Error using the getGEO() patcher

Question

[n,n]

I'm trying to fetch files using the getGEO() function from the GEOQuery package in R. Upon loading the package and trying, I get a known error which can be solved via a patcher function as described in this post: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile

However, after following the steps to solve the error I get a new error:

gset <- getGEO("GSE134231" , GSEMatrix =TRUE, destdir=".")
Error in getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL,  : 
  unused argument (parseCharacteristics = parseCharacteristics)

What could possibly be wrong here? Here is my session info:

R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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

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

other attached packages:
[1] GEOquery_2.52.0     Biobase_2.44.0      BiocGenerics_0.30.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3       tidyr_1.0.2      crayon_1.3.4     dplyr_0.8.4      assertthat_0.2.1
 [6] R6_2.4.1         lifecycle_0.2.0  magrittr_1.5     pillar_1.4.3     rlang_0.4.4     
[11] rstudioapi_0.11  limma_3.40.6     xml2_1.2.2       vctrs_0.2.2      tools_3.6.3     
[16] readr_1.3.1      glue_1.3.1       purrr_0.3.3      hms_0.5.3        compiler_3.6.3  
[21] pkgconfig_2.0.3  tidyselect_1.0.0 tibble_2.1.3

[Kevin Blighe]

Estoy usando / I am using the same version of R, but GEOquery v2.54. The command works for me:

datos <- getGEO("GSE134231" , GSEMatrix =TRUE, destdir=".")
datos
$`GSE134231-GPL18287_series_matrix.txt.gz`
ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 167 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM3939894 GSM3939895 ... GSM3940060 (167 total)
  varLabels: title geo_accession ... location:ch1 (49 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
  pubMedIds: 31934344 
Annotation: GPL18287 

$`GSE134231-GPL26913_series_matrix.txt.gz`
ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 24 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM3940061 GSM3940062 ... GSM3940084 (24 total)
  varLabels: title geo_accession ... location:ch1 (48 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
  pubMedIds: 31934344 
Annotation: GPL26913

I would continue without the patcher function. Do you have write access to the current working directory, i.e., the one specified as destdir="."?

[n,n]

yes, I do have the appropriate permissions. For some reason I can't get the 2.54 version of the package by updating bioconductor.

[Kevin Blighe]

Have you tried the development version via devtools::install_github()?

[n,n]

I successfully installed with devtools::install_github("https://github.com/seandavi/GEOquery"). The version is now 2.55 as shown in the session info, however the same exact problem in the original post persists.

R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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

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

other attached packages:
[1] GEOquery_2.55.1     Biobase_2.46.0      BiocGenerics_0.32.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4        compiler_3.6.3    pillar_1.4.3      prettyunits_1.1.1
 [5] remotes_2.1.1     tools_3.6.3       testthat_2.3.2    digest_0.6.25    
 [9] pkgbuild_1.0.6    pkgload_1.0.2     lifecycle_0.2.0   memoise_1.1.0    
[13] tibble_2.1.3      pkgconfig_2.0.3   rlang_0.4.5       cli_2.0.2        
[17] rstudioapi_0.11   curl_4.3          xml2_1.2.5        withr_2.1.2      
[21] dplyr_0.8.5       vctrs_0.2.4       hms_0.5.3         desc_1.2.0       
[25] fs_1.3.2          devtools_2.2.2    rprojroot_1.3-2   tidyselect_1.0.0 
[29] glue_1.3.2        R6_2.4.1          processx_3.4.2    fansi_0.4.1      
[33] sessioninfo_1.1.1 limma_3.42.2      tidyr_1.0.2       readr_1.3.1      
[37] purrr_0.3.3       callr_3.4.2       magrittr_1.5      backports_1.1.5  
[41] ps_1.3.2          ellipsis_0.3.0    usethis_1.5.1     assertthat_0.2.1 
[45] crayon_1.3.4

[Kevin Blighe]

I see... and you're running Windows 8? I wonder if this does not support some key library that is required. Have you any other system to use?

The files are just located here, by the way; so, you can just download them and read them into R:

• https://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134231/matrix/GSE134231-GPL18287_series_matrix.txt.gz
• https://ftp.ncbi.nlm.nih.gov/geo/series/GSE134nnn/GSE134231/matrix/GSE134231-GPL26913_series_matrix.txt.gz

[n,n]

Tried it on a macOS system without trouble, weird that it just doesn't work in the windows machine.

[Kevin Blighe]

GEOquery needs to pull data from the web, so, I'd say that it relates to some library issue surrounding that, but not sure. Windows 8 is somewhat old, at this stage.