions-options d-flex flex-items-center flex-row flex-wrap"> <div class="js-reactions-container"> <details class="dropdown details-reset details-overlay d-inline-block js-all-reactions-popover" hidden> <summary aria-haspopup="true" data-view-component="true" class="Button--link Button--medium Button"> <span class="Button-content"> <span class="Button-label">All reactions</span> </span> </summary> <ul class="dropdown-menu dropdown-menu-se"> </ul> </details> </div> </div> </form></div> </div> </div> </div> </option></form><form class="js-comment-update" id="issuecomment-1118601256-edit-form" data-turbo="false" action="/grimbough/biomaRt/issue_comments/1118601256" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" data-csrf="true" name="authenticity_token" value="lf220nfbjbfM6IJUV/j2NDH4pY18XLyLLliwlxxb1mexVKJUySvlux09UE6k6hC1dTYpC3Rbr+1P03Em+9hdYg==" /> <include-fragment loading="lazy" src="/grimbough/biomaRt/issue_comments/1118601256/edit_form?textarea_id=issuecomment-1118601256-body&comment_context=" class="previewable-comment-form js-comment-edit-form-deferred-include-fragment" > <p class="text-center mt-3" data-hide-on-error> <span data-view-component="true"> <svg aria-label="Loading..." style="box-sizing: content-box; 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We are actively looking into this issue and can confirm we are seeing the same as you. The error message doesn't make much sense to us, though. I assume this is caused by an error in the error-handling code in biomaRt, so that the original cause is masked?</p> </blockquote> <p dir="auto">Thanks for looking into it. You're correct that the reported error message was a bug in the error handling code. Essential there was a case statement giving advice for known error messages, but I'd missed a default in the case of something unexpected. This has now been patched. The current error message now gives the HTTP response code in this situation:</p> <div class="snippet-clipboard-content notranslate position-relative overflow-auto" data-snippet-clipboard-copy-content="Error: biomaRt has encountered an unknown server error. HTTP error code: 502"><pre class="notranslate"><code class="notranslate">Error: biomaRt has encountered an unknown server error. HTTP error code: 502 </code></pre></div> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container d-none"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" name="authenticity_token" value="720gi3NnpNjUurv6fU2JMKvKpdsZVttzFcczOApf60CG-SllpGaQy8OSTkDvXwyFfcBzgcOv65_AK7LSQ5EFxw" autocomplete="off" /> <input type="hidden" name="input[subjectId]" value="IC_kwDOBgs-bM5CrSMf"> <input type="hidden" name="input[context]" value="" > <div class="js-comment-reactions-options d-flex flex-items-center flex-row flex-wrap"> <div class="js-reactions-container"> <details class="dropdown details-reset details-overlay d-inline-block 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13.132a.25.25 0 0 0 .22.368h12.164a.25.25 0 0 0 .22-.368Zm.53 3.996v2.5a.75.75 0 0 1-1.5 0v-2.5a.75.75 0 0 1 1.5 0ZM9 11a1 1 0 1 1-2 0 1 1 0 0 1 2 0Z"></path> </svg> Sorry, something went wrong. </p> </include-fragment> </form> </div> </div> </div> </div> <div class="js-timeline-item js-timeline-progressive-focus-container" data-gid="CRE_kwDOBgs-bM5Gnfpy"> <div class="TimelineItem"> <div class="TimelineItem-badge"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-cross-reference"> <path d="M2.75 3.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h2a.75.75 0 0 1 .75.75v2.19l2.72-2.72a.749.749 0 0 1 .53-.22h4.5a.25.25 0 0 0 .25-.25v-2.5a.75.75 0 0 1 1.5 0v2.5A1.75 1.75 0 0 1 13.25 13H9.06l-2.573 2.573A1.458 1.458 0 0 1 4 14.543V13H2.75A1.75 1.75 0 0 1 1 11.25v-7.5C1 2.784 1.784 2 2.75 2h5.5a.75.75 0 0 1 0 1.5ZM16 1.25v4.146a.25.25 0 0 1-.427.177L14.03 4.03l-3.75 3.75a.749.749 0 0 1-1.275-.326.749.749 0 0 1 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id="ref-issue-1218782456" > <a href="/grimbough/biomaRt/issues/63" class="Link--primary f4 text-bold markdown-title" data-hovercard-type="issue" data-hovercard-url="/grimbough/biomaRt/issues/63/hovercard"> getLDS Error <span class="color-fg-muted text-normal" >#63</span> </a> </div> <div class="flex-shrink-0 my-1 my-md-0 ml-md-3"> <span title="Status: Closed" data-view-component="true" class="State State--merged State--small d-flex flex-items-center"> <svg aria-hidden="true" height="12" viewBox="0 0 16 16" version="1.1" width="12" data-view-component="true" class="octicon octicon-issue-closed flex-items-center mr-1"> <path d="M11.28 6.78a.75.75 0 0 0-1.06-1.06L7.25 8.69 5.78 7.22a.75.75 0 0 0-1.06 1.06l2 2a.75.75 0 0 0 1.06 0l3.5-3.5Z"></path><path d="M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0Zm-1.5 0a6.5 6.5 0 1 0-13 0 6.5 6.5 0 0 0 13 0Z"></path> </svg> Closed </span> </div> </div> </div> </div> </div> <div class="js-timeline-item js-timeline-progressive-focus-container" data-gid="IC_kwDOBgs-bM5CuiKn"> <div class="TimelineItem js-comment-container" data-gid="IC_kwDOBgs-bM5CuiKn" data-url="/grimbough/biomaRt/comments/IC_kwDOBgs-bM5CuiKn/partials/timeline_issue_comment" > <div class="avatar-parent-child TimelineItem-avatar d-none d-md-block"> <a class="d-inline-block" data-hovercard-type="user" data-hovercard-url="/users/ens-ds23/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/ens-ds23"><img class="avatar rounded-2 avatar-user" src="https://avatars.githubusercontent.com/u/6160073?s=80&v=4" width="40" height="40" alt="@ens-ds23" /></a> </div> <div class=" timeline-comment-group js-minimizable-comment-group