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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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readr troubles remaining #83

Closed powestermark closed 3 years ago

powestermark commented 5 years ago

There seems to be some remaining bugs regarding GEOquery interoperation with readr. Downgrading to readr 1.1.1 and GEOquery 2.46.14 fixed this for me.

` getGEO("GSE80672") Found 1 file(s) GSE80672_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80672/matrix/GSE80672_series_matrix.txt.gz' Content type 'application/x-gzip' length 12745 bytes (12 KB)

downloaded 12 KB

Parsed with column specification: cols()

Error in .subset2(x, i) : subscript out of bounds

Traceback: 5. [[.tbl_df(datamat, 1) 4. datamat[[1]] 3. parseGSEMatrix(destfile, destdir = destdir, AnnotGPL = AnnotGPL, getGPL = getGPL) 2. getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL, parseCharacteristics = parseCharacteristics) 1. getGEO("GSE80672")

sessionInfo() R version 3.5.3 (2019-03-11) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.4

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] GEOquery_2.50.5 Biobase_2.42.0 BiocGenerics_0.28.0 pwrutilities_0.1.0 magrittr_1.5

loaded via a namespace (and not attached): [1] Rcpp_1.0.1 tidyr_0.8.3 crayon_1.3.4 packrat_0.5.0 dplyr_0.8.0.1 assertthat_0.2.1 [7] R6_2.4.0 pillar_1.3.1 stringi_1.4.3 rlang_0.3.2 curl_3.3 rstudioapi_0.10 [13] limma_3.38.3 xml2_1.2.0 tools_3.5.3 readr_1.3.1 glue_1.3.1 purrr_0.3.2
[19] hms_0.4.2 compiler_3.5.3 pkgconfig_2.0.2 tidyselect_0.2.5 tibble_2.1.1 `

seandavi commented 3 years ago

We've entirely removed readr from GEOquery.