Question: Error in "getGSEDataTables" in GSEquery package
gravatar for ajwijeratne.1
22 months ago by
United States
ajwijeratne.110 wrote:


I am trying to use "getGSEDataTables" from GSEquery package, but it gives the following error:

> dfl = getGSEDataTables("GSE3494")
error : Unknown IO error
I/O warning : failed to load external entity ""
Error in UseMethod("xmlRoot") : 
  no applicable method for 'xmlRoot' applied to an object of class "NULL"

My session info:

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin14.5.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] GEOquery_2.36.0              devtools_1.9.1               hgu133ahsentrezg.db_20.0.0          
 [5] pd.hgu133a.hs.entrezg_0.0.1  oligo_1.34.2                 oligoClasses_1.32.0          RSQLite_1.0.0               
 [9] DBI_0.3.1                    Biostrings_2.38.4            XVector_0.10.0               hgu133ahsentrezgprobe_20.0.0
[13] hgu133ahsentrezgcdf_20.0.0   AnnotationDbi_1.32.3         IRanges_2.4.8                S4Vectors_0.8.11            
[17] gcrma_2.42.0                 affy_1.48.0                  Biobase_2.30.0               BiocGenerics_0.16.1         
[21] BiocInstaller_1.20.1        

loaded via a namespace (and not attached):
 [1] GenomeInfoDb_1.6.3         bitops_1.0-6               iterators_1.0.8            tools_3.2.3               
 [5] zlibbioc_1.16.0            digest_0.6.8               bit_1.1-12                 memoise_0.2.1             
 [9] preprocessCore_1.32.0      ff_2.2-13                  foreach_1.4.3              curl_0.9.4                
[13] httr_1.0.0                 stringr_1.0.0              affxparser_1.42.0          R6_2.1.1                  
[17] XML_3.98-1.3               magrittr_1.5               codetools_0.2-14           splines_3.2.3             
[21] GenomicRanges_1.22.4       SummarizedExperiment_1.0.2 stringi_1.0-1              RCurl_1.95-4.7            
[25] affyio_1.40.0           
ADD COMMENTlink modified 14 months ago by Sean Davis21k • written 22 months ago by ajwijeratne.110
gravatar for sharvari gujja
14 months ago by
United States
sharvari gujja10 wrote:


I get the same error, and wondered if you have any suggestions to fix it.



ADD COMMENTlink written 14 months ago by sharvari gujja10
gravatar for Sean Davis
14 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:

Sorry I missed this question the first time.  The solution is to upgrade to GEOquery 2.40 or higher due to a change at NCBI from "http" to "https". 

ADD COMMENTlink written 14 months ago by Sean Davis21k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 100 users visited in the last hour