js-targetable-element TimelineItem-body my-0 " id="issuecomment-1119494823"> <div class="ml-n3 timeline-comment unminimized-comment comment previewable-edit js-task-list-container js-comment timeline-comment--caret" data-body-version="436be1c57188fb7b38b8ddf2f77221472da6170acbf1944db2613a1d03f50c03"> <div 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role="menuitem" data-view-component="true" class="dropdown-item btn-link"> Copy link </clipboard-copy> <div aria-live="polite" aria-atomic="true" class="sr-only" data-clipboard-copy-feedback></div> </span> </details-menu> </details> </div> <div class="d-none d-sm-flex"> </div> <h3 class="f5 text-normal" style="flex: 1 1 auto"> <div> <strong> <a class="author Link--primary text-bold css-overflow-wrap-anywhere " show_full_name="false" data-hovercard-type="user" data-hovercard-url="/users/ens-ds23/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/ens-ds23">ens-ds23</a> </strong> commented <a href="#issuecomment-1119494823" id="issuecomment-1119494823-permalink" class="Link--secondary js-timestamp"><relative-time datetime="2022-05-06T10:57:51Z" class="no-wrap">May 6, 2022</relative-time></a> </div> </h3> </div> <div class="edit-comment-hide"> <task-lists disabled sortable> <table class="d-block user-select-contain" data-paste-markdown-skip> <tbody class="d-block"> <tr class="d-block"> <td class="d-block comment-body markdown-body js-comment-body"> <p dir="auto">Thanks <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/grimbough/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/grimbough">@grimbough</a> . Creating a similar query in the biomart UI leads to an unexpected, but clearer presumed configuration error, which I'm following up with our biomart production people. I'm not 100% sure this is the same issue, but it is a genuine one and may be the cause. When we get to the bottom of that one we can see if it helps with this issue as well. I'll also do a binary search on our archives to see if these issues share the same set of biomart instances. Unfortunately, triaging based on logs is difficult (though possible) given the sheer load and the very high baseline error rate as people author and debug scripts: I'm hoping there will be an easier way through, but that's a fallback.</p> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container d-none"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" name="authenticity_token" value="ZDO-DqM98u_TsRRPxcS2tBSsTvtnFtuY0iuKFrX5zBANp7fgdDzG_MSZ4fVX1jMBwqaYob3v63QHxwv8_Dcilw" autocomplete="off" /> <input type="hidden" name="input[subjectId]" value="IC_kwDOBgs-bM5CuiKn"> <input type="hidden" name="input[context]" value="" > <div class="js-comment-reactions-options d-flex flex-items-center flex-row flex-wrap"> <div class="js-reactions-container"> <details class="dropdown details-reset details-overlay d-inline-block js-all-reactions-popover" hidden> <summary aria-haspopup="true" data-view-component="true" class="Button--link Button--medium Button"> <span class="Button-content"> <span class="Button-label">All reactions</span> </span> </summary> <ul class="dropdown-menu dropdown-menu-se"> </ul> </details> </div> </div> </form></div> </div> </div> </div> </option></form><form class="js-comment-update" id="issuecomment-1119494823-edit-form" data-turbo="false" action="/grimbough/biomaRt/issue_comments/1119494823" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" data-csrf="true" name="authenticity_token" value="adlo7JzeBYEyvCs3LlG8LnzpSSxiRPJg0v26ZVXlHnRMVNgg97kItMrQEPQ1F3LzU+xlPYhwrA1EL/0lAbgKWQ==" /> <include-fragment loading="lazy" src="/grimbough/biomaRt/issue_comments/1119494823/edit_form?textarea_id=issuecomment-1119494823-body&comment_context=" class="previewable-comment-form js-comment-edit-form-deferred-include-fragment" > <p class="text-center mt-3" data-hide-on-error> <span data-view-component="true"> <svg aria-label="Loading..." style="box-sizing: content-box; 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If it's helpful I can strip away all the R package machinery and provide the underlying XML query that can be submitted with cURL at the command line. Let me know if that's of interest to you.</p> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container d-none"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" name="authenticity_token" value="FKbYMz2FPlT4KDAArPFq0Ub2OF1tCTXX0BZ8UF7GDud9MtHd6oQKR-8Axbo-4-9kkPzuB7fwBTsF-v26FwjgYA" autocomplete="off" /> <input type="hidden" name="input[subjectId]" value="IC_kwDOBgs-bM5Cu3VA"> <input type="hidden" name="input[context]" value="" > <div class="js-comment-reactions-options d-flex flex-items-center flex-row flex-wrap"> <div class="js-reactions-container"> <details class="dropdown details-reset details-overlay d-inline-block 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13.132a.25.25 0 0 0 .22.368h12.164a.25.25 0 0 0 .22-.368Zm.53 3.996v2.5a.75.75 0 0 1-1.5 0v-2.5a.75.75 0 0 1 1.5 0ZM9 11a1 1 0 1 1-2 0 1 1 0 0 1 2 0Z"></path> </svg> Sorry, something went wrong. </p> </include-fragment> </form> </div> </div> </div> </div> <div class="js-timeline-item js-timeline-progressive-focus-container" data-gid="CRE_kwDOBgs-bM5GoQwD"> <div class="TimelineItem"> <div class="TimelineItem-badge"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-cross-reference"> <path d="M2.75 3.