Question: Error in "getGSEDataTables" in GSEquery package
gravatar for ajwijeratne.1
2.5 years 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 21 months ago by Sean Davis21k • written 2.5 years ago by ajwijeratne.110
gravatar for sharvari gujja
21 months ago by
United States
sharvari gujja20 wrote:


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



ADD COMMENTlink written 21 months ago by sharvari gujja20
gravatar for Sean Davis
21 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 21 months ago by Sean Davis21k
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