Error in gzfile(fname, open = "rt") : invalid 'description' argument - r

Question

library(Biobase)
library(GEOquery)
gds4577 <- getGEO(filename='c:/test/GDS4577_full.soft.gz')
eset <- GDS2eSet(gds4577, do.log2=TRUE)
> eset <- GDS2eSet(gds4577, do.log2=TRUE)
File stored at:
C:\DOCUME~1\sanya\LOCALS~1\Temp\RtmpQtuak0/GPL1261.annot.gzC:\DOCUME~1\sanya\LOCALS~1\Temp\RtmpQtuak0/GPL1261.annot.gz
Error in gzfile(fname, open = "rt") : invalid 'description' argument
In addition: Warning messages:
1: In if (GSEMatrix & geotype == "GSE") { :
the condition has length > 1 and only the first element will be used
2: In if (geotype == "GDS") { :
the condition has length > 1 and only the first element will be used
3: In if (geotype == "GSE" & amount == "full") { :
the condition has length > 1 and only the first element will be used
4: In if (geotype == "GSE" & amount != "full" & amount != "table") { :
the condition has length > 1 and only the first element will be used
5: In if (geotype == "GPL") { :
the condition has length > 1 and only the first element will be used
6: In if (!file.exists(destfile)) { :
the condition has length > 1 and only the first element will be used
7: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
only first element of 'url' argument used
8: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
only first element of 'destfile' argument used
> eset
Error: object 'eset' not found
what is the matter with my computer?
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Chinese_People's Republic of China.936 LC_CTYPE=Chinese_People's Republic of China.936
[3] LC_MONETARY=Chinese_People's Republic of China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese_People's Republic of China.936
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] GEOquery_2.28.0 BiocInstaller_1.12.0 affy_1.40.0 Biobase_2.22.0 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] affyio_1.30.0 preprocessCore_1.24.0 RCurl_1.95-4.1 tools_3.0.2 XML_3.98-1.1 zlibbioc_1.8.0

Answer 1

GEOquery currently does not handle the case of the "full_soft" file, a file that is a combination of the GDS expression and the GPL information associated with the GDS. I've put parsing the full_soft format on my TODO list. For the time being, avoiding the "full_soft" file format is what I would recommend, also. Doing so is not a problem since GEOquery will reconstruct the "full_soft" file contents when importing a GDS using the standard GEOquery workflow.