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h2a.75.75 0 0 1 .75.75v2.19l2.72-2.72a.749.749 0 0 1 .53-.22h4.5a.25.25 0 0 0 .25-.25v-2.5a.75.75 0 0 1 1.5 0v2.5A1.75 1.75 0 0 1 13.25 13H9.06l-2.573 2.573A1.458 1.458 0 0 1 4 14.543V13H2.75A1.75 1.75 0 0 1 1 11.25v-7.5C1 2.784 1.784 2 2.75 2h5.5a.75.75 0 0 1 0 1.5ZM16 1.25v4.146a.25.25 0 0 1-.427.177L14.03 4.03l-3.75 3.75a.749.749 0 0 1-1.275-.326.749.749 0 0 1 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id="ref-issue-1203539335" > <a href="/grimbough/biomaRt/issues/59" class="Link--primary f4 text-bold markdown-title" data-hovercard-type="issue" data-hovercard-url="/grimbough/biomaRt/issues/59/hovercard"> Recent problem with Ensembl: "object 'err_msg' not found" <span class="color-fg-muted text-normal" >#59</span> </a> </div> <div class="flex-shrink-0 my-1 my-md-0 ml-md-3"> <span title="Status: Closed" data-view-component="true" class="State State--merged State--small d-flex flex-items-center"> <svg aria-hidden="true" height="12" viewBox="0 0 16 16" version="1.1" width="12" data-view-component="true" class="octicon octicon-issue-closed flex-items-center mr-1"> <path d="M11.28 6.78a.75.75 0 0 0-1.06-1.06L7.25 8.69 5.78 7.22a.75.75 0 0 0-1.06 1.06l2 2a.75.75 0 0 0 1.06 0l3.5-3.5Z"></path><path d="M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0Zm-1.5 0a6.5 6.5 0 1 0-13 0 6.5 6.5 0 0 0 13 0Z"></path> </svg> Closed </span> </div> </div> </div> </div> </div> <div class="js-timeline-item 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> <span data-view-component="true"> <clipboard-copy aria-label="Copy link" for="issuecomment-1120893847-permalink" role="menuitem" data-view-component="true" class="dropdown-item btn-link"> Copy link </clipboard-copy> <div aria-live="polite" aria-atomic="true" class="sr-only" data-clipboard-copy-feedback></div> </span> </details-menu> </details> </div> <div class="d-none d-sm-flex"> </div> <h3 class="f5 text-normal" style="flex: 1 1 auto"> <div> <strong> <a class="author Link--primary text-bold css-overflow-wrap-anywhere " show_full_name="false" data-hovercard-type="user" data-hovercard-url="/users/sofiapuvogelvittini/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/sofiapuvogelvittini">sofiapuvogelvittini</a> </strong> commented <a href="#issuecomment-1120893847" id="issuecomment-1120893847-permalink" class="Link--secondary js-timestamp"><relative-time datetime="2022-05-09T09:57:35Z" class="no-wrap">May 9, 2022</relative-time></a> </div> </h3> </div> <div class="edit-comment-hide"> <task-lists disabled sortable> <table class="d-block user-select-contain" data-paste-markdown-skip> <tbody class="d-block"> <tr class="d-block"> <td class="d-block comment-body markdown-body js-comment-body"> <p dir="auto">Hello, thanks for providing solutions.<br> I tried tt342400 solution:human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "<a href="https://dec2021.archive.ensembl.org/" rel="nofollow">https://dec2021.archive.ensembl.org/</a>")<br> mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = "<a href="https://dec2021.archive.ensembl.org/" rel="nofollow">https://dec2021.archive.ensembl.org/</a>")<br> however I recieved this error message<br> Error in .getArchiveList(https, httr_config): argument "httr_config" is missing, with no default<br> Do you know how can i fix it ? Thanks a lot,<br> Sof'ia</p> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container d-none"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" name="authenticity_token" value="hUNHzCV4jSUuUUYGYlidHSaEqVeu_mdygq4ChqS594Ls104i8nm5Njl5s7zwShio8I5_DXQHV55XQoNs7XcZBQ" autocomplete="off" /> <input type="hidden" name="input[subjectId]" value="IC_kwDOBgs-bM5Cz3uX"> <input type="hidden" name="input[context]" value="" > <div class="js-comment-reactions-options d-flex flex-items-center flex-row flex-wrap"> <div class="js-reactions-container"> <details class="dropdown details-reset details-overlay d-inline-block 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1.5 0 0 0 0 3Zm13 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Z"></path> </svg></span> </span> </summary> <details-menu class="dropdown-menu dropdown-menu-sw show-more-popover color-fg-default" style="width:185px" src="" preload > <span data-view-component="true"> <clipboard-copy aria-label="Copy link" for="issuecomment-1121410440-permalink" role="menuitem" data-view-component="true" class="dropdown-item btn-link"> Copy link </clipboard-copy> <div aria-live="polite" aria-atomic="true" class="sr-only" data-clipboard-copy-feedback></div> </span> </details-menu> </details> </div> <div class="d-none d-sm-flex"> </div> <h3 class="f5 text-normal" style="flex: 1 1 auto"> <div> <strong> <a class="author Link--primary text-bold css-overflow-wrap-anywhere " show_full_name="false" data-hovercard-type="user" data-hovercard-url="/users/ens-ds23/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/ens-ds23">ens-ds23</a> </strong> commented <a href="#issuecomment-1121410440" id="issuecomment-1121410440-permalink" class="Link--secondary js-timestamp"><relative-time datetime="2022-05-09T18:02:18Z" class="no-wrap">May 9, 2022</relative-time></a> </div> </h3> </div> <div class="edit-comment-hide"> <task-lists disabled sortable> <table class="d-block user-select-contain" data-paste-markdown-skip> <tbody class="d-block"> <tr class="d-block"> <td class="d-block comment-body markdown-body js-comment-body"> <p dir="auto"><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/grimbough/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/grimbough">@grimbough</a> That XML query would be really useful if you could, thank you.