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namespace error when calling simplifyGO

Open russtafayyazi opened this issue 2 years ago • 0 comments

I am trying to make a simplifyEnrichment heatmap to group my GO:BP terms. I am able to use GO_similarity to create my similarity matrix. But at

simplifyGO(Ureg_mtx, method = "binary_cut", plot = TRUE)

I get the following error message:

Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/d6/hcjc7wbs4sjdsrnycpn7h5zr0000gn/T//Rtmpl3Ngkz/.heatmap_body_8314b6e270871e94cfd6143670a0a2eb_1_117d855554d483.png
In addition: Warning message:
In (function (filename = "Rplot%03d.png", width = 480, height = 480,  :
  failed to load cairo DLL

I am unable to locate the folder that it is referencing, let alone know what to do if I could. I've tried updating my Rstudio and all packages in my session:

R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1

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

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

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

other attached packages:
[1] simplifyEnrichment_1.6.1 BiocGenerics_0.42.0     

loaded via a namespace (and not attached):
 [1] KEGGREST_1.36.3        circlize_0.4.15        shape_1.4.6           
 [4] GetoptLong_1.0.5       NLP_0.2-1              slam_0.1-50           
 [7] lattice_0.20-45        colorspace_2.0-3       vctrs_0.4.2           
[10] stats4_4.2.1           blob_1.2.3             rlang_1.0.6           
[13] DBI_1.1.3              bit64_4.0.5            RColorBrewer_1.1-3    
[16] matrixStats_0.62.0     GenomeInfoDbData_1.2.8 foreach_1.5.2         
[19] zlibbioc_1.42.0        Biostrings_2.64.1      GOSemSim_2.22.0       
[22] proxyC_0.3.2           GlobalOptions_0.1.2    codetools_0.2-18      
[25] memoise_2.0.1          Biobase_2.56.0         ComplexHeatmap_2.13.2 
[28] IRanges_2.30.1         fastmap_1.1.0          doParallel_1.0.17     
[31] GenomeInfoDb_1.32.4    tm_0.7-8               parallel_4.2.1        
[34] AnnotationDbi_1.58.0   Rcpp_1.0.9             BiocManager_1.30.18   
[37] cachem_1.0.6           org.Hs.eg.db_3.15.0    S4Vectors_0.34.0      
[40] RcppParallel_5.1.5     XVector_0.36.0         bit_4.0.4             
[43] rjson_0.2.21           png_0.1-7              digest_0.6.29         
[46] clue_0.3-61            cli_3.4.1              tools_4.2.1           
[49] bitops_1.0-7           RCurl_1.98-1.9         RSQLite_2.2.18        
[52] cluster_2.1.4          crayon_1.5.2           GO.db_3.15.0          
[55] pkgconfig_2.0.3        Matrix_1.5-1           xml2_1.3.3            
[58] org.Mm.eg.db_3.15.0    httr_1.4.4             rstudioapi_0.14       
[61] iterators_1.0.14       R6_2.5.1               compiler_4.2.1  

Not sure how to resolve the issue, and this is my first time using the simplifyEnrichment package so I'm quite amateur in navigating it. Would appreciate any advice!

russtafayyazi avatar Oct 08 '22 17:10 russtafayyazi