seandavi / GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor
http://seandavi.github.io/GEOquery/
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using `parseCharacteristics = FALSE` still parses characteristics #60

Open kalugny opened 6 years ago

kalugny commented 6 years ago

E.g.: $ GEOquery::getGEO('GSE23397', parseCharacteristics = FALSE)


Traceback:

1. GEOquery::getGEO("GSE23397", parseCharacteristics = FALSE)
2. getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, 
 .     parseCharacteristics = parseCharacteristics)
3. parseGSEMatrix(destfile, destdir = destdir, AnnotGPL = AnnotGPL, 
 .     getGPL = getGPL)
4. dplyr::mutate(pd, characteristics = ifelse(grepl("_ch2", characteristics), 
 .     "ch2", "ch1")) %>% tidyr::separate(kvpair, into = c("k", 
 .     "v"), sep = ":", fill = "right") %>% dplyr::mutate(k = paste(k, 
 .     characteristics, sep = ":")) %>% dplyr::select(-characteristics) %>% 
 .     tidyr::spread(k, v)
5. withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
6. eval(quote(`_fseq`(`_lhs`)), env, env)
7. eval(quote(`_fseq`(`_lhs`)), env, env)
8. `_fseq`(`_lhs`)
9. freduce(value, `_function_list`)
10. withVisible(function_list[[k]](value))
11. function_list[[k]](value)
12. tidyr::spread(., k, v)
13. spread.data.frame(., k, v)
14. abort(glue("Duplicate identifiers for rows {rows}"))```