`unused argument (.data$species_name == species)` error

[katwre]

Hi, I've just got unused argument (.data$species_name == species) error, and I don't know how to proceed. Is it a bug or am I doing sth wrong?

> library(msigdbr)
> msigdbr(species = "Homo sapiens")
Error in filter.tbl(msigdbr_orthologs, .data$species_name == species) : 
  unused argument (.data$species_name == species)
> msigdbr(species = "Mus musculus", category = "C2", subcategory = "CGP")
Error in filter.tbl(msigdbr_orthologs, .data$species_name == species) : 
  unused argument (.data$species_name == species)
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /opt/R-4.0.2/lib64/R/lib/libRblas.so
LAPACK: /opt/R-4.0.2/lib64/R/lib/libRlapack.so

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] grid      stats4    parallel  stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] msigdbr_7.2.1               DESeq2_1.28.1              
 [3] SummarizedExperiment_1.18.2 DelayedArray_0.14.1        
 [5] matrixStats_0.57.0          Biobase_2.48.0             
 [7] rtracklayer_1.48.0          genomation_1.20.0          
 [9] gProfileR_0.7.0             ChIPpeakAnno_3.22.4        
[11] Biostrings_2.56.0           XVector_0.28.0             
[13] VennDiagram_1.6.20          futile.logger_1.4.3        
[15] rGREAT_1.20.0               methylKit_1.14.2           
[17] GenomicRanges_1.40.0        GenomeInfoDb_1.24.2        
[19] IRanges_2.22.2              S4Vectors_0.26.1           
[21] BiocGenerics_0.34.0         gprofiler2_0.2.0           
[23] reshape2_1.4.4              ggplot2_3.3.2              
[25] gridExtra_2.3               data.table_1.13.0          
[27] biomaRt_2.44.4              igraph_1.2.6               
[29] STRINGdb_2.0.2             

loaded via a namespace (and not attached):
  [1] circlize_0.4.10          BiocFileCache_1.12.1     plyr_1.8.6              
  [4] lazyeval_0.2.2           splines_4.0.2            BiocParallel_1.22.0     
  [7] gridBase_0.4-7           digest_0.6.25            ensembldb_2.12.1        
 [10] htmltools_0.5.0          GO.db_3.11.4             magrittr_1.5            
 [13] memoise_1.1.0            BSgenome_1.56.0          limma_3.44.3            
 [16] annotate_1.66.0          readr_1.4.0              R.utils_2.10.1          
 [19] askpass_1.1              bdsmatrix_1.3-4          prettyunits_1.1.1       
 [22] colorspace_1.4-1         blob_1.2.1               rappdirs_0.3.1          
 [25] xfun_0.18                dplyr_1.0.2              crayon_1.3.4            
 [28] RCurl_1.98-1.2           jsonlite_1.7.1           graph_1.66.0            
 [31] genefilter_1.70.0        impute_1.62.0            survival_3.1-12         
 [34] glue_1.4.2               hash_2.2.6.1             gtable_0.3.0            
 [37] zlibbioc_1.34.0          seqinr_4.2-4             GetoptLong_1.0.3        
 [40] shape_1.4.5              scales_1.1.1             futile.options_1.0.1    
 [43] mvtnorm_1.1-1            DBI_1.1.0                Rcpp_1.0.5              
 [46] plotrix_3.7-8            xtable_1.8-4             viridisLite_0.3.0       
 [49] progress_1.2.2           emdbook_1.3.12           bit_4.0.4               
 [52] mclust_5.4.6             sqldf_0.4-11             htmlwidgets_1.5.2       
 [55] httr_1.4.2               gplots_3.1.0             RColorBrewer_1.1-2      
 [58] ellipsis_0.3.1           pkgconfig_2.0.3          XML_3.99-0.5            
 [61] R.methodsS3_1.8.1        farver_2.0.3             dbplyr_1.4.4            
 [64] locfit_1.5-9.4           tidyselect_1.1.0         labeling_0.3            
 [67] rlang_0.4.7              AnnotationDbi_1.50.3     munsell_0.5.0           
 [70] tools_4.0.2              gsubfn_0.7               generics_0.0.2          
 [73] RSQLite_2.2.1            ade4_1.7-15              fastseg_1.34.0          
 [76] evaluate_0.14            stringr_1.4.0            yaml_2.2.1              
 [79] knitr_1.30               bit64_4.0.5              caTools_1.18.0          
 [82] purrr_0.3.4              AnnotationFilter_1.12.0  RBGL_1.64.0             
 [85] formatR_1.7              R.oo_1.24.0              xml2_1.3.2              
 [88] compiler_4.0.2           rstudioapi_0.11          plotly_4.9.2.1          
 [91] curl_4.3                 png_0.1-7                geneplotter_1.66.0      
 [94] tibble_3.0.3             idr_1.2                  stringi_1.5.3           
 [97] GenomicFeatures_1.40.1   lattice_0.20-41          ProtGenerics_1.20.0     
[100] Matrix_1.2-18            multtest_2.44.0          vctrs_0.3.4             
[103] pillar_1.4.6             lifecycle_0.2.0          BiocManager_1.30.10     
[106] GlobalOptions_0.1.2      bitops_1.0-6             qvalue_2.20.0           
[109] R6_2.4.1                 KernSmooth_2.23-17       lambda.r_1.2.4          
[112] MASS_7.3-51.6            gtools_3.8.2             assertthat_0.2.1        
[115] chron_2.3-56             proto_1.0.0              openssl_1.4.3           
[118] rjson_0.2.20             withr_2.3.0              regioneR_1.20.1         
[121] GenomicAlignments_1.24.0 Rsamtools_2.4.0          GenomeInfoDbData_1.2.3  
[124] hms_0.5.3                tidyr_1.1.2              coda_0.19-4             
[127] rmarkdown_2.4            seqPattern_1.20.0        bbmle_1.0.23.1          
[130] numDeriv_2016.8-1.1      tinytex_0.26

Best, Kasia

[igordot]

Hi Kasia.

Thanks for trying msigdbr! I have not seen that error before. You are using a recent version of R and not doing anything complicated, so everything should be working.

Did you install the package from CRAN or GitHub?

You have a few other packages loaded in your environment. It's possible that there is a conflict. If you start a new session and just load msigdbr, are you still seeing the error?

[katwre]

@igordot , thank you for a quick reply! Oh, after starting a new session everything seems to be fine, so there must be a conflict with another R package I guess.. I use R version 4.0.2 and I installed it from CRAN. Thanks a lot for your help! Kasia

[igordot]

Glad to hear it works now. Let me know if you figure out which package was was causing the conflict.