</p> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container 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text-normal" style="flex: 1 1 auto"> <div> <strong> <a class="author Link--primary text-bold css-overflow-wrap-anywhere " show_full_name="false" data-hovercard-type="user" data-hovercard-url="/users/grimbough/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/grimbough">grimbough</a> </strong> commented <a href="#issuecomment-1121454896" id="issuecomment-1121454896-permalink" class="Link--secondary js-timestamp"><relative-time datetime="2022-05-09T18:49:08Z" class="no-wrap">May 9, 2022</relative-time></a> </div> </h3> </div> <div class="edit-comment-hide"> <task-lists disabled sortable> <table class="d-block user-select-contain" data-paste-markdown-skip> <tbody class="d-block"> <tr class="d-block"> <td class="d-block comment-body markdown-body js-comment-body"> <blockquote> <p dir="auto"><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/grimbough/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/grimbough">@grimbough</a> That XML query would be really useful if you could, thank you.</p> </blockquote> <p dir="auto">Sure. Here's an example of XML that should do an LDS query for the mouse MGI symbol <code class="notranslate">mt-Co1</code> and return the matching human HGNC symbol:</p> <div class="highlight highlight-text-xml notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE Query> <Query virtualSchemaName = "default" uniqueRows = "1" count = "0" datasetConfigVersion = "0.6" header="1" formatter = "TSV" requestid= "biomaRt"> <Dataset name = "mmusculus_gene_ensembl"> <Attribute name = "mgi_symbol"/> <Filter name = "mgi_symbol" value = "mt-Co1" /> </Dataset> <Dataset name = "hsapiens_gene_ensembl" > <Attribute name = "hgnc_symbol"/> </Dataset> </Query>"><pre class="notranslate"><?<span class="pl-ent">xml</span><span class="pl-e"> version</span>=<span class="pl-s"><span class="pl-pds">"</span>1.0<span class="pl-pds">"</span></span><span class="pl-e"> encoding</span>=<span class="pl-s"><span class="pl-pds">"</span>UTF-8<span class="pl-pds">"</span></span>?> <!<span class="pl-ent">DOCTYPE</span> <span class="pl-e">Query</span>> <<span class="pl-ent">Query</span> virtualSchemaName = <span class="pl-s"><span class="pl-pds">"</span>default<span class="pl-pds">"</span></span> uniqueRows = <span class="pl-s"><span class="pl-pds">"</span>1<span class="pl-pds">"</span></span> count = <span class="pl-s"><span class="pl-pds">"</span>0<span class="pl-pds">"</span></span> datasetConfigVersion = <span class="pl-s"><span class="pl-pds">"</span>0.6<span class="pl-pds">"</span></span> <span class="pl-e">header</span>=<span class="pl-s"><span class="pl-pds">"</span>1<span class="pl-pds">"</span></span> formatter = <span class="pl-s"><span class="pl-pds">"</span>TSV<span class="pl-pds">"</span></span> <span class="pl-e">requestid</span>= <span class="pl-s"><span class="pl-pds">"</span>biomaRt<span class="pl-pds">"</span></span>> <<span class="pl-ent">Dataset</span> name = <span class="pl-s"><span class="pl-pds">"</span>mmusculus_gene_ensembl<span class="pl-pds">"</span></span>> <<span class="pl-ent">Attribute</span> name = <span class="pl-s"><span class="pl-pds">"</span>mgi_symbol<span class="pl-pds">"</span></span>/> <<span class="pl-ent">Filter</span> name = <span class="pl-s"><span class="pl-pds">"</span>mgi_symbol<span class="pl-pds">"</span></span> value = <span class="pl-s"><span class="pl-pds">"</span>mt-Co1<span class="pl-pds">"</span></span> /> </<span class="pl-ent">Dataset</span>> <<span class="pl-ent">Dataset</span> name = <span class="pl-s"><span class="pl-pds">"</span>hsapiens_gene_ensembl<span class="pl-pds">"</span></span> > <<span class="pl-ent">Attribute</span> name = <span class="pl-s"><span class="pl-pds">"</span>hgnc_symbol<span class="pl-pds">"</span></span>/> </<span class="pl-ent">Dataset</span>> </<span class="pl-ent">Query</span>></pre></div> <p dir="auto">Submitting with <strong>wget</strong> gives:</p> <div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="wget -O /dev/stdout 'https://www.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query virtualSchemaName = "default" uniqueRows = "1" count = "0" datasetConfigVersion = "0.6" header="1" formatter = "TSV" requestid= "biomaRt"> <Dataset name = "mmusculus_gene_ensembl"><Attribute name = "mgi_symbol"/><Filter name = "mgi_symbol" value = "mt-Co1" /></Dataset><Dataset name = "hsapiens_gene_ensembl" ><Attribute name = "hgnc_symbol"/></Dataset></Query>' --2022-05-09 20:41:42-- https://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%3C!DOCTYPE%20Query%3E%3CQuery%20virtualSchemaName%20=%20%22default%22%20uniqueRows%20=%20%221%22%20count%20=%20%220%22%20datasetConfigVersion%20=%20%220.6%22%20header=%221%22%20formatter%20=%20%22TSV%22%20requestid=%20%22biomaRt%22%3E%20%3CDataset%20name%20=%20%22mmusculus_gene_ensembl%22%3E%3CAttribute%20name%20=%20%22mgi_symbol%22/%3E%3CFilter%20name%20=%20%22mgi_symbol%22%20value%20=%20%22mt-Co1%22%20/%3E%3C/Dataset%3E%3CDataset%20name%20=%20%22hsapiens_gene_ensembl%22%20%3E%3CAttribute%20name%20=%20%22hgnc_symbol%22/%3E%3C/Dataset%3E%3C/Query%3E Resolving www.ensembl.org (www.ensembl.org)... 193.62.193.83 Connecting to www.ensembl.org (www.ensembl.org)|193.62.193.83|:443... connected. HTTP request sent, awaiting response... 500 Internal Server Error 2022-05-09 20:41:42 ERROR 500: Internal Server Error."><pre class="notranslate">wget -O /dev/stdout <span class="pl-s"><span class="pl-pds">'</span>https://www.