[BioC] Pathview hickups

[Luo Weijun]

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 Outdated packages and Bioconductor may run with unexpected conflicts.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

 > https://www.youtube.com/watch?v=sne_Nb9au20
 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"--------------------------