Error in stopAndCache(title) for DMR

[gbc529]

Hello,

I am trying to generate a DMR using sesame and was able to run preprocessing and modeling steps sucessfully. I went to generate a DMR with my data and get the message below:

> merged <- DMR(se_filtered, smry, "Sample.Region")
Platform set to: EPIC
Error in stopAndCache(title) : 
File EPIC.address needs to be cached to be used in sesame.
Please make sure you have updated ExperimentHub and try
> sesameDataCache()
to retrieve and cache needed sesame data.
> library(ExperimentHub)
> sesameDataCacheAll()
Metadata (N=43):

I tried caching both the specific data as well as caching all and the error persists. My sessionInfo is below. Thank you for your help.

> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.5 (Maipo)

Matrix products: default
BLAS:   /hpc/software/R/4.1.1/lib64/R/lib/libRblas.so
LAPACK: /hpc/software/R/4.1.1/lib64/R/lib/libRlapack.so

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

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

other attached packages:
 [1] sesame_1.15.4               data.table_1.14.2          
 [3] forcats_0.5.1               stringr_1.4.0              
 [5] dplyr_1.0.9                 purrr_0.3.4                
 [7] readr_2.1.2                 tidyr_1.2.0                
 [9] tibble_3.1.7                ggplot2_3.3.6              
[11] tidyverse_1.3.1             sesameData_1.12.0          
[13] ExperimentHub_2.2.1         AnnotationHub_3.2.2        
[15] BiocFileCache_2.2.1         dbplyr_2.2.1               
[17] SummarizedExperiment_1.24.0 Biobase_2.54.0             
[19] GenomicRanges_1.46.1        GenomeInfoDb_1.30.1        
[21] IRanges_2.28.0              MatrixGenerics_1.6.0       
[23] matrixStats_0.62.0          S4Vectors_0.32.4           
[25] BiocGenerics_0.40.0        

loaded via a namespace (and not attached):
 [1] wheatmap_0.2.0                colorspace_2.0-3             
 [3] ellipsis_0.3.2                rprojroot_2.0.3              
 [5] XVector_0.34.0                fs_1.5.2                     
 [7] rstudioapi_0.13               farver_2.1.1                 
 [9] remotes_2.4.2                 bit64_4.0.5                  
[11] interactiveDisplayBase_1.32.0 AnnotationDbi_1.56.2         
[13] fansi_1.0.3                   lubridate_1.8.0              
[15] xml2_1.3.3                    cachem_1.0.6                 
[17] pkgload_1.2.4                 jsonlite_1.8.0               
[19] broom_1.0.0                   png_0.1-7                    
[21] shiny_1.7.1                   BiocManager_1.30.18          
[23] compiler_4.1.1                httr_1.4.3                   
[25] backports_1.4.1               assertthat_0.2.1             
[27] Matrix_1.3-4                  fastmap_1.1.0                
[29] cli_3.3.0                     later_1.3.0                  
[31] htmltools_0.5.2               prettyunits_1.1.1            
[33] tools_4.1.1                   gtable_0.3.0                 
[35] glue_1.6.2                    GenomeInfoDbData_1.2.7       
[37] reshape2_1.4.4                rappdirs_0.3.3               
[39] Rcpp_1.0.9                    cellranger_1.1.0             
[41] vctrs_0.4.1                   Biostrings_2.62.0            
[43] preprocessCore_1.56.0         brio_1.1.3                   
[45] ps_1.7.1                      testthat_3.1.4               
[47] rvest_1.0.2                   mime_0.12                    
[49] lifecycle_1.0.1               zlibbioc_1.40.0              
[51] scales_1.2.0                  hms_1.1.1                    
[53] promises_1.2.0.1              parallel_4.1.1               
[55] RColorBrewer_1.1-3            yaml_2.3.5                   
[57] curl_4.3.2                    memoise_2.0.1                
[59] stringi_1.7.8                 RSQLite_2.2.14               
[61] BiocVersion_3.14.0            desc_1.4.1                   
[63] filelock_1.0.2                pkgbuild_1.3.1               
[65] BiocParallel_1.28.3           rlang_1.0.4                  
[67] pkgconfig_2.0.3               bitops_1.0-7                 
[69] lattice_0.20-44               labeling_0.4.2               
[71] bit_4.0.4                     tidyselect_1.1.2             
[73] processx_3.7.0                plyr_1.8.7                   
[75] magrittr_2.0.3                R6_2.5.1                     
[77] generics_0.1.3                DelayedArray_0.20.0          
[79] DBI_1.1.3                     pillar_1.7.0                 
[81] haven_2.5.0                   withr_2.5.0                  
[83] KEGGREST_1.34.0               RCurl_1.98-1.7               
[85] modelr_0.1.8                  crayon_1.5.1                 
[87] utf8_1.2.2                    tzdb_0.3.0                   
[89] grid_4.1.1                    readxl_1.4.0                 
[91] blob_1.2.3                    callr_3.7.0                  
[93] reprex_2.0.1                  digest_0.6.29                
[95] xtable_1.8-4                  httpuv_1.6.5                 
[97] munsell_0.5.0  

[gbc529]

Hello, I would like to update that I was able to resolve the above issue as I found it was a platform issue on my end and by removing and re-installing the latest sesame package the error dissappeared. However, I am now getting a different error when using "visualizeProbes":

Error in sesameData_check_platform(platform, rownames(betas)) :
could not find function "sesameData_check_platform"

Thank you in advance for any advice!

[zwdzwd]

Hi, sorry for the late response. Looks like you are running sesame 1.15 and sesameData 1.12. The two packages should be matched. That's why the newer sesameData_check_platform cannot be found. Just update the sesameData to 1.15 should solve this issue.