Issues with getGEO() "Error in new(...), unused arguments

[suburbianmantia]

Hi,

I currently begin to work with getGEO but I can't get rid of the following issue (example):

getGEO("GSE11724") Found 1 file(s) GSE11724_series_matrix.txt.gz Using locally cached version: C:\Users\thoma\AppData\Local\Temp\Rtmpk5Cttq/GSE11724_series_matrix.txt.gz Error in new("MIAME", name = ifelse(is.null(headerlist$contact_name), : unused arguments (name = ifelse(is.null(headerlist$contact_name), "", headerlist$contact_name), title = headerlist$title, contact = ifelse(is.null(headerlist$contact_email), "", headerlist$contact_email), pubMedIds = ifelse(is.null(headerlist$pubmed_id), "", headerlist$pubmed_id), abstract = ifelse(is.null(headerlist$summary), "", headerlist$summary), url = link, other = headerlist)

The same error occurs with any other query with getGEO function in my R session. I already update all packages (readr, magrittr, httr, xml2, dplyr, tidyr and limma and my session info looks like this:

R version 4.1.1 (2021-08-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 [4] LC_NUMERIC=C LC_TIME=French_France.1252

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

other attached packages: [1] limma_3.48.3 tidyr_1.1.4 dtplyr_1.1.0 dbplyr_2.1.1 xml2_1.3.2
[6] httr_1.4.2 R.methodsS3_1.8.1 MASS_7.3-54 magrittr_2.0.1 BiocVersion_3.13.1 [11] BiocManager_1.30.16 dplyr_1.0.7 readr_2.0.2 GEOquery_2.60.0 Biobase_2.53.0
[16] BiocGenerics_0.38.0 ROCR_1.0-11 clValid_0.7 cluster_2.1.2

loaded via a namespace (and not attached): [1] bit64_4.0.5 webshot_0.5.2 RColorBrewer_1.1-2 tools_4.1.1 backports_1.2.1
[6] utf8_1.2.2 R6_2.5.1 DBI_1.1.1 colorspace_2.0-2 withr_2.4.2
[11] tidyselect_1.1.1 GGally_2.1.2 bit_4.0.4 curl_4.3.2 compiler_4.1.1
[16] chron_2.3-56 cli_3.0.1 rvest_1.0.2 factoextra_1.0.7 HardyWeinberg_1.7.2 [21] flextable_0.6.9 mice_3.13.0 officer_0.4.0 scales_1.1.1 systemfonts_1.0.3
[26] stringr_1.4.0 digest_0.6.28 foreign_0.8-81 rmarkdown_2.11 svglite_2.0.0
[31] rio_0.5.27 base64enc_0.1-3 pkgconfig_2.0.3 htmltools_0.5.2 fastmap_1.1.0
[36] rlang_0.4.12 readxl_1.3.1 rstudioapi_0.13 generics_0.1.0 vroom_1.5.5
[41] zip_2.2.0 car_3.0-11 kableExtra_1.3.4 Matrix_1.3-4 Rcpp_1.0.7
[46] munsell_0.5.0 fansi_0.5.0 abind_1.4-5 gdtools_0.2.3 lifecycle_1.0.1
[51] stringi_1.7.5 pROC_1.18.0 carData_3.0-4 plyr_1.8.6 grid_4.1.1
[56] ggrepel_0.9.1 forcats_0.5.1 crayon_1.4.1 lattice_0.20-44 haven_2.4.3
[61] splines_4.1.1 hms_1.1.1 knitr_1.36 pillar_1.6.4 ggpubr_0.4.0
[66] uuid_0.1-4 ggsignif_0.6.3 compareGroups_4.5.1 glue_1.4.2 evaluate_0.14
[71] data.table_1.14.2 tzdb_0.1.2 vctrs_0.3.8 cellranger_1.1.0 gtable_0.3.0
[76] purrr_0.3.4 reshape_0.8.8 assertthat_0.2.1 ggplot2_3.3.5 xfun_0.27
[81] openxlsx_4.2.4 broom_0.7.9 coda_0.19-4 Rsolnp_1.16 rstatix_0.7.0
[86] class_7.3-19 survival_3.2-13 rjags_4-12 viridisLite_0.4.0 truncnorm_1.0-8
[91] tibble_3.1.5 writexl_1.4.0 ellipsis_0.3.2

Any idea of what is causing the error and how to get rid of it?

Thanks a lot!

[seandavi]

Hi, @suburbianmantia. The version of GEOquery on Bioconductor is currently broken and no changes are allowed while the next Bioconductor release is being processed. In the meantime, this will get you the newest developer version:

BiocManager::install('seandavi/GEOquery')

I think that should fix your problem.

[suburbianmantia]

Hi again,

Thanks for the prompt response.

Unfortunately, this did not solve the problem. Every time I run the getGEO function, whatever file I choose, I have the same issue with Error in new([...]) and unused arguments.

I also tried to supress and reinstall all packages that I need, but it didn't work either.

Do you have any other ideas?