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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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Loading Window yields issue on R online platform #106

Closed bastienchassagnol closed 3 years ago

bastienchassagnol commented 3 years ago

Hello, Since I have updated to GEOquery 2.54.1, I can't use anymore on RStudio platform online function getGEO (it's the professional one, I don't have possibilities of upgrading R for instance on it).

There's no clear mistake, just a crash from Rstudio platform that reloads the session, without downloading the file. I can't remember the previous version I used, but it seems that the problem appears after adding a window waiting loading (additionally to string loading), as this issue didn't happen before adding of that feature, or doesn't appear with function GEOquery::getGEOSuppFiles.

Is there a possibility of removing that waiting loading window as option? Or maybe could you send me the last link to your package before this update?

Here's my session info:

R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /softhpc/R/3.6.1/lib64/R/lib/libRblas.so LAPACK: /softhpc/R/3.6.1/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached): [1] tidyselect_1.1.0 RSQLite_2.2.1 AnnotationDbi_1.48.0 htmlwidgets_1.5.2 FactoMineR_2.3 grid_3.6.1
[7] devtools_2.3.2 munsell_0.5.0 preprocessCore_1.48.0 DT_0.16 withr_2.3.0 colorspace_2.0-0
[13] Biobase_2.46.0 knitr_1.30 uuid_0.1-4 rstudioapi_0.12 leaps_3.1 stats4_3.6.1
[19] ggsignif_0.6.0 officer_0.3.15 yarrr_0.1.5 simpleaffy_2.62.0 polyclip_1.10-0 bit64_4.0.5
[25] farver_2.0.3 rprojroot_2.0.2 coda_0.19-4 vctrs_0.3.5 generics_0.1.0 xfun_0.19
[31] fastcluster_1.1.25 R6_2.5.0 clue_0.3-57 BayesFactor_0.9.12-4.2 librarian_1.7.0 bitops_1.0-6
[37] assertthat_0.2.1 scales_1.1.1 gtable_0.3.0 affy_1.64.0 processx_3.4.5 rlang_0.4.9
[43] MatrixModels_0.4-1 genefilter_1.68.0 systemfonts_0.3.2 scatterplot3d_0.3-41 GlobalOptions_0.1.2 splines_3.6.1
[49] rstatix_0.6.0 lazyeval_0.2.2 GEOquery_2.54.1 broom_0.7.2 BiocManager_1.30.10 reshape2_1.4.4
[55] abind_1.4-5 backports_1.2.0 qvalue_2.18.0 usethis_1.6.3 tools_3.6.1 ggplot2_3.3.2
[61] affyio_1.56.0 ellipsis_0.3.1 RColorBrewer_1.1-2 BiocGenerics_0.32.0 sessioninfo_1.1.1 Rcpp_1.0.5
[67] plyr_1.8.6 base64enc_0.1-3 zlibbioc_1.32.0 purrr_0.3.4 RCurl_1.98-1.2 ps_1.4.0
[73] prettyunits_1.1.1 ggpubr_0.4.0 pbapply_1.4-3 GetoptLong_1.0.4 viridis_0.5.1 S4Vectors_0.24.4
[79] haven_2.3.1 ggrepel_0.8.2 cluster_2.1.0 fs_1.5.0 factoextra_1.0.7 tinytex_0.27
[85] magrittr_2.0.1 data.table_1.13.2 RSpectra_0.16-0 openxlsx_4.2.3 flextable_0.6.0 circlize_0.4.11
[91] mvtnorm_1.1-1 matrixStats_0.57.0 pkgload_1.1.0 hms_0.5.3 evaluate_0.14 xtable_1.8-4
[97] XML_3.99-0.3 rio_0.5.16 jpeg_0.1-8.1 gcrma_2.58.0 readxl_1.3.1 IRanges_2.20.2
[103] gridExtra_2.3 shape_1.4.5 testthat_3.0.0 compiler_3.6.1 ellipse_0.4.2 tibble_3.0.4
[109] crayon_1.3.4 htmltools_0.5.0 segmented_1.3-0 corpcor_1.6.9 tidyr_1.1.2 DBI_1.1.0
[115] tweenr_1.0.1 ComplexHeatmap_2.2.0 MASS_7.3-53 Matrix_1.2-17 car_3.0-10 readr_1.4.0
[121] cli_2.1.0 parallel_3.6.1 igraph_1.2.6 forcats_0.5.0 pkgconfig_2.0.3 flashClust_1.01-2
[127] foreign_0.8-72 plotly_4.9.2.1 xml2_1.3.2 rARPACK_0.11-0 annotate_1.64.0 EnhancedVolcano_1.4.0 [133] XVector_0.26.0 iheatmapr_0.5.1 stringr_1.4.0 callr_3.5.1 digest_0.6.27 Biostrings_2.54.0
[139] rmarkdown_2.5 cellranger_1.1.0 gdtools_0.2.2 curl_4.3 kernlab_0.9-29 gtools_3.8.2
[145] rjson_0.2.20 lifecycle_0.2.0 jsonlite_1.7.1 carData_3.0-4 mixOmics_6.10.9 desc_1.2.0
[151] viridisLite_0.3.0 limma_3.42.2 fansi_0.4.1 pillar_1.4.7 lattice_0.20-38 httr_1.4.2
[157] pkgbuild_1.1.0 survival_3.2-7 glue_1.4.2 remotes_2.2.0 zip_2.1.1 png_0.1-7
[163] bit_4.0.4 ggforce_0.3.2 stringi_1.5.3 mixtools_1.2.0 blob_1.2.1 memoise_1.1.0
[169] renv_0.12.0 dplyr_1.0.2

bastienchassagnol commented 3 years ago

After further tests, I can now clearly confirm that the issue on R studio Server happens between version 2.54.0 and 2.54.1, only difference between 2 versions for function getGEO seeming to be the adding of progress bar.

seandavi commented 3 years ago

I'm closing this for now since this uses an older version of R and Bioconductor.