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query virtualSchemaName = "default" uniqueRows = "1" count = "0" datasetConfigVersion = "0.6" header="1" formatter = "TSV" requestid= "biomaRt"> <Dataset name = "mmusculus_gene_ensembl"><Attribute name = "mgi_symbol"/><Filter name = "mgi_symbol" value = "mt-Co1" /></Dataset><Dataset name = "hsapiens_gene_ensembl" ><Attribute name = "hgnc_symbol"/></Dataset></Query><span class="pl-pds">'</span></span> --2022-05-09 20:41:42-- https://www.ensembl.org/biomart/martservice<span class="pl-k">?</span>query=%3C<span class="pl-k">?</span>xml%20version=%221.0%22%20encoding=%22UTF-8%22<span class="pl-k">?</span>%3E%3C<span class="pl-k">!</span>DOCTYPE%20Query%3E%3CQuery%20virtualSchemaName%20=%20%22default%22%20uniqueRows%20=%20%221%22%20count%20=%20%220%22%20datasetConfigVersion%20=%20%220.6%22%20header=%221%22%20formatter%20=%20%22TSV%22%20requestid=%20%22biomaRt%22%3E%20%3CDataset%20name%20=%20%22mmusculus_gene_ensembl%22%3E%3CAttribute%20name%20=%20%22mgi_symbol%22/%3E%3CFilter%20name%20=%20%22mgi_symbol%22%20value%20=%20%22mt-Co1%22%20/%3E%3C/Dataset%3E%3CDataset%20name%20=%20%22hsapiens_gene_ensembl%22%20%3E%3CAttribute%20name%20=%20%22hgnc_symbol%22/%3E%3C/Dataset%3E%3C/Query%3E Resolving www.ensembl.org (www.ensembl.org)... 193.62.193.83 Connecting to www.ensembl.org (www.ensembl.org)<span class="pl-k">|</span>193.62.193.83<span class="pl-k">|</span>:443... connected. HTTP request sent, awaiting response... 500 Internal Server Error 2022-05-09 20:41:42 ERROR 500: Internal Server Error.</pre></div> <p dir="auto">Just to check the XML isn't the culprit here's the same thing submitted to the 105 archive:</p> <div class="highlight highlight-source-shell notranslate position-relative overflow-auto" dir="auto" data-snippet-clipboard-copy-content="wget -q -O /dev/stdout 'https://dec2021.archive.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query virtualSchemaName = "default" uniqueRows = "1" count = "0" datasetConfigVersion = "0.6" header="1" formatter = "TSV" requestid= "biomaRt"> <Dataset name = "mmusculus_gene_ensembl"><Attribute name = "mgi_symbol"/><Filter name = "mgi_symbol" value = "mt-Co1" /></Dataset><Dataset name = "hsapiens_gene_ensembl" ><Attribute name = "hgnc_symbol"/></Dataset></Query>' MGI symbol HGNC symbol mt-Co1 MT-CO1"><pre class="notranslate">wget -q -O /dev/stdout <span class="pl-s"><span class="pl-pds">'</span>https://dec2021.archive.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query virtualSchemaName = "default" uniqueRows = "1" count = "0" datasetConfigVersion = "0.6" header="1" formatter = "TSV" requestid= "biomaRt"> <Dataset name = "mmusculus_gene_ensembl"><Attribute name = "mgi_symbol"/><Filter name = "mgi_symbol" value = "mt-Co1" /></Dataset><Dataset name = "hsapiens_gene_ensembl" ><Attribute name = "hgnc_symbol"/></Dataset></Query><span class="pl-pds">'</span></span> MGI symbol HGNC symbol mt-Co1 MT-CO1</pre></div> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container d-none"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" name="authenticity_token" value="sCeB8shlRe2AtglrFFRqJrbm2Vsfy4ewpzKMRe7h8bbZs4gcH2Rx_pee_NGGRu-TYOwPAcUyt1xy3g2vpy8fMQ" autocomplete="off" /> <input type="hidden" name="input[subjectId]" value="IC_kwDOBgs-bM5C2Asw"> <input type="hidden" name="input[context]" value="" > <div class="js-comment-reactions-options d-flex flex-items-center flex-row flex-wrap"> <div class="js-reactions-container"> <details class="dropdown details-reset details-overlay d-inline-block js-all-reactions-popover" hidden> <summary aria-haspopup="true" data-view-component="true" class="Button--link Button--medium Button"> <span class="Button-content"> <span class="Button-label">All reactions</span> </span> </summary> <ul class="dropdown-menu dropdown-menu-se"> </ul> </details> </div> </div> </form></div> </div> </div> </div> </option></form><form class="js-comment-update" id="issuecomment-1121454896-edit-form" data-turbo="false" action="/grimbough/biomaRt/issue_comments/1121454896" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" data-csrf="true" name="authenticity_token" value="vVonYbuJSYQJIFWTI5deJEP2sZ6VUWYB3G/wOM5GSlOrzVQ3FF26xPR1EekH92/I8/F5pTBLlCgHBjLtoLA4NA==" /> <include-fragment loading="lazy" src="/grimbough/biomaRt/issue_comments/1121454896/edit_form?textarea_id=issuecomment-1121454896-body&comment_context=" class="previewable-comment-form js-comment-edit-form-deferred-include-fragment" > <p class="text-center mt-3" data-hide-on-error> <span data-view-component="true"> <svg aria-label="Loading..." style="box-sizing: content-box; 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I'll close this issue.</p> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container d-none"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" name="authenticity_token" value="6pROdO2Y1IvU4BavLRVWJ2nqWIamsYLTxFpGs8PIX12DAEeaOpngmMPI4xW_B9OSv-CO3HxIsj8RtsdZigax2g" autocomplete="off" /> <input type="hidden" name="input[subjectId]" value="IC_kwDOBgs-bM5DIVV5"> <input type="hidden" name="input[context]" value="" > <div class="js-comment-reactions-options d-flex flex-items-center flex-row flex-wrap"> <div class="js-reactions-container"> <details class="dropdown details-reset details-overlay d-inline-block 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height-full"></div> </div> <div class="js-timeline-item js-timeline-progressive-focus-container" data-gid="IC_kwDOBgs-bM5DWjeF"> <div class="TimelineItem js-comment-container" data-gid="IC_kwDOBgs-bM5DWjeF" data-url="/grimbough/biomaRt/comments/IC_kwDOBgs-bM5DWjeF/partials/timeline_issue_comment" > <div class="avatar-parent-child TimelineItem-avatar