search

seandavi / GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor
http://seandavi.github.io/GEOquery/
Other
88 stars 36 forks source link

Issues with installing GEOquery package #153

Open nilanjana1996 opened 2 months ago

nilanjana1996 commented 2 months ago

I'm facing problem with installing GEOquery packge.

Tried to install the packag wityh the code below,

if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

Opening R as administrator didn't help either. The error message I got is,

Session Info is as follows. sessioninfo::platform_info() setting value version R version 4.3.1 (2023-06-16 ucrt) os Windows 11 x64 (build 22631) system x86_64, mingw32 ui RStudio language (EN) collate English_United States.utf8 ctype English_United States.utf8 tz Asia/Calcutta date 2024-08-27 rstudio 2023.06.1+524 Mountain Hydrangea (desktop) pandoc NA

sessioninfo::package_info() ! package version date (UTC) lib source abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0) affy 1.80.0 2023-10-24 [1] Bioconductor affyio 1.72.0 2023-10-24 [1] Bioconductor AnnotationDbi 1.64.1 2023-11-03 [1] Bioconductor Biobase 2.62.0 2023-10-24 [1] Bioconductor BiocFileCache 2.10.2 2024-03-27 [1] Bioconductor 3.18 (R 4.3.3) BiocGenerics 0.48.1 2023-11-01 [1] Bioconductor BiocIO 1.12.0 2023-10-24 [1] Bioconductor BiocManager 1.30.24 2024-08-20 [1] CRAN (R 4.3.3) BiocParallel 1.36.0 2023-10-24 [1] Bioconductor biomaRt 2.58.2 2024-01-30 [1] Bioconductor 3.18 (R 4.3.2) Biostrings 2.70.2 2024-01-28 [1] Bioconductor 3.18 (R 4.3.2) bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.1) bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.1) bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0) blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.1) cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.1) cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.1) V codetools 0.2-19 2024-03-31 [2] CRAN (R 4.3.3) (on disk 0.2.20) colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.1) cowplot 1.1.3 2024-01-22 [1] CRAN (R 4.3.2) crayon 1.5.3 2024-06-20 [1] CRAN (R 4.3.3) curl 5.1.0 2023-10-02 [1] CRAN (R 4.3.1) data.table 1.15.0 2024-01-30 [1] CRAN (R 4.3.2) DBI 1.2.3 2024-06-02 [1] CRAN (R 4.3.3) dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.3.1) DelayedArray 0.28.0 2023-10-24 [1] Bioconductor digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.1) dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.3.2) fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.2) fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.1) fastmatch 1.1-4 2023-08-18 [1] CRAN (R 4.3.1) fgsea 1.28.0 2023-10-24 [1] Bioconductor filelock 1.0.3 2023-12-11 [1] CRAN (R 4.3.2) generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.1) GenomeInfoDb 1.38.8 2024-03-15 [1] Bioconductor 3.18 (R 4.3.3) GenomeInfoDbData 1.2.11 2023-10-31 [1] Bioconductor GenomicAlignments 1.38.2 2024-01-16 [1] Bioconductor 3.18 (R 4.3.2) GenomicFeatures 1.54.4 2024-03-13 [1] Bioconductor 3.18 (R 4.3.3) GenomicRanges 1.54.1 2023-10-29 [1] Bioconductor ggplot2 3.5.1 2024-04-23 [1] CRAN (R 4.3.3) glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.1) gtable 0.3.5 2024-04-22 [1] CRAN (R 4.3.3) hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.1) httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.1) IRanges 2.36.0 2023-10-24 [1] Bioconductor KEGGREST 1.42.0 2023-10-24 [1] Bioconductor lattice 0.22-5 2023-10-24 [1] CRAN (R 4.3.2) lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.2) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.1) Matrix 1.6-5 2024-01-11 [1] CRAN (R 4.3.2) MatrixGenerics 1.14.0 2023-10-24 [1] Bioconductor matrixStats 1.2.0 2023-12-11 [1] CRAN (R 4.3.2) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.1) munsell 0.5.1 2024-04-01 [1] CRAN (R 4.3.3) openxlsx 4.2.5.2 2023-02-06 [1] CRAN (R 4.3.1) pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.1) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.1) png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0) preprocessCore 1.64.0 2023-10-24 [1] Bioconductor prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.3.1) progress 1.2.3 2023-12-06 [1] CRAN (R 4.3.2) R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.1) rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.3.1) Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.2) RCurl 1.98-1.12 2023-03-27 [1] CRAN (R 4.3.0) remotes 2.5.0 2024-03-17 [1] CRAN (R 4.3.3) restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.3.1) rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0) rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.1) Rsamtools 2.18.0 2023-10-24 [1] Bioconductor RSQLite 2.3.5 2024-01-21 [1] CRAN (R 4.3.2) rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.3.1) rtracklayer 1.62.0 2023-10-24 [1] Bioconductor S4Arrays 1.2.0 2023-10-24 [1] Bioconductor S4Vectors 0.40.2 2023-11-23 [1] Bioconductor scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.2) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.1) SparseArray 1.2.3 2023-12-25 [1] Bioconductor 3.18 (R 4.3.2) stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.0) stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.2) SummarizedExperiment 1.32.0 2023-10-24 [1] Bioconductor tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.1) tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.3.3) utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.2) vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.2) XML 3.99-0.16.1 2024-01-22 [1] CRAN (R 4.3.2) xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.2) XVector 0.42.0 2023-10-24 [1] Bioconductor yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0) zip 2.3.1 2024-01-27 [1] CRAN (R 4.3.2) zlibbioc 1.48.0 2023-10-24 [1] Bioconductor

[1] C:/Users/nilm9/AppData/Local/R/win-library/4.3 [2] C:/Program Files/R/R-4.3.1/library

V ── Loaded and on-disk version mismatch.

Code example

Output of Session Info:

Cut-and-paste output of sessionInfo