Question: Problem with getGEO (GEOquery)
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gravatar for luciano.anselmino
16 months ago by
luciano.anselmino0 wrote:

Good morning everyone, I'm having problems with the getGEO function, every time I try I get this message (below). I already updated my version of R and Bioconductor, I tested on other computers and it works but not on mine. Also try to execute the code by deactivating the firewall, without answer. Someone help me?

GSE72970<- getGEO("GSE72970", GSEMatrix = TRUE) Found 1 file(s) GSE72970_series_matrix.txt.gz testing the URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72970/matrix/GSE72970_series_matrix.txt.gz' Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", : not possible open the URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72970/matrix/GSE72970_series_matrix.txt.gz' In addition: Warning message: In download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", : InternetOpenUrl failed: 'An error occurred in the secure channel support'

sessionInfo() R version 3.5.1 Patched (2018-07-02 r74950) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=Spanish_Argentina.1252 LC_CTYPE=Spanish_Argentina.1252
[3] LC_MONETARY=Spanish_Argentina.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Argentina.1252

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

other attached packages: [1] GEOquery_2.48.0 Biobase_2.40.0 BiocGenerics_0.26.0

loaded via a namespace (and not attached): [1] Rcpp_0.12.17 tidyr_0.8.1 dplyr_0.7.6 assertthat_0.2.0 R6_2.2.2
[6] magrittr_1.5 pillar_1.2.3 rlang_0.2.1 curl_3.2 bindrcpp_0.2.2
[11] limma_3.36.2 xml2_1.2.0 readr_1.1.1 glue_1.2.0 purrr_0.2.5
[16] hms_0.4.2 compiler_3.5.1 pkgconfig_2.0.1 bindr_0.1.1 tidyselect_0.2.4 [21] tibble_1.4.2

geoquery R getgeo • 599 views
ADD COMMENTlink written 16 months ago by luciano.anselmino0

Good time Did you solve this problem? I have the same problem. Can you help me?

ADD REPLYlink written 20 days ago by mahal13660
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