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seandavi / GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor
http://seandavi.github.io/GEOquery/
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findFirstEntity enters infinite loop on GSEMatrix file stored locally #57

Closed seandavi closed 6 years ago

seandavi commented 6 years ago

Reported by Mike Love and Mike Smith who noted that the GSEMatrix file parsing seemed to not end. GEOquery enters an infinite loop in findFirstEntity.

This code from http://bioconductor.org/packages/3.6/data/experiment/vignettes/airway/inst/doc/airway.html produced the bug:

suppressPackageStartupMessages( library( "GEOquery" ) )
suppressPackageStartupMessages( library( "airway" ) )
dir <- system.file("extdata",package="airway")
geofile <- file.path(dir, "GSE52778_series_matrix.txt")
gse <- getGEO(filename=geofile)