<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi again Türküler<div class=""><br class=""></div><div class="">Just to help me debug things a bit more, could you let me know when you ran your script? I can then check if that time coincides with any known issues at our end.</div><div class=""><br class=""></div><div class="">Thanks</div><div class=""><br class=""></div><div class="">Anne</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 19 Mar 2020, at 22:42, Türküler Özgümüş <<a href="mailto:turkulerc@gmail.com" class="">turkulerc@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi,</div><div class=""><br class=""></div><div class="">I had a problem with the below code. It is not about the code itself since the first time I ran it I got the results. But then because of a downstream error, unrelated to this one, I had to run it again. I ran it several times and every time there were different error messages until at the end it ran as expected. I got my results but I don't understand the problem here. So, I am reporting :) <br class=""></div><div class=""><br class=""></div><div class="">Best regards,</div><div class="">Turkuler<br class=""></div><div class=""><br class=""></div><div class=""><b class="">Code:</b><br class=""></div><div class="">library(biomaRt)<br class="">mart <- useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL", version=99, dataset = "hsapiens_gene_ensembl")<br class="">tx2gene <- getBM(attributes = c("ensembl_transcript_id", "transcript_version", "ensembl_gene_id", "external_gene_name","entrezgene_id"), mart = mart)</div><div class=""><br class=""></div><div class=""><b class="">Message #1</b></div><div class="">Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE, : <br class=""> Unexpected format to the list of available marts.<br class="">Please check the following URL manually, and try ?listMarts for advice.<br class=""><a href="http://dec2019.archive.ensembl.org/biomart/martservice?type=registry&requestid=biomaRt" target="_blank" class="">http://dec2019.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt</a><br class="">Calls: useEnsembl -> useMart -> listMarts<br class="">Execution halted</div><div class=""><br class=""></div><div class=""><b class="">Message #2 </b>(Archive version changes but error message stays the same here)<br class=""><b class=""></b></div><div class="">Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE, : <br class=""> Unexpected format to the list of available marts.<br class="">Please check the following URL manually, and try ?listMarts for advice.<br class=""><a href="http://jan2020.archive.ensembl.org/biomart/martservice?type=registry&requestid=biomaRt" target="_blank" class="">http://jan2020.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt</a><br class="">Calls: useEnsembl -> useMart -> listMarts<br class="">Execution halted</div><div class=""><br class=""></div><div class=""><b class="">Message #3</b></div><div class="">Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : <br class=""> line 1 did not have 3 elements<br class="">Calls: getBM -> read.table -> scan<br class="">Execution halted</div><div class=""><br class=""></div><div class=""><b class="">Message #4</b><br class=""></div><div class="">Error in useMart(biomart = biomart, dataset = dataset, host = host, verbose = verbose) : <br class=""> Incorrect BioMart name, use the listMarts function to see which BioMart databases are available<br class="">Calls: useEnsembl -> useMart<br class="">Execution halted</div><div class=""><br class=""></div><div class=""><b class="">Message #5 </b>(In this case it continues to the following lines without any problem)<br class=""><b class=""></b></div><div class="">Note: requested host was redirected from<br class=""><a href="http://jan2020.archive.ensembl.org/" target="_blank" class="">http://jan2020.archive.ensembl.org</a> to <a href="http://www.ensembl.org/biomart/martservice" target="_blank" class="">http://www.ensembl.org:80/biomart/martservice</a><br class="">This often occurs when connecting to the archive URL for the current Ensembl release<br class="">You can check the current version number using listEnsemblArchives()</div><div class=""><br class=""></div><div class=""><b class="">sessionInfo()</b></div><div class="">R version 3.5.2 (2018-12-20)<br class="">Platform: x86_64-pc-linux-gnu (64-bit)<br class="">Running under: Red Hat Enterprise Linux<br class=""><br class="">Matrix products: default<br class="">BLAS: /gpfs/gpfs0/RHEL7-Tools/Software/R/3.5.2/lib64/R/lib/libRblas.so<br class="">LAPACK: /gpfs/gpfs0/RHEL7-Tools/Software/R/3.5.2/lib64/R/lib/libRlapack.so<br class=""><br class="">locale:<br class=""> [1] LC_CTYPE=C LC_NUMERIC=C <br class=""> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 <br class=""> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 <br class=""> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C <br class=""> [9] LC_ADDRESS=C LC_TELEPHONE=C <br class="">[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C <br class=""><b class=""><br class=""></b>attached base packages:<b class=""><br class=""></b>[1] stats graphics grDevices utils datasets methods base <br class=""><br class="">other attached packages:<br class=""> [1] biomaRt_2.38.0 forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3 <br class=""> [5] purrr_0.3.2 readr_1.3.1 tidyr_0.8.3 tibble_2.1.3 <br class=""> [9] ggplot2_3.2.0 tidyverse_1.2.1</div></div>
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