installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
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0
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Hannah • 0
@02a93254
Last seen 7 weeks ago
United States

Hi, I am running into some issues with installing chromVAR and VariantAnnotation through BioConductor. I am working in R/4.0.1 and BioConductor 3.12. This occurs whether it is installed via the development version from GitHub or through BioConductor and I believe both packages are compatible with this version of BioConductor and R. Any help would be greatly appreciated!

Thanks!

# chromVAR
# installation command:

BiocManager::install('chromVAR')

Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE,  : 
  class “chromVARDeviations” cannot extend class “Vector”: slot in class “chromVARDeviations” must extend corresponding slot in class “Vector”: fails for elementMetadata
Error in setClass("chromVARDeviations", contains = "SummarizedExperiment") : 
  error in contained classes ("SummarizedExperiment") for class “chromVARDeviations”; class definition removed from ‘chromVAR’
Error: unable to load R code in package ‘chromVAR’
Execution halted
ERROR: lazy loading failed for package ‘chromVAR’
* removing ‘~R-4.0.1-IRkernel/library/chromVAR’

The downloaded source packages are in
    ‘/tmp/RtmprPOorE/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /n/app/R/4.0.1/lib64/R/library
  packages:
    boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS,
    Matrix, mgcv, nlme, nnet, spatial, survival
Old packages: 'leiden', 'RJSONIO', 'VariantAnnotation'

#############

# VariantAnnotation

Warning: undefined slot classes in definition of "VcfFileList": elementMetadata(class "DataTable_OR_NULL")
Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE,  : 
  class “VcfFileList” cannot extend class “SimpleList”: slot in class “VcfFileList” must extend corresponding slot in class “SimpleList”: fails for elementMetadata
Error in setClass("VcfFileList", contains = "TabixFileList", prototype = prototype(elementType = "VcfFile")) : 
  error in contained classes ("TabixFileList") for class “VcfFileList”; class definition removed from ‘VariantAnnotation’
Error: unable to load R code in package ‘VariantAnnotation’
Execution halted
ERROR: lazy loading failed for package ‘VariantAnnotation’
* removing ‘/~/R-4.0.1-IRkernel/library/VariantAnnotation’
* restoring previous ‘~/R-4.0.1-IRkernel/library/VariantAnnotation’

The downloaded source packages are in
    ‘/tmp/RtmprPOorE/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /n/app/R/4.0.1/lib64/R/library
  packages:
    boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS,
    Matrix, mgcv, nlme, nnet, spatial, survival
Old packages: 'leiden', 'RJSONIO', 'VariantAnnotation'

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /n/app/openblas/0.2.19/lib/libopenblas_core2p-r0.2.19.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=en_US.UTF-8   
 [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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.16 compiler_4.0.1      tools_4.0.1
Install VariantAnnotation Bioconductor chromVAR • 231 views
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You mentioned installing through github and I'm not sure how you mean; if you installed a devel github version that version would not be compatible with the version of Bioc/R you are using. I would recommend running BiocManager::valid() and doing any recommendations it provides. Also try reinstalling VariantAnnotation BiocManager::install('VariantAnnotation') to ensure you have the correct version.

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Entering edit mode

Thanks for the response! What I meant was I initially tried installing through BiocManager and when that failed I attempted to install with devtools install_github() and in both cases ran into the same error with chromVAR when doing lazy loading:

** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE,  : 
  class “chromVARDeviations” cannot extend class “Vector”: slot in class “chromVARDeviations” must extend corresponding slot in class “Vector”: fails for elementMetadata
Error in setClass("chromVARDeviations", contains = "SummarizedExperiment") : 
  error in contained classes ("SummarizedExperiment") for class “chromVARDeviations”; class definition removed from ‘chromVAR’
Error: unable to load R code in package ‘chromVAR’
Execution halted

ERROR: lazy loading failed for package ‘chromVAR’

etc...

As for VariantAnnotation, I removed my previous installation of VariantAnnotation and attempted reinstalled it, and again, same error. The error I got in my original post was when trying to upgrade VariantAnnotation (as per recommendation of BiocManager::valid() when previously troubleshooting the chromVAR error).

BiocManager::valid() now reports only one unrelated package being out of date and no packages as too new.

Any suggestions would be greatly appreciated!

