Problem with dyplr dependency (I think)

[rebeelouise]

I am getting this error when trying to use msigdbr:

`> msigdbr(species = "Homo sapiens")
Error in `select()`:
! <text>:1:5: unexpected symbol
1: Use of
        ^
Run `rlang::last_error()` to see where the error occurred.
> rlang::last_error()
<simpleError in select(., .data$human_ensembl_gene, gene_symbol = .data$human_gene_symbol,     entrez_gene = .data$human_entrez_gene): <text>:1:5: unexpected symbol
1: Use of
        ^>`

session info:

`> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] EnrichmentBrowser_2.26.0    graph_1.74.0               
 [3] SummarizedExperiment_1.26.1 Biobase_2.56.0             
 [5] GenomicRanges_1.48.0        GenomeInfoDb_1.32.4        
 [7] IRanges_2.30.1              S4Vectors_0.34.0           
 [9] BiocGenerics_0.42.0         MatrixGenerics_1.8.1       
[11] matrixStats_0.63.0          msigdbr_7.5.1              
[13] fgsea_1.22.0                biomaRt_2.52.0             
[15] dplyr_1.0.10                clusterProfiler_4.4.4      `

Any ideas...?

[igordot]

I am not seeing this error with the latest CRAN version of msigdbr.

I notice you have some other packages loaded. Do you still get this error if you only load msigdbr?

For reference, here is my session info:

R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6.3

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] msigdbr_7.5.1

loaded via a namespace (and not attached):
 [1] fansi_1.0.4      withr_2.5.0      utf8_1.2.3       dplyr_1.1.1      R6_2.5.1        
 [6] lifecycle_1.0.3  magrittr_2.0.3   pillar_1.9.0     rlang_1.1.0      cli_3.6.1       
[11] rstudioapi_0.14  generics_0.1.3   vctrs_0.6.1      tools_4.2.2      glue_1.6.2      
[16] compiler_4.2.2   pkgconfig_2.0.3  babelgene_22.9   tidyselect_1.2.0 tibble_3.2.1