Issue with BSgenome installation

[joseverdezoto]

Hello,

I'm having issues with the installation of the BSgenome package that I had not experienced before. I was hoping to get your input on this issue. When trying to install the package, I get the following error:

Error in setMethod("releaseName", "SNPlocs", function(x) x@release_name) : 
  no existing definition for function ‘releaseName’
Error: unable to load R code in package ‘BSgenome’
Execution halted
ERROR: lazy loading failed for package ‘BSgenome’
* removing ‘/home/jer4xy/R/x86_64-pc-linux-gnu-library/4.0/BSgenome’

Below my session Info:

sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.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=C             
 [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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] GenomicDistributions_0.99.0 GenomicRanges_1.41.5       
[3] GenomeInfoDb_1.25.5         IRanges_2.23.10            
[5] S4Vectors_0.27.12           BiocGenerics_0.35.4        
[7] LOLA_1.19.0                 BiocManager_1.30.10        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6           compiler_4.0.0         pillar_1.4.4          
 [4] plyr_1.8.6             XVector_0.29.3         bitops_1.0-6          
 [7] tools_4.0.0            zlibbioc_1.35.0        lifecycle_0.2.0       
[10] tibble_3.0.1           gtable_0.3.0           pkgconfig_2.0.3       
[13] rlang_0.4.6            GenomeInfoDbData_1.2.3 stringr_1.4.0         
[16] dplyr_1.0.0            generics_0.0.2         Biostrings_2.57.2     
[19] vctrs_0.3.1            grid_4.0.0             tidyselect_1.1.0      
[22] glue_1.4.1             data.table_1.12.8      R6_2.4.1              
[25] ggplot2_3.3.2          reshape2_1.4.4         purrr_0.3.4           
[28] magrittr_1.5           scales_1.1.1           ellipsis_0.3.1        
[31] colorspace_1.4-1       stringi_1.4.6          RCurl_1.98-1.2        
[34] munsell_0.5.0          crayon_1.3.4  

[mtmorgan]

Are your packages consistent with the Bioconductor version you are trying to use?

BiocManager::version()
BiocManager::valid()

[hpages]

Hi @joseverdezoto ,

This is a regression I introduced recently while working on improvements to the seqlevelsStyle() setter, sorry. It should be fixed in the latest version of GenomeInfoDb (version 1.25.6, see https://github.com/Bioconductor/GenomeInfoDb/commit/0a1cf2ec6abbaa1c8368005a57f4c92c80a4d5f9) and BSgenome (version 1.57.3, see commit b5c3f3aedf7973ba0968259efb842a40e55cbdc7). Both packages will become available via BiocManager::install() in the next 24h-48h.

Note that you can get them immediately by installing from GitHub:

BiocManager::install(c("Bioconductor/GenomeInfoDb", "Bioconductor/BSgenome"))

Please be aware that we usually don't recommend installing Bioconductor packages from GitHub so consider this an exception.

Best, H.

[joseverdezoto]

Dear @hpages,

Thank you so much for the pointer. I was able to successfully install both packages.