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Question: getGEO: not all columns named in 'colClasses' exist and invalid 'nlines' argument
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gravatar for Shicheng Guo
11 months ago by
United States
Shicheng Guo0 wrote:

Hi All,

When I try to download GSE49656 with GEOquery, errors were always reported: such as not all columns named in 'colClasses' exist

 

When I change to server (linux), some other error reported:

Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :  invalid 'nlines' argument

 

Any idea? 

 

> library("GEOquery")

> GEO <- getGEO("GSE49656")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49656/matrix/
Found 1 file(s)
GSE49656_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49656/matrix/GSE49656_series_matrix.txt.gz'
downloaded 79.6 MB

File stored at:
C:\Users\shicheng\AppData\Local\Temp\RtmpopB434/GPL13534.soft
Warning message:
In read.table(file = file, header = header, sep = sep, quote = quote,  :  not all columns named in 'colClasses' exist


Using locally cached version of GPL13534 found here:
/tmp/Rtmppjr6CA/GPL13534.soft
Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :  invalid 'nlines' argument

 

 

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    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] GEOquery_2.38.4     Biobase_2.32.0      BiocGenerics_0.18.0 mypackage_0.1.0     roxygen2_5.0.1      devtools_1.12.0    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7    XML_3.98-1.4   digest_0.6.10  withr_1.0.2    bitops_1.0-6   R6_2.2.0       magrittr_1.5   httr_1.2.1     stringi_1.1.2  tools_3.3.1   
[11] stringr_1.1.0  RCurl_1.95-4.8 memoise_1.0.0 

 

ADD COMMENTlink modified 11 months ago • written 11 months ago by Shicheng Guo0
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