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Entering edit mode
@james-w-macdonald-5106
Last seen 42 minutes ago
United States

FWIW, I can't get chromVAR to install on a linux install of R-4.0.0, but I can get it to install on R-4.1.0 on the same computer. We don't really support old versions anyway, so the best thing is for you to upgrade and see if that helps.

0
Entering edit mode

For completeness:

> library(chromVAR)

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /share/apps/MKL/mkl-2019.3/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.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=en_US.UTF-8   
 [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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] chromVAR_1.14.0     BiocManager_1.30.16

loaded via a namespace (and not attached):
  [1] bitops_1.0-7                matrixStats_0.60.1         
  [3] DirichletMultinomial_1.34.0 TFBSTools_1.30.0           
  [5] bit64_4.0.5                 httr_1.4.2                 
  [7] GenomeInfoDb_1.28.1         tools_4.1.0                
  [9] utf8_1.2.2                  R6_2.5.1                   
 [11] DT_0.18                     lazyeval_0.2.2             
 [13] seqLogo_1.58.0              DBI_1.1.1                  
 [15] BiocGenerics_0.38.0         colorspace_2.0-2           
 [17] tidyselect_1.1.1            bit_4.0.4                  
 [19] compiler_4.1.0              Biobase_2.52.0             
 [21] plotly_4.9.4.1              DelayedArray_0.18.0        
 [23] rtracklayer_1.52.1          caTools_1.18.2             
 [25] scales_1.1.1                readr_2.0.1                
 [27] stringr_1.4.0               digest_0.6.27              
 [29] Rsamtools_2.8.0             R.utils_2.10.1             
 [31] XVector_0.32.0              pkgconfig_2.0.3            
 [33] htmltools_0.5.1.1           MatrixGenerics_1.4.2       
 [35] fastmap_1.1.0               BSgenome_1.60.0            
 [37] htmlwidgets_1.5.3           rlang_0.4.11               
 [39] rstudioapi_0.13             RSQLite_2.2.8              
 [41] shiny_1.6.0                 BiocIO_1.2.0               
 [43] generics_0.1.0              jsonlite_1.7.2             
 [45] BiocParallel_1.26.1         gtools_3.9.2               
 [47] R.oo_1.24.0                 dplyr_1.0.7                
 [49] RCurl_1.98-1.4              magrittr_2.0.1             
 [51] GO.db_3.13.0                GenomeInfoDbData_1.2.6     
 [53] Matrix_1.3-3                Rcpp_1.0.7                 
 [55] munsell_0.5.0               S4Vectors_0.30.0           
 [57] fansi_0.5.0                 R.methodsS3_1.8.1          
 [59] lifecycle_1.0.0             stringi_1.7.3              
 [61] yaml_2.2.1                  SummarizedExperiment_1.22.0
 [63] zlibbioc_1.38.0             plyr_1.8.6                 
 [65] grid_4.1.0                  blob_1.2.2                 
 [67] parallel_4.1.0              promises_1.2.0.1           
 [69] crayon_1.4.1                miniUI_0.1.1.1             
 [71] CNEr_1.28.0                 lattice_0.20-44            
 [73] Biostrings_2.60.2           annotate_1.70.0            
 [75] hms_1.1.0                   KEGGREST_1.32.0            
 [77] pillar_1.6.2                GenomicRanges_1.44.0       
 [79] rjson_0.2.20                reshape2_1.4.4             
 [81] stats4_4.1.0                TFMPvalue_0.0.8            
 [83] XML_3.99-0.7                glue_1.4.2                 
 [85] data.table_1.14.0           vctrs_0.3.8                
 [87] png_0.1-7                   tzdb_0.1.2                 
 [89] httpuv_1.6.2                tidyr_1.1.3                
 [91] gtable_0.3.0                poweRlaw_0.70.6            
 [93] purrr_0.3.4                 assertthat_0.2.1           
 [95] cachem_1.0.6                ggplot2_3.3.5              
 [97] mime_0.11                   xtable_1.8-4               
 [99] restfulr_0.0.13             pracma_2.3.3               
[101] later_1.3.0                 viridisLite_0.4.0          
[103] tibble_3.1.3                GenomicAlignments_1.28.0   
[105] AnnotationDbi_1.54.1        memoise_2.0.0              
[107] IRanges_2.26.0              ellipsis_0.3.2             
>
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Entering edit mode

removing ‘/~/R-4.0.1-IRkernel/library/VariantAnnotation’ indicates that user is running into this situation in Jupyter

Please use BiocManager::valid() for a suitable version of R.

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