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Question: Pathview hickups
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gravatar for Luo Weijun
4.3 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
Animesh, I notice that you are using an old version pathview_1.2.4. This should be the problem. Please always use the updated pathview (currently 1.4.1) with the updated Bioconductor (currently 2.14). Outdated packages and Bioconductor may run with unexpected conflicts. In addition, new functionalities have been added to pathview recently too. It shouldn?t be a KEGG API problem, which has been very stable. Nor should this be a windows problem. Pathview has been test the same way for all operating systems by Bioconductor. HTHs, Weijun -------------------------------------------- On Wed, 7/16/14, Animesh wrote: Subject: Re: Pathview hickups Date: Wednesday, July 16, 2014, 6:22 AM Thanks for the prompt reply Lou. I tried on another machine, with the same problem. Could it be due to Windows or some restriction on KEGG REST API. Do you remember doing any special parameter tuneup? The sessionInfo() is below: > sessionInfo()R version 3.0.3 (2014-03-06)Platform: x86_64-w64-mingw32/x64 (64-bit) locale:[1] LC_COLLATE=English_United States.1252?[2] LC_CTYPE=English_United States.1252 ?? [3] LC_MONETARY=English_United States.1252[4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ?[5] LC_TIME=English_United States.1252 ? ? attached base packages:[1] parallel ?stats ? ? graphics ?grDevices utils ? ? datasets? [7] methods ? base ? ?? other attached packages:?[1] pathview_1.2.4 ? ? ? org.Hs.eg.db_2.10.1??[3] RSQLite_0.11.4 ? ? ? DBI_0.2-7 ? ? ? ? ???[5] AnnotationDbi_1.24.0 Biobase_2.22.0 ? ? ? ?[7] BiocGenerics_0.8.0 ? KEGGgraph_1.20.0 ? ??[9] graph_1.40.1 ? ? ? ? XML_3.98-1.1 ? ? ? ?[11] BiocInstaller_1.12.1 loaded via a namespace (and not attached): ?[1] Biostrings_2.30.1 grid_3.0.3 ? ? ? ?httr_0.3 ? ? ? ???[4] IRanges_1.20.7 ? ?KEGGREST_1.2.2 ? ?png_0.1-7 ? ? ? ??[7] RCurl_1.95-4.1 ? ?Rgraphviz_2.6.0 ? stats4_3.0.3 ? ??[10] stringr_0.6.2 ? ? tools_3.0.3 ? ? ? XVector_0.2.0 ? ? Regards, Animesh --------------------------"The Answer Lies In The Genome"-------------------------- On Wed, Jul 16, 2014 at wrote: I can not reproduce your error. All codes from the tutorial have been extensively tested on Bioconductor servers and by numerous users. I doubt this could be due to your local conflicts. You may want to try the same code or tutorial examples out in a different machine, or start a new and clean R session and try it again. On 7/15/2014 8:58 AM, Animesh wrote:> Dear Weijun, > > I just came across your wonderful tool via your seminar > presentation and found it > useful, something which i would like to try on my own data now :) So i > started with your tutorial, but got stuck on the very first line of > codes, namely: > > library(pathview) > data(gse16873.d) > pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id > <http: pathway.id=""> = "04110", species = "hsa", out.suffix = "gse16873") > > which gives following error: > > In download.file(xml.url, xml.target, quiet = T) : > ? ?downloaded length 45020 != reported length 200 > > I think this has something to do with limited access of REST API to > KEGG? Is there a restriction on how much data can be pulled out in a go? > Kindly share your insight on what might be wrong here? Appended below > the email is the session information for your perusal :) > > > Regards, > Animesh > > > ?> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] parallel ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods > ? ?base > > other attached packages: > ? [1] goProfiles_1.24.0 ? ?GO.db_2.10.1 ? ? ? ? gage_2.12.3 > ? pathview_1.2.4 ? ? ? org.Hs.eg.db_2.10.1 > ? [6] RSQLite_0.11.4 ? ? ? DBI_0.2-7 ? ? ? ? ? ?AnnotationDbi_1.24.0 > Biobase_2.22.0 ? ? ? BiocGenerics_0.8.0 > [11] KEGGgraph_1.20.0 ? ? graph_1.40.1 ? ? ? ? XML_3.98-1.1 > BiocInstaller_1.12.1 > > loaded via a namespace (and not attached): > ? [1] Biostrings_2.30.1 grid_3.0.2 ? ? ? ?httr_0.3 > ? IRanges_1.20.7 ? ?KEGGREST_1.2.2 ? ?png_0.1-7 > ? [7] RCurl_1.95-4.1 ? ?Rgraphviz_2.6.0 ? stats4_3.0.2 > ? stringr_0.6.2 ? ? tools_3.0.2 ? ? ? XVector_0.2.0 > ?> > > --------------------------"The Answer Lies In The > Genome"--------------------------
ADD COMMENTlink written 4.3 years ago by Luo Weijun1.4k
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