d-none d-md-block"> <a class="d-inline-block" data-hovercard-type="user" data-hovercard-url="/users/sofiapuvogelvittini/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/sofiapuvogelvittini"><img class="avatar rounded-2 avatar-user" src="https://avatars.githubusercontent.com/u/48957422?s=80&u=6ffeeeb376cb1cc47d177e104134c70423431aac&v=4" width="40" height="40" alt="@sofiapuvogelvittini" /></a> </div> <div class=" timeline-comment-group js-minimizable-comment-group js-targetable-element TimelineItem-body my-0 " id="issuecomment-1129985925"> <div class="ml-n3 timeline-comment unminimized-comment 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show-more-popover color-fg-default" style="width:185px" src="" preload > <span data-view-component="true"> <clipboard-copy aria-label="Copy link" for="issuecomment-1129985925-permalink" role="menuitem" data-view-component="true" class="dropdown-item btn-link"> Copy link </clipboard-copy> <div aria-live="polite" aria-atomic="true" class="sr-only" data-clipboard-copy-feedback></div> </span> </details-menu> </details> </div> <div class="d-none d-sm-flex"> </div> <h3 class="f5 text-normal" style="flex: 1 1 auto"> <div> <strong> <a class="author Link--primary text-bold css-overflow-wrap-anywhere " show_full_name="false" data-hovercard-type="user" data-hovercard-url="/users/sofiapuvogelvittini/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/sofiapuvogelvittini">sofiapuvogelvittini</a> </strong> commented <a href="#issuecomment-1129985925" id="issuecomment-1129985925-permalink" class="Link--secondary js-timestamp"><relative-time datetime="2022-05-18T12:58:57Z" class="no-wrap">May 18, 2022</relative-time></a> </div> </h3> </div> <div class="edit-comment-hide"> <task-lists disabled sortable> <table class="d-block user-select-contain" data-paste-markdown-skip> <tbody class="d-block"> <tr class="d-block"> <td class="d-block comment-body markdown-body js-comment-body"> <p dir="auto">Hello, @<a href="https://github.com/PallaviSurana1">PallaviSurana</a> How did you solve it? I still can't use it</p> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container d-none"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" name="authenticity_token" value="LXCBX6IK6Vf3K4QZz96OD02IgXObF0z_ODN9cb8R8bRE5IixdQvdROADcaNdzAu6m4JXKUHufBPt3_yb9t8fMw" autocomplete="off" /> <input type="hidden" name="input[subjectId]" value="IC_kwDOBgs-bM5DWjeF"> <input type="hidden" name="input[context]" value="" > <div class="js-comment-reactions-options d-flex flex-items-center flex-row flex-wrap"> <div class="js-reactions-container"> <details class="dropdown details-reset details-overlay d-inline-block 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13.132a.25.25 0 0 0 .22.368h12.164a.25.25 0 0 0 .22-.368Zm.53 3.996v2.5a.75.75 0 0 1-1.5 0v-2.5a.75.75 0 0 1 1.5 0ZM9 11a1 1 0 1 1-2 0 1 1 0 0 1 2 0Z"></path> </svg> Sorry, something went wrong. </p> </include-fragment> </form> </div> </div> </div> </div> <div class="js-timeline-item js-timeline-progressive-focus-container" data-gid="IC_kwDOBgs-bM5DkLb5"> <div class="TimelineItem js-comment-container" data-gid="IC_kwDOBgs-bM5DkLb5" data-url="/grimbough/biomaRt/comments/IC_kwDOBgs-bM5DkLb5/partials/timeline_issue_comment" > <div class="avatar-parent-child TimelineItem-avatar d-none d-md-block"> <a class="d-inline-block" data-hovercard-type="user" data-hovercard-url="/users/MertDemirdizen/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/MertDemirdizen"><img class="avatar rounded-2 avatar-user" src="https://avatars.githubusercontent.com/u/68648070?s=80&v=4" width="40" height="40" alt="@MertDemirdizen" /></a> </div> <div class=" 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9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Zm13 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Z"></path> </svg></span> </span> </summary> <details-menu class="dropdown-menu dropdown-menu-sw show-more-popover color-fg-default" style="width:185px" src="" preload > <span data-view-component="true"> <clipboard-copy aria-label="Copy link" for="issuecomment-1133557497-permalink" role="menuitem" data-view-component="true" class="dropdown-item btn-link"> Copy link </clipboard-copy> <div aria-live="polite" aria-atomic="true" class="sr-only" data-clipboard-copy-feedback></div> </span> </details-menu> </details> </div> <div class="d-none d-sm-flex"> </div> <h3 class="f5 text-normal" style="flex: 1 1 auto"> <div> <strong> <a class="author Link--primary text-bold css-overflow-wrap-anywhere " show_full_name="false" data-hovercard-type="user" data-hovercard-url="/users/MertDemirdizen/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/MertDemirdizen">MertDemirdizen</a> </strong> commented <a href="#issuecomment-1133557497" id="issuecomment-1133557497-permalink" class="Link--secondary js-timestamp"><relative-time datetime="2022-05-21T07:41:51Z" class="no-wrap">May 21, 2022</relative-time></a> </div> </h3> </div> <div class="edit-comment-hide"> <task-lists disabled sortable> <table class="d-block user-select-contain" data-paste-markdown-skip> <tbody class="d-block"> <tr class="d-block"> <td class="d-block comment-body markdown-body js-comment-body"> <p dir="auto">I could not fix it too.