Question

sesameDataCache is not work properly on my system

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alos_diallo • 0

@alos_diallo-23297

Last seen 5 months ago

United States

I am trying to use sesame, but I am not able to run sesameDataCache() I have the latest version of Sesame, SesameData, R, and ExperimentHub. I tried to create a new cache folder but the results are the same. This has worked previously. Any advice would be greatly appreciated. Thank you!

Here is what my current system has:

R version 4.3.2 (2023-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.2.1 [1] sesame_1.18.4 sesameData_1.18.0 ExperimentHub_2.8.1 AnnotationHub_3.8.0 [5] BiocFileCache_2.8.0 dbplyr_2.4.0 BiocGenerics_0.46.0

Here is what I have tried to run: sesameDataCache() Here is the error message:

Blockquote enter code here error in evaluating the argument 'x' in selecting a method for function 'query': Failed to collect lazy table. Caused by error in >db_collect(): ! Arguments in ... must be used. X Problematic argument: \ ..1 = Inf i Did you misspell an argument name?

sesameData sesameDataCache sesame ExperimentalHub • 654 views

ADD COMMENT • link updated 4 months ago by alyssa-daniel • 0 • written 5 months ago by alos_diallo • 0

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Here is my SessionInfo:

sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.2.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] sesame_1.18.4       sesameData_1.18.0   ExperimentHub_2.8.1 AnnotationHub_3.8.0
[5] BiocFileCache_2.8.0 dbplyr_2.4.0        BiocGenerics_0.46.0

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0              dplyr_1.1.3                   blob_1.2.4                   
 [4] filelock_1.0.2                Biostrings_2.68.1             bitops_1.0-7                 
 [7] fastmap_1.1.1                 RCurl_1.98-1.13               promises_1.2.1               
[10] digest_0.6.33                 mime_0.12                     lifecycle_1.0.3              
[13] ellipsis_0.3.2                KEGGREST_1.40.1               interactiveDisplayBase_1.38.0
[16] RSQLite_2.3.2                 magrittr_2.0.3                compiler_4.3.2               
[19] rlang_1.1.1                   tools_4.3.2                   utf8_1.2.4                   
[22] yaml_2.3.7                    knitr_1.45                    S4Arrays_1.0.6               
[25] bit_4.0.5                     curl_5.1.0                    DelayedArray_0.26.7          
[28] plyr_1.8.9                    RColorBrewer_1.1-3            abind_1.4-5                  
[31] BiocParallel_1.34.2           purrr_1.0.2                   grid_4.3.2                   
[34] stats4_4.3.2                  preprocessCore_1.62.1         fansi_1.0.5                  
[37] wheatmap_0.2.0                xtable_1.8-4                  colorspace_2.1-0             
[40] ggplot2_3.4.4                 scales_1.2.1                  SummarizedExperiment_1.30.2  
[43] cli_3.6.1                     crayon_1.5.2                  generics_0.1.3               
[46] rstudioapi_0.15.0             reshape2_1.4.4                httr_1.4.7                   
[49] tzdb_0.4.0                    DBI_1.1.3                     cachem_1.0.8                 
[52] stringr_1.5.0                 zlibbioc_1.46.0               parallel_4.3.2               
[55] AnnotationDbi_1.62.2          BiocManager_1.30.22           XVector_0.40.0               
[58] matrixStats_1.0.0             vctrs_0.6.4                   Matrix_1.6-1.1               
[61] IRanges_2.34.1                hms_1.1.3                     S4Vectors_0.38.2             
[64] bit64_4.0.5                   glue_1.6.2                    codetools_0.2-19             
[67] stringi_1.7.12                gtable_0.3.4                  BiocVersion_3.17.1           
[70] later_1.3.1                   GenomeInfoDb_1.36.4           GenomicRanges_1.52.1         
[73] munsell_0.5.0                 tibble_3.2.1                  pillar_1.9.0                 
[76] rappdirs_0.3.3                htmltools_0.5.7               GenomeInfoDbData_1.2.10      
[79] R6_2.5.1                      lattice_0.22-5                shiny_1.7.5.1                
[82] Biobase_2.60.0                readr_2.1.4                   png_0.1-8                    
[85] memoise_2.0.1                 httpuv_1.6.12                 Rcpp_1.0.11                  
[88] xfun_0.41                     MatrixGenerics_1.12.3         pkgconfig_2.0.3

ADD REPLY • link 5 months ago alos_diallo • 0

score 0 · Answer 1 · 2023-11-12

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alos_diallo • 0

@alos_diallo-23297

Last seen 5 months ago

United States

So I updated sesameData, sesame,BiocFileCache, and ExperimentHub then I removed the ExperimentHub cache, and deleted my rdata files. Re-booted and it now works. I am not sure which of these changes has fixed it though. I will continue to investigate and will update here if I find anything.

ADD COMMENT • link 5 months ago alos_diallo • 0

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Could you please post your code here? I am having a heck of a time trying to get mine to work... and I am newer to R so I am not sure I know how to do those things you mentioned. My sesame was working fine with version 3.17 and then I ran into this same issue... Thanks!

ADD REPLY • link 4 months ago alyssa-daniel • 0