GEOquery::getGEO warning: not all columns named in 'colClasses' exist
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@alexvpickering
Last seen 11 weeks ago
Canada

I'm getting a warning message from GEOquery function getGEO (only seems to happen with GSEMatrix = TRUE).  May be a bug (I believe everything is up to date).

library(GEOquery)
gse <- getGEO("GSE61538", GSEMatrix=TRUE)

Warning message:
In read.table(file = file, header = header, sep = sep, quote = quote,  :
  not all columns named in 'colClasses' exist

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
[1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8      
[4] LC_COLLATE=en_CA.UTF-8     LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8  
[7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                  LC_ADDRESS=C             
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GEOquery_2.38.4     Biobase_2.32.0      BiocGenerics_0.18.0

loaded via a namespace (and not attached):
[1] httr_1.1.0     R6_2.1.2       tools_3.3.0    RCurl_1.95-4.8 bitops_1.0-6   XML_3.98-1.4  
GEOquery • 1.5k views
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2
Entering edit mode
@sean-davis-490
Last seen 18 days ago
United States
I need to do a little cleanup, but this is just a warning and will not affect your ability to use GEOquery.
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