</p> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container d-none"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" 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src="https://avatars.githubusercontent.com/u/971237?s=40&v=4" width="20" height="20" alt="@grimbough" /></a> <a class="author Link--primary text-bold" data-hovercard-type="user" data-hovercard-url="/users/grimbough/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/grimbough">grimbough</a> reopened this <a href="#event-6655251016" class="Link--secondary"><relative-time datetime="2022-05-21T18:26:47Z" class="no-wrap">May 21, 2022</relative-time></a> </div> </div> <div class="TimelineItem"> <div class="TimelineItem-badge"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-cross-reference"> <path d="M2.75 3.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h2a.75.75 0 0 1 .75.75v2.19l2.72-2.72a.749.749 0 0 1 .53-.22h4.5a.25.25 0 0 0 .25-.25v-2.5a.75.75 0 0 1 1.5 0v2.5A1.75 1.75 0 0 1 13.25 13H9.06l-2.573 2.573A1.458 1.458 0 0 1 4 14.543V13H2.75A1.75 1.75 0 0 1 1 11.25v-7.5C1 2.784 1.784 2 2.75 2h5.5a.75.75 0 0 1 0 1.5ZM16 1.25v4.146a.25.25 0 0 1-.427.177L14.03 4.03l-3.75 3.75a.749.749 0 0 1-1.275-.326.749.749 0 0 1 .215-.734l3.75-3.75-1.543-1.543A.25.25 0 0 1 11.604 1h4.146a.25.25 0 0 1 .25.25Z"></path> </svg> </div> <div class="TimelineItem-body" > <div > <a class="d-inline-block" data-hovercard-type="user" data-hovercard-url="/users/grimbough/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/grimbough"><img class="avatar avatar-user" src="https://avatars.githubusercontent.com/u/971237?s=40&v=4" width="20" height="20" alt="@grimbough" /></a> <a class="author Link--primary text-bold" data-hovercard-type="user" data-hovercard-url="/users/grimbough/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/grimbough">grimbough</a> mentioned this issue <a class="Link--secondary" href="#ref-issue-1246776850" > <relative-time datetime="2022-05-31T06:57:49Z" class="no-wrap">May 31, 2022</relative-time> </a> </div> <div class="mt-2 d-flex flex-items-start flex-column flex-md-row"> <div class="flex-auto wb-break-word" id="ref-issue-1246776850" > <a href="/grimbough/biomaRt/issues/66" class="Link--primary f4 text-bold markdown-title" data-hovercard-type="issue" data-hovercard-url="/grimbough/biomaRt/issues/66/hovercard"> Error getLDS() - Error in attributes(.Data) <span class="color-fg-muted text-normal" >#66</span> </a> </div> <div class="flex-shrink-0 my-1 my-md-0 ml-md-3"> <span title="Status: Open" data-view-component="true" class="State State--open State--small d-flex flex-items-center"> <svg aria-hidden="true" height="12" viewBox="0 0 16 16" version="1.1" width="12" data-view-component="true" class="octicon octicon-issue-opened flex-items-center mr-1"> <path d="M8 9.5a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Z"></path><path d="M8 0a8 8 0 1 1 0 16A8 8 0 0 1 8 0ZM1.5 8a6.5 6.5 0 1 0 13 0 6.5 6.5 0 0 0-13 0Z"></path> </svg> Open </span> </div> </div> </div> </div> </div> <div class="js-timeline-item js-timeline-progressive-focus-container" data-gid="IC_kwDOBgs-bM5IYG2-"> <div class="TimelineItem js-comment-container" data-gid="IC_kwDOBgs-bM5IYG2-" data-url="/grimbough/biomaRt/comments/IC_kwDOBgs-bM5IYG2-/partials/timeline_issue_comment" > <div class="avatar-parent-child TimelineItem-avatar d-none d-md-block"> <a class="d-inline-block" data-hovercard-type="user" data-hovercard-url="/users/yujhao/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/yujhao"><img class="avatar rounded-2 avatar-user" src="https://avatars.githubusercontent.com/u/74956161?s=80&u=84e83f926cbdbf81b3aa26dae3fdf9d181a2758e&v=4" width="40" height="40" alt="@yujhao" /></a> </div> <div class=" timeline-comment-group js-minimizable-comment-group js-targetable-element TimelineItem-body my-0 " id="issuecomment-1214279102"> <div class="ml-n3 timeline-comment unminimized-comment comment previewable-edit js-task-list-container js-comment timeline-comment--caret" data-body-version="0a2748bcce9a7dfca566d19387715ad70723570bedaca88e5ea9125eba8866f2"> <div class="timeline-comment-header clearfix d-flex" data-morpheus-enabled="false"> <div class="timeline-comment-actions flex-shrink-0 d-flex flex-items-center"> <details class="details-overlay details-reset position-relative d-inline-block"> <summary data-view-component="true" class="timeline-comment-action Link--secondary Button--link Button--medium Button"> <span class="Button-content"> <span class="Button-label"><svg aria-label="Show options" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-kebab-horizontal"> <path d="M8 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3ZM1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Zm13 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Z"></path> </svg></span> </span> </summary> <details-menu class="dropdown-menu dropdown-menu-sw show-more-popover color-fg-default" style="width:185px" src="" preload > <span data-view-component="true"> <clipboard-copy aria-label="Copy link" for="issuecomment-1214279102-permalink" role="menuitem" data-view-component="true" class="dropdown-item btn-link"> Copy link </clipboard-copy> <div aria-live="polite" aria-atomic="true" class="sr-only" data-clipboard-copy-feedback></div> </span> </details-menu> </details> </div> <div class="d-none d-sm-flex"> </div> <h3 class="f5 text-normal" style="flex: 1 1 auto"> <div> <strong> <a class="author Link--primary text-bold css-overflow-wrap-anywhere " show_full_name="false" data-hovercard-type="user" data-hovercard-url="/users/yujhao/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/yujhao">yujhao</a> </strong> commented <a href="#issuecomment-1214279102" id="issuecomment-1214279102-permalink" class="Link--secondary js-timestamp"><relative-time datetime="2022-08-14T03:48:35Z" class="no-wrap">Aug 14, 2022</relative-time></a> </div> </h3> </div> <div class="edit-comment-hide"> <task-lists disabled sortable> <table class="d-block user-select-contain" data-paste-markdown-skip> <tbody class="d-block"> <tr class="d-block"> <td class="d-block comment-body markdown-body js-comment-body"> <p dir="auto">IF the error messages: # ERROR messages Error in .createErrorMessage(error_code = status_code(res), host = host) : object 'err_msg' not found.