sesameDataCache is not work properly on my system
1
0
Entering edit mode
@alos_diallo-23297
Last seen 3 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 • 482 views
ADD COMMENT
0
Entering edit mode

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
0
Entering edit mode
@alos_diallo-23297
Last seen 3 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
0
Entering edit mode

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

Login before adding your answer.

Traffic: 767 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6