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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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Error parsing GSE6030_family.soft.gz #100

Closed ghost closed 3 years ago

ghost commented 4 years ago

Data File

SOFT file obtained from NCBI.

Steps To Reproduce

Launch R from dir with downloaded GSE6030 SOFT file:

library(GEOquery)
soft <- getGEO(filename= "./GSE6030_family.soft.gz")

Error Message

Using locally cached version of GSE6030 found here:
/home/allen/GSE6030.soft.gz
Reading file....
Parsing....
Found 7 entities...
GPL1261 (1 of 8 entities)
Warning: 64 parsing failures.
  row     col           expected    actual         file
45038 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
45039 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
45040 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
45041 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
45042 SPOT_ID 1/0/T/F/TRUE/FALSE --Control literal data
..... ....... .................. ......... ............
See problems(...) for more details.

GSM139983 (2 of 8 entities)
GSM139984 (3 of 8 entities)
GSM139985 (4 of 8 entities)
GSM139986 (5 of 8 entities)
GSM139987 (6 of 8 entities)
GSM139988 (7 of 8 entities)

Any help is appreciated. Thanks.

seandavi commented 3 years ago

Sorry, @ghost, for taking so long to get back to you. I don't see any errors with the current devel (soon to be release) version of GEOquery. If you still see problems, feel free to post a new issue.