</p> <p dir="auto">Please reload : human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "<a href="https://dec2021.archive.ensembl.org/" rel="nofollow">https://dec2021.archive.ensembl.org/</a>"); mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = "<a href="https://dec2021.archive.ensembl.org/" rel="nofollow">https://dec2021.archive.ensembl.org/</a>"), I can use biomart now. <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/sofiapuvogelvittini/hovercard" data-octo-click="hovercard-link-click" 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class="Button-content"> <span class="Button-label"><svg aria-label="Show options" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-kebab-horizontal"> <path d="M8 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3ZM1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Zm13 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3Z"></path> </svg></span> </span> </summary> <details-menu class="dropdown-menu dropdown-menu-sw show-more-popover color-fg-default" style="width:185px" src="" preload > <span data-view-component="true"> <clipboard-copy aria-label="Copy link" for="issuecomment-1921482174-permalink" role="menuitem" data-view-component="true" class="dropdown-item btn-link"> Copy link </clipboard-copy> <div aria-live="polite" aria-atomic="true" class="sr-only" data-clipboard-copy-feedback></div> </span> </details-menu> </details> </div> <div class="d-none d-sm-flex"> </div> <h3 class="f5 text-normal" style="flex: 1 1 auto"> <div> <strong> <a class="author Link--primary text-bold css-overflow-wrap-anywhere " show_full_name="false" data-hovercard-type="user" data-hovercard-url="/users/andrewyatz/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/andrewyatz">andrewyatz</a> </strong> commented <a href="#issuecomment-1921482174" id="issuecomment-1921482174-permalink" class="Link--secondary js-timestamp"><relative-time datetime="2024-02-01T14:36:42Z" class="no-wrap">Feb 1, 2024</relative-time></a> </div> </h3> </div> <div class="edit-comment-hide"> <task-lists disabled sortable> <table class="d-block user-select-contain" data-paste-markdown-skip> <tbody class="d-block"> <tr class="d-block"> <td class="d-block comment-body markdown-body js-comment-body"> <p dir="auto">Hi all. Just dropping a line as we in Ensembl have had this issue re-raised. I am sorry we haven't been able to fix this and from the thread above it's obvious this is an issue at our end and not in biomaRt. Unfortunately our engineer who commented on the ticket previously was unable to resolve the issue and left EMBL last year. It's collectively on Ensembl's radar to see if there is an obvious regression in our build or configuration of BioMart but initial tests are not yielding much success.</p> <p dir="auto">If we do manage to make progress we will report it back here.</p> <p dir="auto">As for temporary solutions, using the 105 archive is the best course of action but obviously is now quite an old archive</p> </td> </tr> </tbody> </table> </task-lists> <div class="d-flex"> <div class="pr-review-reactions"> <div data-view-component="true" class="comment-reactions js-reactions-container js-reaction-buttons-container social-reactions reactions-container d-none"> </option></form><form class="js-pick-reaction" data-turbo="false" action="/grimbough/biomaRt/reactions" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" name="authenticity_token" value="F2FRFIDJAuO6XrlZG-hHg7M3qsSEFVDzBdUDs29dD4h-9Vj6V8g28K12TOOJ-sI2ZT18nl7sYB_QOYJZJpPhDw" autocomplete="off" /> <input type="hidden" name="input[subjectId]" value="IC_kwDOBgs-bM5yh32-"> <input type="hidden" name="input[context]" value="" > <div class="js-comment-reactions-options d-flex flex-items-center flex-row flex-wrap"> <div class="js-reactions-container"> <details class="dropdown details-reset details-overlay d-inline-block js-all-reactions-popover" hidden> <summary aria-haspopup="true" data-view-component="true" class="Button--link Button--medium Button"> <span class="Button-content"> <span class="Button-label">All reactions</span> </span> </summary> <ul class="dropdown-menu dropdown-menu-se"> </ul> </details> </div> </div> </form></div> </div> </div> </div> </option></form><form class="js-comment-update" id="issuecomment-1921482174-edit-form" data-turbo="false" action="/grimbough/biomaRt/issue_comments/1921482174" accept-charset="UTF-8" method="post"><input type="hidden" name="_method" value="put" autocomplete="off" /><input type="hidden" data-csrf="true" name="authenticity_token" value="/KQm6be6M/KRKYoEdMsEk2Tosm86kiMLIfy2dnDmdcHrTSD584SVa+mHW6bqJlxrft7NiemOIyMPRt4+CcTwBg==" /> <include-fragment loading="lazy" src="/grimbough/biomaRt/issue_comments/1921482174/edit_form?textarea_id=issuecomment-1921482174-body&comment_context=" class="previewable-comment-form js-comment-edit-form-deferred-include-fragment" > <p class="text-center mt-3" data-hide-on-error> <span data-view-component="true"> <svg aria-label="Loading..." style="box-sizing: content-box; 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biomaRt error in converting mouse to hg gene orthologs · Issue #61 · grimbough/biomaRt · GitHub